Sox17 SRY-box transcription factor 17 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sox17provided by RGD
Official Full Name: SRY-box transcription factor 17provided by RGD
Primary source: RGD:1305371
See related: EnsemblRapid:ENSRNOG00000027357 AllianceGenome:RGD:1305371
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 sequence-specific double-stranded DNA binding activity. Involved in response to alkaloid. Located in nucleus. Biomarker of cholangiocarcinoma and pulmonary hypertension. Human ortholog(s) of this gene implicated in intracranial aneurysm; patent ductus arteriosus; and vesicoureteral reflux. Orthologous to human SOX17 (SRY-box transcription factor 17). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 81.0), Uterus (RPKM 51.2) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q12

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (19814345..19819859)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (15016660..15022228)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (14890318..14895907)

Chromosome 5 - NC_086023.1 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
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?

SOX17 Deficiency Mediates Pulmonary Hypertension: At the Crossroads of Sex, Metabolism, and Genetics.
Title: SOX17 Deficiency Mediates Pulmonary Hypertension: At the Crossroads of Sex, Metabolism, and Genetics.

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 activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology 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	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-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in angiogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within angiogenesis	ISO Inferred from Sequence Orthology more info
involved_in cardiac cell fate determination	ISO Inferred from Sequence Orthology more info
involved_in cardiogenic plate morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell migration involved in gastrulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to leukemia inhibitory factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within common bile duct development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic foregut morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in embryonic foregut morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic heart tube development	ISO Inferred from Sequence Orthology more info
involved_in embryonic heart tube morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endocardial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endocardium formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endoderm development	ISO Inferred from Sequence Orthology more info
involved_in endoderm development	ISO Inferred from Sequence Orthology more info
involved_in endoderm formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoderm formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endodermal cell fate determination	ISO Inferred from Sequence Orthology more info
involved_in endodermal cell fate specification	ISO Inferred from Sequence Orthology more info
involved_in endodermal digestive tract morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gallbladder development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gastrulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of gene expression	ISO Inferred from Sequence Orthology more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart looping	ISO Inferred from Sequence Orthology more info
involved_in heart looping	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner cell mass cellular morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in metanephros development	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in outflow tract morphogenesis	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
acts_upstream_of_or_within positive regulation of endodermal cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein catabolic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein destabilization	ISO Inferred from Sequence Orthology more info
involved_in protein stabilization	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of cardiac cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of embryonic development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of stem cell division	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of stem cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to alkaloid	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within rostrocaudal neural tube patterning	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within signal transduction involved in regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell fate specification	ISO Inferred from Sequence Orthology more info
involved_in ureter development	ISO Inferred from Sequence Orthology more info
involved_in vasculogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within vasculogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology 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-17

Names: SRY (sex determining region Y)-box 17; SRY box 17; SRY-box containing gene 17

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_001107902.1 → NP_001101372.1 transcription factor SOX-17

See identical proteins and their annotated locations for NP_001101372.1

Status: PROVISIONAL

Source sequence(s)

CH473984

UniProtKB/TrEMBL

A6JFJ9, G3V923

Conserved Domains (2) summary

cd01388
Location:67 → 138

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 ...

pfam12067
Location:203 → 253

Sox17_18_mid; Sox 17/18 central domain

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_086023.1 Reference GRCr8

Range

19814345..19819859

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063287521.1 → XP_063143591.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923
XM_063287523.1 → XP_063143593.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923
XM_039109753.2 → XP_038965681.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923

Related

ENSRNOP00000033962.4, ENSRNOT00000033116.6

Conserved Domains (2) summary

cd01388
Location:67 → 138

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 ...

pfam12067
Location:203 → 253

Sox17_18_mid; Sox 17/18 central domain
XM_039109752.2 → XP_038965680.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923

Conserved Domains (2) summary

cd01388
Location:67 → 138

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 ...

pfam12067
Location:203 → 253

Sox17_18_mid; Sox 17/18 central domain
XM_039109751.2 → XP_038965679.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923

Conserved Domains (2) summary

cd01388
Location:67 → 138

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 ...

pfam12067
Location:203 → 253

Sox17_18_mid; Sox 17/18 central domain
XM_063287522.1 → XP_063143592.1 transcription factor SOX-17 isoform X1

UniProtKB/TrEMBL

A6JFJ9, G3V923
XM_008763538.4 → XP_008761760.1 transcription factor SOX-17 isoform X1

See identical proteins and their annotated locations for XP_008761760.1

UniProtKB/TrEMBL

A6JFJ9, G3V923

Conserved Domains (2) summary

cd01388
Location:67 → 138

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 ...

pfam12067
Location:203 → 253

Sox17_18_mid; Sox 17/18 central domain