Sox13 SRY-box transcription factor 13 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sox13provided by RGD
Official Full Name: SRY-box transcription factor 13provided by RGD
Primary source: RGD:1309674
See related: EnsemblRapid:ENSRNOG00000028353 AllianceGenome:RGD:1309674
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: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and identical protein binding activity. Predicted to be involved in several processes, including negative regulation of canonical Wnt signaling pathway; positive regulation of cell differentiation; and spinal cord oligodendrocyte cell differentiation. Predicted to act upstream of or within regulation of gamma-delta T cell differentiation. Predicted to be located in cytoplasm and nucleoplasm. Predicted to be active in nucleus. Orthologous to human SOX13 (SRY-box transcription factor 13). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 149.9), Kidney (RPKM 113.3) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q13

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (47383145..47427572, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (44831097..44875522, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (50434702..50479118)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology 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 transcription regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell fate commitment	IBA Inferred from Biological aspect of Ancestor more info
involved_in gamma-delta T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of brown fat cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gamma-delta T cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gamma-delta T cell differentiation	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	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription factor SOX-13

Names: SRY (sex determining region Y)-box 13; SRY box 13; SRY-box containing gene 13

NCBI Reference Sequences (RefSeq)

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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)

NM_001105952.1 → NP_001099422.1 transcription factor SOX-13

See identical proteins and their annotated locations for NP_001099422.1

Status: PROVISIONAL

Source sequence(s)

CH473958

UniProtKB/TrEMBL

A6IC79, A6IC80

Related

ENSRNOP00000068223.3, ENSRNOT00000076857.3

Conserved Domains (2) summary

PHA03195
Location:250 → 418

PHA03195; tegument protein VP11/12; Provisional

cd01388
Location:414 → 485

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 ...

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

NC_086031.1 Reference GRCr8

Range

47383145..47427572 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006249762.5 → XP_006249824.1 transcription factor SOX-13 isoform X3

UniProtKB/TrEMBL

A6IC80, D4A8S0

Conserved Domains (2) summary

cd01388
Location:415 → 486

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 ...

cl28045
Location:251 → 419

Herpes_UL46; Herpesvirus UL46 protein
XM_039090434.2 → XP_038946362.1 transcription factor SOX-13 isoform X3

UniProtKB/TrEMBL

A6IC80, D4A8S0

Related

ENSRNOP00000030216.6, ENSRNOT00000032244.9

Conserved Domains (2) summary

cd01388
Location:415 → 486

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 ...

cl28045
Location:251 → 419

Herpes_UL46; Herpesvirus UL46 protein
XM_063272079.1 → XP_063128149.1 transcription factor SOX-13 isoform X4

UniProtKB/TrEMBL

A6IC79, A6IC80
XM_063272078.1 → XP_063128148.1 transcription factor SOX-13 isoform X2
XM_063272077.1 → XP_063128147.1 transcription factor SOX-13 isoform X1