Arid1b AT-rich interaction domain 1B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Arid1bprovided by RGD
Official Full Name: AT-rich interaction domain 1Bprovided by RGD
Primary source: RGD:708504
See related: EnsemblRapid:ENSRNOG00000017030 AllianceGenome:RGD:708504
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: 6A3-5; Smcf1; smcf-1
Summary: Predicted to enable DNA binding activity. Predicted to contribute to nucleosome binding activity. Involved in cellular response to angiotensin and response to ischemia. Predicted to be located in several cellular components, including cytosol; nucleus; and synapse. Predicted to be part of SWI/SNF complex and nBAF complex. Predicted to be active in nucleoplasm. Used to study ischemia. Biomarker of hypertension and ischemia. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome; Coffin-Siris syndrome 1; intellectual disability; lung non-small cell carcinoma; and neuroblastoma. Orthologous to human ARID1B (AT-rich interaction domain 1B). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 141.7), Kidney (RPKM 111.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q11

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (47973199..48328793)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (45567991..45923644)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (45923119..46232301)

Chromosome 1 - NC_086019.1 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?

The molecular mechanism of the transcriptional activator SWI regulating gene ARID1B affecting swallowing dysfunction after stroke in rats.
Title: The molecular mechanism of the transcriptional activator SWI regulating gene ARID1B affecting swallowing dysfunction after stroke in rats.
6A3-5 expression is associated with alpha-smooth muscle cell actin in mesangial cells, arteriolar smooth muscle cells, and interstitial myofibroblasts. could potentially be a novel early vascular marker of acute and chronic renal ischemic stress
Title: Ischemia induces early expression of a new transcription factor (6A3-5) in kidney vascular smooth muscle cells: studies in rat and human renal pathology.

Submit: New GeneRIF Correction

General gene information

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Markers

RH138115 (e-PCR)
- UniSTS:220202

D1Rat313 (e-PCR), detects polymorphism
- UniSTS:227120

AW531100 (e-PCR)
- UniSTS:245075

AU046724 (e-PCR)
- UniSTS:111191

RH138438 (e-PCR)
- UniSTS:220525

STS-T31821 (e-PCR)
- UniSTS:25009

D1Mgh3 (e-PCR)
- UniSTS:240581

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	TAS Traceable Author Statement more info	PubMed
contributes_to nucleosome binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cellular response to angiotensin	IEP Inferred from Expression Pattern more info	PubMed
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dendritic cell dendrite assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within dendritic spine development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron-neuron synaptic transmission	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to ischemia	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of SWI/SNF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of SWI/SNF complex	ISO Inferred from Sequence Orthology more info
part_of brahma complex	IEA Inferred from Electronic Annotation more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
part_of nBAF complex	IBA Inferred from Biological aspect of Ancestor more info
part_of nBAF complex	ISO Inferred from Sequence Orthology more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: AT-rich interactive domain-containing protein 1B

Names: AT rich interactive domain 1B (Swi1 like); transcription factor 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_001419802.1 → NP_001406731.1 AT-rich interactive domain-containing protein 1B

Status: VALIDATED

Source sequence(s)

JAXUCZ010000001

UniProtKB/TrEMBL

A0A0G2JVD3

Related

ENSRNOP00000110916.1, ENSRNOT00000161412.1

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_086019.1 Reference GRCr8

Range

47973199..48328793

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039099697.2 → XP_038955625.1 AT-rich interactive domain-containing protein 1B isoform X4

UniProtKB/TrEMBL

F1LNP1

Related

ENSRNOP00000022939.7, ENSRNOT00000022939.9

Conserved Domains (4) summary

PHA03247
Location:126 → 391

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:703 → 1080

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd16877
Location:590 → 682

ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins

pfam12031
Location:1473 → 1728

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
XM_039099688.2 → XP_038955616.1 AT-rich interactive domain-containing protein 1B isoform X1

Conserved Domains (4) summary

PHA03247
Location:719 → 984

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:1296 → 1672

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd16877
Location:1183 → 1275

ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins

pfam12031
Location:2065 → 2320

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
XM_039099696.2 → XP_038955624.1 AT-rich interactive domain-containing protein 1B isoform X3

Related

ENSRNOP00000076073.3, ENSRNOT00000092976.3

Conserved Domains (4) summary

PHA03247
Location:575 → 924

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:1236 → 1613

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd16877
Location:1123 → 1215

ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins

pfam12031
Location:2006 → 2261

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa
XM_039099692.2 → XP_038955620.1 AT-rich interactive domain-containing protein 1B isoform X2

Related

ENSRNOP00000109702.1, ENSRNOT00000126261.1

Conserved Domains (4) summary

PHA03247
Location:575 → 945

PHA03247; large tegument protein UL36; Provisional

pfam09606
Location:1259 → 1636

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd16877
Location:1146 → 1238

ARID_ARID1B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 1B (ARID1B) and similar proteins

pfam12031
Location:2029 → 2284

BAF250_C; SWI/SNF-like complex subunit BAF250/Osa

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_172157.1: Suppressed sequence

Description

NM_172157.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.