Arid4a AT-rich interaction domain 4A [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Arid4aprovided by RGD
Official Full Name: AT-rich interaction domain 4Aprovided by RGD
Primary source: RGD:1307442
See related: EnsemblRapid:ENSRNOG00000026239 AllianceGenome:RGD:1307442
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
Summary: Predicted to enable transcription cis-regulatory region binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including erythrocyte development; establishment of Sertoli cell barrier; and regulation of gene expression. Predicted to be located in nucleoplasm and plasma membrane. Predicted to be part of transcription repressor complex. Predicted to be active in nucleus. Orthologous to human ARID4A (AT-rich interaction domain 4A). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 119.6), Spleen (RPKM 110.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 6q24

Exon count:: 27

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	6	NC_086024.1 (95258429..95335987)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	6	NC_051341.1 (89522459..89593868)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	6	NC_005105.4 (93461713..93532901)

Chromosome 6 - NC_086024.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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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?

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General gene information

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Markers

D12Mit200.3 (e-PCR), detects polymorphism
- UniSTS:126757

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within chromatin organization	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within erythrocyte development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within establishment of Sertoli cell barrier	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within genomic imprinting	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	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
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
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
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of transcription repressor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: AT-rich interactive domain-containing protein 4A

Names: AT rich interactive domain 4A (Rbp1 like)

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_001395713.1 → NP_001382642.1 AT-rich interactive domain-containing protein 4A

Status: VALIDATED

Source sequence(s)

JAXUCZ010000006

UniProtKB/TrEMBL

A0A8I6AQP2

Related

ENSRNOP00000029718.5, ENSRNOT00000031595.7

Conserved Domains (5) summary

cd18641
Location:578 → 636

CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins

cl28902
Location:312 → 397

ARID; ARID/BRIGHT DNA binding domain family

pfam08169
Location:170 → 262

RBB1NT; RBB1NT (NUC162) domain

cd20459
Location:4 → 61

Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins

cl02573
Location:62 → 118

Tudor_SF; Tudor domain superfamily

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_086024.1 Reference GRCr8

Range

95258429..95335987

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039112256.2 → XP_038968184.1 AT-rich interactive domain-containing protein 4A isoform X1

UniProtKB/TrEMBL

A0A0G2K094, A0A8I6AQP2

Related

ENSRNOP00000071353.2, ENSRNOT00000089473.3

Conserved Domains (5) summary

cd18641
Location:597 → 655

CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins

cl28902
Location:331 → 416

ARID; ARID/BRIGHT DNA binding domain family

pfam08169
Location:189 → 281

RBB1NT; RBB1NT (NUC162) domain

cd20459
Location:23 → 80

Tudor_ARID4A_rpt1; first Tudor domain found in AT-rich interactive domain-containing protein 4A (ARID4A) and similar proteins

cl02573
Location:81 → 137

Tudor_SF; Tudor domain superfamily
XM_039112258.2 → XP_038968186.1 AT-rich interactive domain-containing protein 4A isoform X2

UniProtKB/TrEMBL

A0A8I6APL4

Conserved Domains (2) summary

cd18641
Location:256 → 314

CBD_RBP1_like; chromo barrel domain of retinoblastoma binding protein 1, and similar proteins

cl28902
Location:1 → 75

ARID; ARID/BRIGHT DNA binding domain family
XM_039112259.2 → XP_038968187.1 AT-rich interactive domain-containing protein 4A isoform X3

Conserved Domains (1) summary

cl28914
Location:1 → 33

CD_CSD; CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains

RNA

XR_010052092.1 RNA Sequence
XR_010052090.1 RNA Sequence
XR_010052094.1 RNA Sequence
XR_010052089.1 RNA Sequence
XR_010052091.1 RNA Sequence
XR_010052093.1 RNA Sequence
XR_010052095.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001108029.1: Suppressed sequence

Description

NM_001108029.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.