Sox5 SRY-box transcription factor 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sox5provided by RGD
Official Full Name: SRY-box transcription factor 5provided by RGD
Primary source: RGD:620471
See related: EnsemblRapid:ENSRNOG00000027869 AllianceGenome:RGD:620471
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Sox5l1
Summary: Enables cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including asymmetric neuroblast division; cartilage development; and positive regulation of cell differentiation. Predicted to act upstream of or within several processes, including neurogenesis; regulation of timing of neuron differentiation; and regulation of transcription, DNA-templated. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Orthologous to human SOX5 (SRY-box transcription factor 5). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Testes (RPKM 79.6), Liver (RPKM 52.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q44

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (178512272..179467686, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (176781375..177736833, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (178062267..179031991, complement)

Chromosome 4 - NC_086022.1 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

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study revealed that Sox5 and Sox6 prevent oligodendroglial differentiation, thus ensuring that the progenitor cells first reach their proper destination and only then lose their migratory capacity
Title: Transcription factors Sox5 and Sox6 exert direct and indirect influences on oligodendroglial migration in spinal cord and forebrain.
a spatially loaded combination of RUNX2 and SOX trio DNA loading significantly improved healing relative to empty hydrogels or either factor alone.
Title: Osteochondral tissue regeneration through polymeric delivery of DNA encoding for the SOX trio and RUNX2.
The gene expressions of SOX-5, -6, -9 decreased by 58, 20 and 40%, respectively, in the osteoarthritis cartilage, while their respective protein expressions increased.
Title: The expressions of the SOX trio, PTHrP (parathyroid hormone-related peptide)/IHH (Indian hedgehog protein) in surgically induced osteoarthritis of the rat.

Submit: New GeneRIF Correction

General gene information

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Markers

D4Got154 (e-PCR)
- UniSTS:111618

BE108803 (e-PCR)
- UniSTS:247898

Sox5 (e-PCR), detects polymorphism
- UniSTS:507239

Sox5 (e-PCR), detects polymorphism
- UniSTS:265085

Sox5 (e-PCR), detects polymorphism
- UniSTS:265086

D9Rat28 (e-PCR)
- UniSTS:119166

Sox5 (e-PCR), detects polymorphism
- UniSTS:265087

RH134712 (e-PCR)
- UniSTS:217990

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	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, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor 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 cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in asymmetric neuroblast division	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
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within central nervous system neuron differentiation	ISO Inferred from Sequence Orthology 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 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
acts_upstream_of_or_within oligodendrocyte differentiation	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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of mesenchymal stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of timing of neuron 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

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription factor SOX-5

Names: SRY (sex determining region Y)-box 5; SRY box 5; SRY-box containing gene 5; SRY-box containing gene 5-like 1

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_001014060.2 → NP_001014082.1 transcription factor SOX-5 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004
NM_001271267.2 → NP_001258196.1 transcription factor SOX-5 isoform 2

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

F1LQN4, F1M8W4, Q5U1X4

UniProtKB/TrEMBL

A6IMY0

Related

ENSRNOP00000052404.3, ENSRNOT00000055542.5

Conserved Domains (1) summary

cd01388
Location:555 → 626

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 ...
NM_001415821.1 → NP_001402750.1 transcription factor SOX-5 isoform 3

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

Related

ENSRNOP00000020729.8, ENSRNOT00000020729.8
NM_001415822.1 → NP_001402751.1 transcription factor SOX-5 isoform 4

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

Related

ENSRNOP00000073853.2, ENSRNOT00000087434.3
NM_001415823.1 → NP_001402752.1 transcription factor SOX-5 isoform 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

Related

ENSRNOP00000079278.2, ENSRNOT00000096663.2

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_086022.1 Reference GRCr8

Range

178512272..179467686 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017592402.3 → XP_017447891.1 transcription factor SOX-5 isoform X3

UniProtKB/TrEMBL

A6IMY0

Conserved Domains (1) summary

cd01388
Location:543 → 614

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 ...
XM_039106953.2 → XP_038962881.1 transcription factor SOX-5 isoform X3

UniProtKB/TrEMBL

A6IMY0

Conserved Domains (1) summary

cd01388
Location:543 → 614

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 ...
XM_063285440.1 → XP_063141510.1 transcription factor SOX-5 isoform X3
XM_039106952.2 → XP_038962880.1 transcription factor SOX-5 isoform X2

UniProtKB/TrEMBL

A6IMY0

Conserved Domains (1) summary

cd01388
Location:556 → 627

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 ...
XM_008763349.3 → XP_008761571.1 transcription factor SOX-5 isoform X4

UniProtKB/TrEMBL

A0A8I5ZMP4

Conserved Domains (1) summary

cd01388
Location:521 → 592

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 ...
XM_063285441.1 → XP_063141511.1 transcription factor SOX-5 isoform X5
XM_006237604.5 → XP_006237666.1 transcription factor SOX-5 isoform X1

UniProtKB/TrEMBL

A6IMY0

Conserved Domains (1) summary

cd01388
Location:556 → 627

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 ...
XM_017592410.3 → XP_017447899.1 transcription factor SOX-5 isoform X7
XM_063285442.1 → XP_063141512.1 transcription factor SOX-5 isoform X6
XM_063285443.1 → XP_063141513.1 transcription factor SOX-5 isoform X8