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Journal articles on the topic 'Sox genes'

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Published: 4 June 2021
Last updated: 6 July 2024

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1

Dong, C., D. Wilhelm, and P. Koopman. "Sox genes and cancer." Cytogenetic and Genome Research 105, no. 2-4 (2004): 442–47. http://dx.doi.org/10.1159/000078217.

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2

Wang, Yubin, Xiangzhong Luo, Chunjuan Qu, Tao Xu, Guiwei Zou, and Hongwei Liang. "The Important Role of Sex-Related Sox Family Genes in the Sex Reversal of the Chinese Soft-Shelled Turtle (Pelodiscus sinensis)." Biology 11, no. 1 (January 6, 2022): 83. http://dx.doi.org/10.3390/biology11010083.

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The Chinese soft-shelled turtle Pelodiscus sinensis shows obvious sexual dimorphism. The economic and nutrition value of male individuals are significantly higher than those of female individuals. Pseudo-females which are base to all-male breeding have been obtained by estrogen induction, while the gene function and molecular mechanism of sex reversal remain unclear in P. sinensis. Here, comparative transcriptome analyses of female, male, and pseudo-female gonads were performed, and 14,430 genes differentially expressed were identified in the pairwise comparison of three groups. GO and KEGG analyses were performed on the differentially expressed genes (DEGs), which mainly concentrated on steroid hormone synthesis. Furthermore, the results of gonadal transcriptome analysis revealed that 10 sex-related sox genes were differentially expressed in males vs. female, male vs. pseudo-female, and female vs. pseudo-female. Through the differential expression analysis of these 10 sox genes in mature gonads, six sox genes related to sex reversal were further screened. The molecular mechanism of the six sox genes in the embryo were analyzed during sex reversal after E2 treatment. In mature gonads, some sox family genes, such as sox9sox12, and sox30 were highly expressed in the testis, while sox1, sox3, sox6, sox11, and sox17 were lowly expressed. In the male embryos, exogenous estrogen can activate the expression of sox3 and inhibit the expression of sox8, sox9, and sox11. In summary, sox3 may have a role in the process of sex reversal from male to pseudo-female, when sox8 and sox9 are inhibited. Sox family genes affect both female and male pathways in the process of sex reversal, which provides a new insight for the all-male breeding of the Chinese soft-shelled turtle.
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3

Wood, Stephanie, Kenji Ishida, James R. Hagerty, Anida Karahodza, Janay N. Dennis, and Emmitt R. Jolly. "Characterization of Schistosome Sox Genes and Identification of a Flatworm Class of Sox Regulators." Pathogens 12, no. 5 (May 9, 2023): 690. http://dx.doi.org/10.3390/pathogens12050690.

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Schistosome helminths infect over 200 million people across 78 countries and are responsible for nearly 300,000 deaths annually. However, our understanding of basic genetic pathways crucial for schistosome development is limited. The sex determining region Y-box 2 (Sox2) protein is a Sox B type transcriptional activator that is expressed prior to blastulation in mammals and is necessary for embryogenesis. Sox expression is associated with pluripotency and stem cells, neuronal differentiation, gut development, and cancer. Schistosomes express a Sox-like gene expressed in the schistosomula after infecting a mammalian host when schistosomes have about 900 cells. Here, we characterized and named this Sox-like gene SmSOXS1. SmSoxS1 protein is a developmentally regulated activator that localizes to the anterior and posterior ends of the schistosomula and binds to Sox-specific DNA elements. In addition to SmSoxS1, we have also identified an additional six Sox genes in schistosomes, two Sox B, one SoxC, and three Sox genes that may establish a flatworm-specific class of Sox genes with planarians. These data identify novel Sox genes in schistosomes to expand the potential functional roles for Sox2 and may provide interesting insights into early multicellular development of flatworms.
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4

Phochanukul, Nichanun, and Steven Russell. "No backbone but lots of Sox: Invertebrate Sox genes." International Journal of Biochemistry & Cell Biology 42, no. 3 (March 2010): 453–64. http://dx.doi.org/10.1016/j.biocel.2009.06.013.

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5

Koopman, Peter. "Sex determination: a tale of two Sox genes." Trends in Genetics 21, no. 7 (July 2005): 367–70. http://dx.doi.org/10.1016/j.tig.2005.05.006.

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6

Hett, Anne Kathrin, and Arne Ludwig. "SRY-related (Sox) genes in the genome of European Atlantic sturgeon (Acipenser sturio)." Genome 48, no. 2 (April 1, 2005): 181–86. http://dx.doi.org/10.1139/g04-112.

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The Sox-gene family represents an ancient group of transcription factors involved in numerous developmental processes and sex determination in vertebrates. SOX proteins are characterized by a conserved high mobility group (HMG)-box domain, which is responsible for DNA binding and bending. We studied Sox genes in sturgeon, one of the most primitive groups of fishes characterized by a high chromosome number. Male and female genomes were screened for Sox genes using highly degenerate primers that amplified a broad range of HMG boxes. A total of 102 clones, representing 22 different sequences coding for 8 Sox genes, was detected and classified according to their orthologues. Sox2, Sox3, Sox4, Sox9, Sox11, Sox17, Sox19, and Sox21 were found in sturgeon; these genes represent Sox groups B, C, E, and F. In a phylogenetic analysis (neighbor-joining, maximum likelihood, maximum parsimony), these genes clustered with their mouse orthologues. In the case of Sox4, Sox17, and Sox21, we found evidence of gene duplication.Key words: Acipenseridae, gene evolution, sex determination, Sox genes.
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7

Pevny, Larysa H., and Robin Lovell-Badge. "Sox genes find their feet." Current Opinion in Genetics & Development 7, no. 3 (June 1997): 338–44. http://dx.doi.org/10.1016/s0959-437x(97)80147-5.

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8

Prior, Heather M., and Michael A. Walter. "SOX Genes: Architects of Development." Molecular Medicine 2, no. 4 (July 1996): 405–12. http://dx.doi.org/10.1007/bf03401900.

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9

Gozé, Catherine, Francis Poulat, and Philippe Berta. "Partial cloning of SOX-11 and SOX-12, two new human SOX genes." Nucleic Acids Research 21, no. 12 (1993): 2943. http://dx.doi.org/10.1093/nar/21.12.2943.

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10

Ma, Fang, Yali Zou, Ruilin Ma, Xin Chen, and Lanfang Ma. "Evolution, characterization and expression analysis of Sox gene family in rainbow trout (Oncorhynchus mykiss)." Czech Journal of Animal Science 67, No. 4 (April 30, 2022): 157–66. http://dx.doi.org/10.17221/4/2022-cjas.

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The Sox transcription factor family plays an important role in various biological processes such as animal sex determination and multiple organ development. We used online databases to analyze the gene structure, chemical characteristics, and evolutionary relationship of Sox family genes through bioinformatics, and we studied the expression profiles and regulatory mechanisms of Sox family genes. A total of 29 rainbow trout Sox genes were identified. The phylogenetic analysis found that Sox genes of rainbow trout were clustered in seven subfamilies (B1, B2, C, D, E, F and H), and the gene structure of each subfamily was relatively conserved. Furthermore, Sox1, Sox4, Sox6, Sox8, Sox9, Sox11, Sox17, Sox18, and Sox19 developed into two copies, which might be the result of teleost fish-specific genome replication. Multiple HMG box domain alignments indicated that the motifs for all Sox sequences are conserved. Gene expression studies reveal that Sox expression is tissue-specific and that multiple Sox genes are involved in rainbow trout gonad and central nervous system development. Our study provides valuable information on the evolution of teleosts, and will also help to further research the functional characteristics of Sox genes.
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11

Leon, Anthony. "EVOLUTIONARY HISTORY OF THE SOX GENES THROUGHOUT GENE DUPLICATION." REBIOL 39, no. 2 (December 31, 2019): 58–69. http://dx.doi.org/10.17268/rebiol.2019.39.02.06.

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12

Pevny, Larysa, and Marysia Placzek. "SOX genes and neural progenitor identity." Current Opinion in Neurobiology 15, no. 1 (February 2005): 7–13. http://dx.doi.org/10.1016/j.conb.2005.01.016.

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13

Wilson, Megan J., and Peter K. Dearden. "Evolution of the insect Sox genes." BMC Evolutionary Biology 8, no. 1 (2008): 120. http://dx.doi.org/10.1186/1471-2148-8-120.

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14

Zhou, Rongjia, Hanhua Cheng, Qixing Yu, and Yaping Zhang. "Sox andZfx genes in giant panda." Science in China Series C: Life Sciences 41, no. 6 (December 1998): 623–27. http://dx.doi.org/10.1007/bf02882904.

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15

Collignon, J., S. Sockanathan, A. Hacker, M. Cohen-Tannoudji, D. Norris, S. Rastan, M. Stevanovic, P. N. Goodfellow, and R. Lovell-Badge. "A comparison of the properties of Sox-3 with Sry and two related genes, Sox-1 and Sox-2." Development 122, no. 2 (February 1, 1996): 509–20. http://dx.doi.org/10.1242/dev.122.2.509.

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The Sox gene family consists of a large number of embryonically expressed genes related via the possession of a 79-amino-acid DNA-binding domain known as the HMG box. Partial clones for the first three Sox genes (al-a3) were isolated by homology to the HMG box of the testis-determining gene Sry and are now termed Sox-1, Sox-2 and Sox-3, Sox-3 is highly conserved amongst mammalian species and is located on the X chromosome. This has led to the proposal that Sry evolved from Sox-3. We present the cloning and sequencing of Sox-1, Sox-2 and Sox-3 from the mouse and show that Sox-3 is most closely relate to Sry. We also confirm that mouse Sox-3 is located on the X chromosome between Hprt and Dmd. Analysis of the distribution of Sox-3 RNA shows that its main site of expression is in the developing central nervous system, suggesting a role for Sox-3 in neural development. Moreover, we demonstrate that Sox-3, as well as Sox-1 and Sox-2, are expressed in the urogenital ridge and that their protein products are able to bind the same DNA sequence motif as Sry in vitro, but with different affinities. These observations prompt discussion of an evolutionary link between the genes and support the model that Sry has evolved from Sox-3. However our findings imply that if this is true, then Sry has undergone concomitant changes resulting in loss of CNS expression and altered DNA-binding properties.
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16

Marshall Graves, Jennifer A. "Interactions between SRY and SOX genes in mammalian sex determination." BioEssays 20, no. 3 (December 6, 1998): 264–69. http://dx.doi.org/10.1002/(sici)1521-1878(199803)20:3<264::aid-bies10>3.0.co;2-1.

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17

Hu, Yacheng, Binzhong Wang, and Hejun Du. "A review on sox genes in fish." Reviews in Aquaculture 13, no. 4 (March 22, 2021): 1986–2003. http://dx.doi.org/10.1111/raq.12554.

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18

Nagai, K. "Molecular evolution of Sry and Sox genes." Biochemical Society Transactions 28, no. 5 (October 1, 2000): A186. http://dx.doi.org/10.1042/bst028a186.

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19

Kawasaki, Katsushige, Maiko Kawasaki, Momoko Watanabe, Erik Idrus, Takahiro Nagai, Shelly Oommen, Takeyasu Maeda, et al. "Expression of Sox genes in tooth development." International Journal of Developmental Biology 59, no. 10-11-12 (2015): 471–78. http://dx.doi.org/10.1387/ijdb.150192ao.

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20

Lovell-Badge, Robin. "The early history of the Sox genes." International Journal of Biochemistry & Cell Biology 42, no. 3 (March 2010): 378–80. http://dx.doi.org/10.1016/j.biocel.2009.12.003.

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21

Abdullah, Muhammad, Muhammad Saif-ur Rehman, Muhammad Shah Nawaz-ul Rehman, Abdullah A. AlKahtane, Tahani Mohamed Al-Hazani, Faiz-ul Hassan, and Saif ur Rehman. "Genome-Wide Identification, Evolutionary and Mutational Analysis of the Buffalo Sox Gene Family." Animals 13, no. 14 (July 8, 2023): 2246. http://dx.doi.org/10.3390/ani13142246.

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The Sox gene family constitutes transcription factors with a conserved high mobility group box (HMG) that regulate a variety of developmental processes, including sex differentiation, neural, cartilage, and early embryonic development. In this study, we systematically analyzed and characterized the 20 Sox genes from the whole buffalo genome, using comparative genomic and evolutionary analyses. All the buffalo Sox genes were divided into nine sub-groups, and each gene had a specific number of exons and introns, which contributed to different gene structures. Molecular phylogeny revealed more sequence similarity of buffalo Sox genes with those of cattle. Furthermore, evolutionary analysis revealed that the HMG domain remained conserved in the all members of the Sox gene family. Similarly, all the genes are under strong purifying selection pressure; seven segmental duplications occurred from 9.65 to 21.41 million years ago (MYA), and four potential recombination breakpoints were also predicted. Mutational analysis revealed twenty non-synonymous mutations with potential effects on physiological functions, including embryonic development and cell differentiation in the buffalo. The present study provides insights into the genetic architecture of the Sox gene family in buffalo, highlights the significance of mutations, and provides their potential utility for marker-assisted selection for targeted genetic improvement in buffalo.
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22

Jiang, Lan, De Bi, Hengwu Ding, Xuan Wu, Ran Zhu, Juhua Zeng, Xiaojun Yang, and Xianzhao Kan. "Systematic Identification and Evolution Analysis of Sox Genes in Coturnix japonica Based on Comparative Genomics." Genes 10, no. 4 (April 22, 2019): 314. http://dx.doi.org/10.3390/genes10040314.

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Coturnix japonica (Japanese quail) has been extensively used as a model animal for biological studies. The Sox gene family, which was systematically characterized by a high-mobility group (HMG-box) in many animal species, encodes transcription factors that play central roles during multiple developmental processes. However, genome-wide investigations on the Sox gene family in birds are scarce. In the current study, we first performed a genome-wide study to explore the Sox gene family in galliform birds. Based on available genomic sequences retrieved from the NCBI database, we focused on the global identification of the Sox gene family in C. japonica and other species in Galliformes, and the evolutionary relationships of Sox genes. In our result, a total of 35 Sox genes in seven groups were identified in the C. japonica genome. Our results also revealed that dispersed gene duplications contributed the most to the expansion of the Sox gene family in Galliform birds. Evolutionary analyses indicated that Sox genes are an ancient gene family, and strong purifying selections played key roles in the evolution of CjSox genes of C. japonica. More interestingly, we observed that most Sox genes exhibited highly embryo-specific expression in both gonads. Our findings provided new insights into the molecular function and phylogeny of Sox gene family in birds.
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23

Seok, Jaekwon, Minchan Gil, Ahmed Abdal Dayem, Subbroto Kumar Saha, and Ssang-Goo Cho. "Multi-Omics Analysis of SOX4, SOX11, and SOX12 Expression and the Associated Pathways in Human Cancers." Journal of Personalized Medicine 11, no. 8 (August 23, 2021): 823. http://dx.doi.org/10.3390/jpm11080823.

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The Sry-related HMG BOX (SOX) gene family encodes transcription factors containing highly conserved high-mobility group domains that bind to the minor groove in DNA. Although some SOX genes are known to be associated with tumorigenesis and cancer progression, their expression and prognostic value have not been systematically studied. We performed multi-omic analysis to investigate the expression of SOX genes in human cancers. Expression and phylogenetic tree analyses of the SOX gene family revealed that the expression of three closely related SOX members, SOX4, SOX11, and SOX12, was increased in multiple cancers. Expression, mutation, and alteration of the three SOX members were evaluated using the Oncomine and cBioPortal databases, and the correlation between these genes and clinical outcomes in various cancers was examined using the Kaplan–Meier, PrognoScan, and R2 database analyses. The genes commonly correlated with the three SOX members were categorized in key pathways related to the cell cycle, mitosis, immune system, and cancer progression in liver cancer and sarcoma. Additionally, functional protein partners with three SOX proteins and their probable signaling pathways were explored using the STRING database. This study suggests the prognostic value of the expression of three SOX genes and their associated pathways in various human cancers.
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24

Ishikawa, Ryuichi, Maiko Kawasaki, Katsushige Kawasaki, Akane Yamada, Supaluk Trakanant, Fumiya Meguro, Atsushi Kitamura, Takehisa Kudo, Takeyasu Maeda, and Atsushi Ohazama. "Sox Genes Show Spatiotemporal Expression during Murine Tongue and Eyelid Development." International Journal of Dentistry 2018 (October 9, 2018): 1–13. http://dx.doi.org/10.1155/2018/1601363.

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The tongue is a critical organ, involved in functions such as speaking, swallowing, mastication, and degustation. Although Sox genes are known to play critical roles in many biological processes, including organogenesis, the expression of the Sox family members during tongue development remains unclear. We therefore performed a comparative in situ hybridization analysis of 17 Sox genes (Sox1–14, 17, 18, and 21) during murine tongue development. Sox2, 4, 6, 8, 9, 10, 11, 12, and 21 were found to be expressed in the tongue epithelium, whereas Sox2, 4–6, 8–11, 13, and 21 showed expression in the mesenchyme of the developing tongue. Expression of Sox1, 4, 6, 8–12, and 21 were observed in the developing tongue muscle. Sox5 and 13 showed expression only at E12, while Sox1 expression was observed only on E18. Sox6, 8, 9, and 12 showed expression at several stages. Although the expression of Sox2, 4, 10, 11, and 21 was detected during all the four stages of tongue development, their expression patterns differed among the stages. We thus identified a dynamic spatiotemporal expression pattern of the Sox genes during murine tongue development. To understand whether Sox genes are involved in the development of other craniofacial organs through similar roles to those in tongue development, we also examined the expression of Sox genes in eyelid primordia, which also contain epithelium, mesenchyme, and muscle. However, expression patterns and timing of Sox genes differed between tongue and eyelid development. Sox genes are thus related to organogenesis through different functions in each craniofacial organ.
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25

Kim, Hye-Joung, and Gun-Il Im. "Electroporation-Mediated Transfer of SOX Trio Genes (SOX-5, SOX-6, and SOX-9) to Enhance the Chondrogenesis of Mesenchymal Stem Cells." Stem Cells and Development 20, no. 12 (December 2011): 2103–14. http://dx.doi.org/10.1089/scd.2010.0516.

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26

Sun, Yubo, David R. Mauerhan, Nury M. Steuerwald, Jane Ingram, Jeffrey S. Kneisl, and Edward N. Hanley. "Expression of Phosphocitrate-Targeted Genes in Osteoarthritis Menisci." BioMed Research International 2014 (2014): 1–17. http://dx.doi.org/10.1155/2014/210469.

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Phosphocitrate (PC) inhibited calcium crystal-associated osteoarthritis (OA) in Hartley guinea pigs. However, the molecular mechanisms remain elusive. This study sought to determine PC targeted genes and the expression of select PC targeted genes in OA menisci to test hypothesis that PC exerts its disease modifying activity in part by reversing abnormal expressions of genes involved in OA. We found that PC downregulated the expression of numerous genes classified in immune response, inflammatory response, and angiogenesis, including chemokine (C-C motif) ligand 5, Fc fragment of IgG, low affinity IIIb receptor (FCGR3B), and leukocyte immunoglobulin-like receptor, subfamily B member 3 (LILRB3). In contrast, PC upregulated the expression of many genes classified in skeletal development, including collagen type II alpha1, fibroblast growth factor receptor 3 (FGFR3), and SRY- (sex determining region Y-) box 9 (SOX-9). Immunohistochemical examinations revealed higher levels of FCGR3B and LILRB3 and lower level of SOX-9 in OA menisci. These findings indicate that OA is a disease associated with immune system activation and decreased expression of SOX-9 gene in OA menisci. PC exerts its disease modifying activity on OA, at least in part, by targeting immune system activation and the production of extracellular matrix and selecting chondroprotective proteins.
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27

Li, Jingyuan, Jacson Shen, Kunzheng Wang, Francis Hornicek, and Zhenfeng Duan. "The Roles of Sox Family Genes in Sarcoma." Current Drug Targets 17, no. 15 (October 19, 2016): 1761–72. http://dx.doi.org/10.2174/1389450117666160502145311.

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28

Akinyemi, Mabel O., Jessica Finucan, Anastasia Grytsay, Osamede H. Osaiyuwu, Muyiwa S. Adegbaju, Ibukun M. Ogunade, Bolaji N. Thomas, Sunday O. Peters, and Olanrewaju B. Morenikeji. "Molecular Evolution and Inheritance Pattern of Sox Gene Family among Bovidae." Genes 13, no. 10 (October 2, 2022): 1783. http://dx.doi.org/10.3390/genes13101783.

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Sox genes are an evolutionarily conserved family of transcription factors that play important roles in cellular differentiation and numerous complex developmental processes. In vertebrates, Sox proteins are required for cell fate decisions, morphogenesis, and the control of self-renewal in embryonic and adult stem cells. The Sox gene family has been well-studied in multiple species including humans but there has been scanty or no research into Bovidae. In this study, we conducted a detailed evolutionary analysis of this gene family in Bovidae, including their physicochemical properties, biological functions, and patterns of inheritance. We performed a genome-wide cataloguing procedure to explore the Sox gene family using multiple bioinformatics tools. Our analysis revealed a significant inheritance pattern including conserved motifs that are critical to the ability of Sox proteins to interact with the regulatory regions of target genes and orchestrate multiple developmental and physiological processes. Importantly, we report an important conserved motif, EFDQYL/ELDQYL, found in the SoxE and SoxF groups but not in other Sox groups. Further analysis revealed that this motif sequence accounts for the binding and transactivation potential of Sox proteins. The degree of protein–protein interaction showed significant interactions among Sox genes and related genes implicated in embryonic development and the regulation of cell differentiation. We conclude that the Sox gene family uniquely evolved in Bovidae, with a few exhibiting important motifs that drive several developmental and physiological processes.
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29

Underwood, Adam, Daniel T. Rasicci, David Hinds, Jackson T. Mitchell, Jacob K. Zieba, Joshua Mills, Nicholas E. Arnold, et al. "Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships." Genes 14, no. 1 (January 14, 2023): 222. http://dx.doi.org/10.3390/genes14010222.

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The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype–phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood–brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
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30

Stevanovic, Milena, Natasa Kovacevic-Grujicic, Isidora Petrovic, Danijela Drakulic, Milena Milivojevic, and Marija Mojsin. "Crosstalk between SOX Genes and Long Non-Coding RNAs in Glioblastoma." International Journal of Molecular Sciences 24, no. 7 (March 28, 2023): 6392. http://dx.doi.org/10.3390/ijms24076392.

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Glioblastoma (GBM) continues to be the most devastating primary brain malignancy. Despite significant advancements in understanding basic GBM biology and enormous efforts in developing new therapeutic approaches, the prognosis for most GBM patients remains poor with a median survival time of 15 months. Recently, the interplay between the SOX (SRY-related HMG-box) genes and lncRNAs (long non-coding RNAs) has become the focus of GBM research. Both classes of molecules have an aberrant expression in GBM and play essential roles in tumor initiation, progression, therapy resistance, and recurrence. In GBM, SOX and lncRNAs crosstalk through numerous functional axes, some of which are part of the complex transcriptional and epigenetic regulatory mechanisms. This review provides a systematic summary of current literature data on the complex interplay between SOX genes and lncRNAs and represents an effort to underscore the effects of SOX/lncRNA crosstalk on the malignant properties of GBM cells. Furthermore, we highlight the significance of this crosstalk in searching for new biomarkers and therapeutic approaches in GBM treatment.
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31

Dehshahri, Ali, Alessio Biagioni, Hadi Bayat, E. Hui Clarissa Lee, Mohammad Hashemabadi, Hojjat Samareh Fekri, Ali Zarrabi, Reza Mohammadinejad, and Alan Prem Kumar. "Editing SOX Genes by CRISPR-Cas: Current Insights and Future Perspectives." International Journal of Molecular Sciences 22, no. 21 (October 20, 2021): 11321. http://dx.doi.org/10.3390/ijms222111321.

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Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and its associated proteins (Cas) is an adaptive immune system in archaea and most bacteria. By repurposing these systems for use in eukaryote cells, a substantial revolution has arisen in the genome engineering field. In recent years, CRISPR-Cas technology was rapidly developed and different types of DNA or RNA sequence editors, gene activator or repressor, and epigenome modulators established. The versatility and feasibility of CRISPR-Cas technology has introduced this system as the most suitable tool for discovering and studying the mechanism of specific genes and also for generating appropriate cell and animal models. SOX genes play crucial roles in development processes and stemness. To elucidate the exact roles of SOX factors and their partners in tissue hemostasis and cell regeneration, generating appropriate in vitro and in vivo models is crucial. In line with these premises, CRISPR-Cas technology is a promising tool for studying different family members of SOX transcription factors. In this review, we aim to highlight the importance of CRISPR-Cas and summarize the applications of this novel, promising technology in studying and decoding the function of different members of the SOX gene family.
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32

Lyu, Xiao, Xi Zhang, Li-bin Sun, Xiao-ming Cao, and Xu-hui Zhang. "Identification of SOX6 and SOX12 as Prognostic Biomarkers for Clear Cell Renal Cell Carcinoma: A Retrospective Study Based on TCGA Database." Disease Markers 2021 (November 26, 2021): 1–17. http://dx.doi.org/10.1155/2021/7190301.

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Background. The SOX gene family has been proven to display regulatory effects on numerous diseases, particularly in the malignant progression of neoplasms. However, the molecular functions and action mechanisms of SOX genes have not been clearly elucidated in clear cell renal cell carcinoma (ccRCC). We aimed to explore the expression status, prognostic values, clinical significances, and regulatory actions of SOX genes in ccRCC. Methods. RNA-sequence data and clinical information derived from The Cancer Genome Atlas (TCGA) database was used for this study. Dysregulated SOX genes between the normal group and ccRCC group were screened using the Wilcoxon signed-rank test. The Kaplan-Meier analysis and univariate Cox analysis methods were used to estimate the overall survival (OS) and disease-specific survival (DSS) differences between different groups. The independent prognostic factors were identified by the use of uni- and multivariate assays. Subsequently, the Wilcoxon signed-rank test or Kruskal-Wallis test and the chi-square test or Fisher exact probability methods were employed to explore the association between clinicopathological variables and SOX genes. Finally, CIBERSORT was applied to study the samples and examine the infiltration of immune cells between different groups. Results. Herein, 12 dysregulated SOX genes in ccRCC were screened. Among them, two independent prognostic SOX genes (SOX6 and SOX12) were identified. Further investigation results showed that SOX6 and SOX12 were distinctly associated with clinicopathological features. Furthermore, functional enrichment analysis revealed that SOX6 and SOX12 were enriched in essential biological processes and signaling pathways. Finally, we found that the SOX6 and SOX12 expression levels were correlated with tumor-infiltrating immune cells (TIICs). Conclusion. The pooled analyses showed that SOX6 and SOX12 could serve as promising biomarkers and therapeutic targets of patients with ccRCC.
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33

Uy, Benjamin R., Marcos Simoes-Costa, Tatjana Sauka-Spengler, and Marianne E. Bronner. "Expression of Sox family genes in early lamprey development." International Journal of Developmental Biology 56, no. 5 (2012): 377–83. http://dx.doi.org/10.1387/ijdb.113416bu.

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Crémazy, Frédéric, Philippe Berta, and Franck Girard. "Genome-wide analysis of Sox genes in Drosophila melanogaster." Mechanisms of Development 109, no. 2 (December 2001): 371–75. http://dx.doi.org/10.1016/s0925-4773(01)00529-9.

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Watanabe, Momoko, Katsushige Kawasaki, Maiko Kawasaki, Thantrira Portaveetus, Shelly Oommen, James Blackburn, Takahiro Nagai, et al. "Spatio-temporal expression of Sox genes in murine palatogenesis." Gene Expression Patterns 21, no. 2 (July 2016): 111–18. http://dx.doi.org/10.1016/j.gep.2016.05.002.

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36

Wittstatt, Jan, Simone Reiprich, and Melanie Küspert. "Crazy Little Thing Called Sox—New Insights in Oligodendroglial Sox Protein Function." International Journal of Molecular Sciences 20, no. 11 (June 2, 2019): 2713. http://dx.doi.org/10.3390/ijms20112713.

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In the central nervous system, oligodendrocytes wrap axons with myelin sheaths, which is essential for rapid transfer of electric signals and their trophic support. In oligodendroglia, transcription factors of the Sox protein family are pivotal regulators of a variety of developmental processes. These include specification, proliferation, and migration of oligodendrocyte precursor cells as well as terminal differentiation to mature myelinating oligodendrocytes. Sox proteins are further affected in demyelinating diseases and are involved in remyelination following damage of the central nervous system. Here we summarize and discuss latest findings on transcriptional regulation of Sox proteins, their function, target genes, and interaction with other transcription factors and chromatin remodelers in oligodendroglia with physiological and pathophysiological relevance.
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Garifulin, O. M., K. O. Shostak, V. V. Dmitrenko, V. D. Rozumenko, O. V. Khomenko, Yu P. Zozulya, G. Zehetner, and V. M. Kavsan. "The genes SOX-2 and HC gp-39 are overexpressed in astrocytic gliomas." Biopolymers and Cell 18, no. 4 (July 20, 2002): 324–29. http://dx.doi.org/10.7124/bc.000613.

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38

Fontijn, Ruud D., Oscar L. Volger, Joost O. Fledderus, Arie Reijerkerk, Helga E. de Vries, and Anton J. G. Horrevoets. "SOX-18 controls endothelial-specific claudin-5 gene expression and barrier function." American Journal of Physiology-Heart and Circulatory Physiology 294, no. 2 (February 2008): H891—H900. http://dx.doi.org/10.1152/ajpheart.01248.2007.

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Members of the claudin family constitute tight junction strands and are major determinants in specificity and selectivity of paracellular barriers. Transcriptional control of claudin gene expression is essential to establish individual claudin expression patterns and barrier properties. Using full genome expression profiling, we now identify sex-determining region Y-box (SOX)-18, a member of the SOX family of high-mobility group box transcription factors, as one of the most differentially induced genes during establishment of the endothelial barrier. We show that overexpression of SOX-18 and a dominant-negative mutant thereof, as well as SOX-18 silencing, greatly affect levels of claudin-5 (CLDN5). The relevance of an evolutionary conserved SOX-binding site in the CLDN5 promoter is shown using sequential promoter deletions, as well as point mutations. Furthermore, SOX-18 silencing abrogates endothelial barrier function, as measured by electric cell-substrate impedance sensing. Thus an obligatory role for SOX-18 in the regulation of CLDN5 gene expression in an endothelial-specific and cell density-dependent manner is established, as well as a crucial, nonredundant role for specifically SOX-18 in the formation of the endothelial barrier.
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39

Anitha, Arumugam, and Balasubramanian Senthilkumaran. "Role of sox family genes in teleostean reproduction-an overview." Reproduction and Breeding 1, no. 1 (March 2021): 22–31. http://dx.doi.org/10.1016/j.repbre.2021.02.004.

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40

Zhu, Yongzhao, Yong Li, Jun Wei Jun Wei, and Xiaoming Liu. "The Role of Sox Genes in Lung Morphogenesis and Cancer." International Journal of Molecular Sciences 13, no. 12 (November 26, 2012): 15767–83. http://dx.doi.org/10.3390/ijms131215767.

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41

Barrionuevo, Francisco, and Gerd Scherer. "SOX E genes: SOX9 and SOX8 in mammalian testis development." International Journal of Biochemistry & Cell Biology 42, no. 3 (March 2010): 433–36. http://dx.doi.org/10.1016/j.biocel.2009.07.015.

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42

Wallis, M. C., M. L. Delbridge, A. J. Pask, A. E. Alsop, F. Grützner, P. C. M. O’Brien, W. Rens, M. A. Ferguson-Smith, and J. A. M. Graves. "Mapping platypus SOX genes; autosomal location of SOX9 excludes it from sex determining role." Cytogenetic and Genome Research 116, no. 3 (2007): 232–34. http://dx.doi.org/10.1159/000098192.

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43

Coley, L. W., R. A. Godke, and K. R. Bondioli. "235 EXPRESSION OF PLURIPOTENCY-ASSOCIATED GENES IN BOVINE FETAL FIBROBLAST CELLS AND ADIPOSE-DERIVED STEM CELLS." Reproduction, Fertility and Development 22, no. 1 (2010): 275. http://dx.doi.org/10.1071/rdv22n1ab235.

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The extraordinary nature of embryonic stem cells (ESC) lends them the remarkable ability to give rise to all the cell types of a mammalian organism, an attribute known as pluripotency. The pluripotent state of ESC is dependent on the expression of the genes Oct-4, Nanog, and Sox-2, which have also been identified as the key transcriptional regulators of pluripotency. Until recently, Oct-4, Nanog, and Sox-2 were believed to be expressed solely in ESC; however, studies have reported the expression of these genes in some sources of adult stem cells (ASC) of both the mouse and pig. In the current study, we examined cells derived from bovine adipose tissue and fetal fibroblast for the expression of Nanog and Sox-2. Cells were isolated from the adipose tissue of an adult cow and the skin of 2 male fetuses, approximately 70 and 80 d old, and cultured through 6 passages. Total RNA was isolated from each of the 3 cell lines at passages 2, 4, and 6 using TRI Reagent®. Using the Bio-Rad iScript™ cDNA Synthesis Kit, the resulting RNA products were transcribed into cDNA 3 times for separate RT-PCR reactions. RT-PCR was performed with primers for Nanog, Sox-2, and Poly A Polymerase (PAP), as a reference gene for normalization. Primer sets for Nanog and PAP have previously been verified to amplify their respective transcripts in bovine embryos. Reaction products of PCR were subjected to electrophoresis and analyzed by Quantity One software (Bio-Rad). The number of pixels in each electrophoresis band was used to determine the relative transcript levels and was expressed as a ratio of Nanog or Sox-2 to PAP (Table 1). Both Nanog and Sox-2 were present in all cell lines at all 3 passages. Because Oct-4 is known to function synergistically with Nanog and Sox-2 to confer pluripotency, we are currently examining these samples for the presence of Oct-4. The presence of transcripts for the pluripotency-associated genes Nanog and Sox-2 in cells that are not inherently pluripotent suggests that there might be another level of regulation at the translational level for these genes. Table 1.Transcript abundance of pluripotency-associated genes relative to PA P in bovine fetal fibroblast (BFF) and adipose-derived adult stem cells (ADAS)
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44

Zygar, C. A., T. L. Cook, and R. M. Grainger. "Gene activation during early stages of lens induction in Xenopus." Development 125, no. 17 (September 1, 1998): 3509–19. http://dx.doi.org/10.1242/dev.125.17.3509.

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Several stages in the lens determination process have been defined, though it is not known which gene products control these events. At mid-gastrula stages in Xenopus, ectoderm is transiently competent to respond to lens-inducing signals. Between late gastrula and neural tube stages, the presumptive lens ectoderm acquires a lens-forming bias, becomes specified to form lens and begins differentiation. Several genes have been identified, either by expression pattern, mutant phenotype or involvement in crystallin gene regulation, that may play a role in lens bias and specification, and we focus on these roles here. Fate mapping shows that the transcriptional regulators Otx-2, Pax-6 and Sox-3 are expressed in the presumptive lens ectoderm prior to lens differentiation. Otx-2 appears first, followed by Pax-6, during the stages of lens bias (late neural plate stages); expression of Sox-3 follows neural tube closure and lens specification. We also demonstrate the expression of these genes in competent ectoderm transplanted to the lens-forming region. Expression of these genes is maintained or activated preferentially in ectoderm in response to the anterior head environment. Finally, we examined activation of these genes in response to early and late lens-inducing signals. Activation of Otx-2, Pax-6 and Sox-3 in competent ectoderm occurs in response to the early inducing tissue, the anterior neural plate. Since Sox-3 is activated following neural tube closure, we tested its dependence on the later inducing tissue, the optic vesicle, which contacts lens ectoderm at this stage. Sox-3 is not expressed in lens ectoderm, nor does a lens form, when the optic vesicle anlage is removed at late neural plate stages. Expression of these genes demarcates patterning events preceding differentiation and is tightly coupled to particular phases of lens induction.
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45

Bardischewsky, Frank, Jörg Fischer, Bettina Höller, and Cornelius G. Friedrich. "SoxV transfers electrons to the periplasm of Paracoccus pantotrophus – an essential reaction for chemotrophic sulfur oxidation." Microbiology 152, no. 2 (February 1, 2006): 465–72. http://dx.doi.org/10.1099/mic.0.28523-0.

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The soxVW genes are located upstream of the sox gene cluster encoding the sulfur-oxidizing ability of Paracoccus pantotrophus. SoxV is highly homologous to CcdA, which is involved in cytochrome c maturation of P. pantotrophus. SoxV was shown to function in reduction of the periplasmic SoxW, which shows a CysXaaXaaCys motif characteristic for thioredoxins. From strain GBΩV, which carries an Ω-kanamycin-resistance-encoding interposon in soxV, and complementation analysis it was evident that SoxV but not the periplasmic SoxW was essential for lithoautotrophic growth of P. pantotrophus with thiosulfate. However, the thiosulfate-oxidizing activities of cell extracts from the wild-type and from strain GBΩV were similar, demonstrating that the low thiosulfate-oxidizing activity of strain GBΩV in vivo was not due to a defect in biosynthesis or maturation of proteins of the Sox system and suggesting that SoxV is part of a regulatory or catalytic system of the Sox system. Analysis of DNA sequences available from different organisms harbouring a Sox system revealed that soxVW genes are exclusively present in sox operons harbouring the soxCD genes, encoding sulfur dehydrogenase, suggesting that SoxCD might be a redox partner of SoxV. No complementation of the ccdA mutant P. pantotrophus TP43 defective in cytochrome c maturation was achieved by expression of soxV in trans, demonstrating that the high identity of SoxV and CcdA does not correspond to functional homology.
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46

Mizuseki, K., M. Kishi, M. Matsui, S. Nakanishi, and Y. Sasai. "Xenopus Zic-related-1 and Sox-2, two factors induced by chordin, have distinct activities in the initiation of neural induction." Development 125, no. 4 (February 15, 1998): 579–87. http://dx.doi.org/10.1242/dev.125.4.579.

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In a differential screen for downstream genes of the neural inducers, we identified two extremely early neural genes induced by Chordin and suppressed by BMP-4: Zic-related-1 (Zic-r1), a zinc finger factor related to the Drosophila pair-rule gene odd-paired, and Sox-2, a Sry-related HMG factor. Expression of the two genes is first detected widely in the prospective neuroectoderm at the beginning of gastrulation, following the onset of Chordin expression and preceding that of Neurogenin (Xngnr-1). Zic-r1 mRNA injection activates the proneural gene Xngnr-1, and initiates neural and neuronal differentiation in isolated animal caps and in vivo. In contrast, Sox-2 alone is not sufficient to cause neural differentiation, but can work synergistically with FGF signaling to initiate neural induction. Thus, Zic-r1 acts in the pathway bridging the neural inducer with the downstream proneural genes, while Sox-2 makes the ectoderm responsive to extracellular signals, demonstrating that the early phase of neural induction involves simultaneous activation of multiple functions.
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47

Mistri, Tapan Kumar, Wibowo Arindrarto, Wei Ping Ng, Choayang Wang, Leng Hiong Lim, Lili Sun, Ian Chambers, Thorsten Wohland, and Paul Robson. "Dynamic changes in Sox2 spatio-temporal expression promote the second cell fate decision through Fgf4/Fgfr2 signaling in preimplantation mouse embryos." Biochemical Journal 475, no. 6 (March 20, 2018): 1075–89. http://dx.doi.org/10.1042/bcj20170418.

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Oct4 and Sox2 regulate the expression of target genes such as Nanog, Fgf4, and Utf1, by binding to their respective regulatory motifs. Their functional cooperation is reflected in their ability to heterodimerize on adjacent cis regulatory motifs, the composite Sox/Oct motif. Given that Oct4 and Sox2 regulate many developmental genes, a quantitative analysis of their synergistic action on different Sox/Oct motifs would yield valuable insights into the mechanisms of early embryonic development. In the present study, we measured binding affinities of Oct4 and Sox2 to different Sox/Oct motifs using fluorescence correlation spectroscopy. We found that the synergistic binding interaction is driven mainly by the level of Sox2 in the case of the Fgf4 Sox/Oct motif. Taking into account Sox2 expression levels fluctuate more than Oct4, our finding provides an explanation on how Sox2 controls the segregation of the epiblast and primitive endoderm populations within the inner cell mass of the developing rodent blastocyst.
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48

Kuroiwa, A., M. Uchikawa, Y. Kamachi, H. Kondoh, C. Nishida-Umehara, J. Masabanda, D. K. Griffin, and Y. Matsuda. "Chromosome assignment of eight SOX family genes in chicken." Cytogenetic and Genome Research 98, no. 2-3 (2002): 189–93. http://dx.doi.org/10.1159/000069803.

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49

Chen, Lin, Wei Li, Shaojun Liu, Min Tao, Yu Long, Wei Duan, Chun Zhang, et al. "Novel genetic markers derived from the DNA fragments of Sox genes." Molecular and Cellular Probes 23, no. 3-4 (June 2009): 157–65. http://dx.doi.org/10.1016/j.mcp.2009.03.001.

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50

Xin, Y., X. Tang, F. Yue, D. Zhang, X. Yan, C. Wang, and Q. Chen. "Isolation and sequence analysis of Sox genes from lizard Eremias multiocellata." Russian Journal of Genetics 48, no. 1 (January 2012): 79–85. http://dx.doi.org/10.1134/s102279541201019x.

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