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Sox6 SRY-box transcription factor 6 [ Rattus norvegicus (Norway rat) ]

Gene ID: 293165, updated on 2-Nov-2024

Summary

Symbol
Sox6provided by RGD
Full Name
SRY-box transcription factor 6provided by RGD
Primary source
RGD:1309000
See related
EnsemblRapid:ENSRNOG00000020514 AllianceGenome:RGD:1309000
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Enables cis-regulatory region sequence-specific DNA binding activity. Involved in astrocyte differentiation. Predicted to be located in nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in high grade glioma. Orthologous to human SOX6 (SRY-box transcription factor 6). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Biased expression in Muscle (RPKM 95.6), Kidney (RPKM 44.9) and 9 other tissues See more
Orthologs
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Genomic context

See Sox6 in Genome Data Viewer
Location:
1q35
Exon count:
33
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (179157678..179769243, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (169723306..170334846, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (185631702..186186192)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484912 Neighboring gene uncharacterized LOC120097959 Neighboring gene transfer RNA valine (anticodon AAC) 35 Neighboring gene similar to human chromosome 11 open reading frame 58 Neighboring gene pleckstrin homology domain containing A7 Neighboring gene uncharacterized LOC120099912

Genomic regions, transcripts, and products

Expression

  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription factor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 
enables DNA-binding transcription repressor activity ISO
Inferred from Sequence Orthology
more info
 
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
 
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
enables protein homodimerization activity ISO
Inferred from Sequence Orthology
more info
 
enables protein homodimerization activity ISS
Inferred from Sequence or Structural Similarity
more info
 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
 
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
involved_in astrocyte differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in brain development IEA
Inferred from Electronic Annotation
more info
 
involved_in brain development ISO
Inferred from Sequence Orthology
more info
 
involved_in brain development ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cardiac muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in cartilage condensation ISO
Inferred from Sequence Orthology
more info
 
involved_in cartilage condensation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within cartilage development ISO
Inferred from Sequence Orthology
more info
 
involved_in cartilage development ISO
Inferred from Sequence Orthology
more info
 
involved_in cartilage development ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cell fate commitment IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within cell fate commitment ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within cell morphogenesis ISO
Inferred from Sequence Orthology
more info
 
involved_in cellular response to transforming growth factor beta stimulus IEA
Inferred from Electronic Annotation
more info
 
involved_in cellular response to transforming growth factor beta stimulus ISO
Inferred from Sequence Orthology
more info
 
involved_in central nervous system development IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in chondrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in chondrocyte differentiation ISS
Inferred from Sequence or Structural Similarity
more info
 
acts_upstream_of_or_within erythrocyte development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within erythrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in gene expression ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within hemopoiesis ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within in utero embryonic development ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in negative regulation of cardiac muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in negative regulation of cardiac muscle cell differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within oligodendrocyte cell fate specification ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within oligodendrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of cartilage development ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of chondrocyte differentiation IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in positive regulation of chondrocyte differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of chondrocyte differentiation ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of mesenchymal stem cell differentiation IEA
Inferred from Electronic Annotation
more info
 
involved_in positive regulation of mesenchymal stem cell differentiation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within post-embryonic development ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in spinal cord oligodendrocyte cell differentiation ISO
Inferred from Sequence Orthology
more info
 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
transcription factor SOX-6
Names
SRY (sex determining region Y)-box 6
SRY box 6
SRY-box containing gene 6

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001024751.1NP_001019922.1  transcription factor SOX-6

    See identical proteins and their annotated locations for NP_001019922.1

    Status: PROVISIONAL

    Source sequence(s)
    BC097403
    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Related
    ENSRNOP00000079879.1, ENSRNOT00000094350.2
    Conserved Domains (1) summary
    cd01388
    Location:579650
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    179157678..179769243 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039106334.2XP_038962262.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  2. XM_063285244.1XP_063141314.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  3. XM_063285274.1XP_063141344.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  4. XM_039106327.2XP_038962255.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  5. XM_063285251.1XP_063141321.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  6. XM_063285245.1XP_063141315.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  7. XM_039106354.2XP_038962282.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  8. XM_063285282.1XP_063141352.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  9. XM_063285278.1XP_063141348.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  10. XM_039106338.2XP_038962266.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  11. XM_039106363.2XP_038962291.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  12. XM_039106343.2XP_038962271.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  13. XM_063285281.1XP_063141351.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  14. XM_039106328.1XP_038962256.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Related
    ENSRNOP00000044088.4, ENSRNOT00000048020.6
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  15. XM_039106374.2XP_038962302.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  16. XM_063285283.1XP_063141353.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  17. XM_063285280.1XP_063141350.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  18. XM_039106360.2XP_038962288.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  19. XM_063285275.1XP_063141345.1  transcription factor SOX-6 isoform X5

    UniProtKB/TrEMBL
    A0A6I8PLH1
  20. XM_039106377.2XP_038962305.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  21. XM_006230091.5XP_006230153.1  transcription factor SOX-6 isoform X5

    See identical proteins and their annotated locations for XP_006230153.1

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  22. XM_039106304.2XP_038962232.1  transcription factor SOX-6 isoform X3

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:627698
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  23. XM_039106313.2XP_038962241.1  transcription factor SOX-6 isoform X4

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:626697
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  24. XM_039106301.2XP_038962229.1  transcription factor SOX-6 isoform X1

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Related
    ENSRNOP00000068898.3, ENSRNOT00000079072.3
    Conserved Domains (1) summary
    cd01388
    Location:647718
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...
  25. XM_006230087.5XP_006230149.1  transcription factor SOX-6 isoform X2

    See identical proteins and their annotated locations for XP_006230149.1

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:646717
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
  26. XM_006230094.5XP_006230156.1  transcription factor SOX-6 isoform X8

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:585656
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
  27. XM_006230092.5XP_006230154.1  transcription factor SOX-6 isoform X6

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:606677
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
  28. XM_006230093.5XP_006230155.1  transcription factor SOX-6 isoform X7

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6R0V8A0, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:605676
    SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...
  29. XM_017588968.3XP_017444457.1  transcription factor SOX-6 isoform X5

    UniProtKB/Swiss-Prot
    A0A0G2JTZ2, F1MAJ5, Q4V8G3
    UniProtKB/TrEMBL
    A0A6I8PLH1, A6I8C8
    Conserved Domains (1) summary
    cd01388
    Location:620691
    SOX-TCF_HMG-box; class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and ...