Arid5b AT-rich interaction domain 5B [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Arid5bprovided by RGD
Official Full Name: AT-rich interaction domain 5Bprovided by RGD
Primary source: RGD:1311735
See related: EnsemblRapid:ENSRNOG00000000635 AllianceGenome:RGD:1311735
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 transcription cis-regulatory region binding activity and transcription coactivator activity. Predicted to be involved in adipose tissue development and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including cellular response to leukemia inhibitory factor; face morphogenesis; and gonad development. Predicted to be located in nucleus. Orthologous to human ARID5B (AT-rich interaction domain 5B). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Lung (RPKM 104.7), Kidney (RPKM 98.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 20p11

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	20	NC_086038.1 (20305693..20489689)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	20	NC_051355.1 (20307731..20490746)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	20	NC_005119.4 (21713900..21881193)

Chromosome 20 - NC_086038.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Gene expression of type II collagen is regulated by direct interaction with Kruppel-like factor 4 and AT-rich interactive domain 5B.
Title: Gene expression of type II collagen is regulated by direct interaction with Kruppel-like factor 4 and AT-rich interactive domain 5B.

Submit: New GeneRIF Correction

General gene information

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Markers

BG377178 (e-PCR)
- UniSTS:244489

AU022012 (e-PCR)
- UniSTS:207632

D20Rat23 (e-PCR)
- UniSTS:118637

RH142848 (e-PCR)
- UniSTS:232095

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
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in adipose tissue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adrenal gland development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell development	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 face morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fat cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fat pad development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within female gonad development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within fibroblast migration	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within kidney development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male gonad development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within muscle organ morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within platelet-derived growth factor receptor signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic development	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 roof of mouth development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within skeletal system morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: AT-rich interactive domain-containing protein 5B

Names: AT rich interactive domain 5B (Mrf1 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_001107624.1 → NP_001101094.1 AT-rich interactive domain-containing protein 5B

See identical proteins and their annotated locations for NP_001101094.1

Status: PROVISIONAL

Source sequence(s)

CH473988

UniProtKB/TrEMBL

A0A8I6AEL5, A6JKU7

Related

ENSRNOP00000090849.1, ENSRNOT00000000787.10

Conserved Domains (3) summary

smart00501
Location:320 → 412

BRIGHT; BRIGHT, ARID (A/T-rich interaction domain) domain

pfam05466
Location:422 → 618

BASP1; Brain acid soluble protein 1 (BASP1 protein)

cl02608
Location:35 → 108

BAH; BAH, or Bromo Adjacent Homology domain (also called ELM1 and BAM for Bromo Adjacent Motif). BAH domains have first been described as domains found in the polybromo protein and Yeast Rsc1/Rsc2 (Remodeling of the Structure of Chromatin). They also occur in ...

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_086038.1 Reference GRCr8

Range

20305693..20489689

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063279167.1 → XP_063135237.1 AT-rich interactive domain-containing protein 5B isoform X3

UniProtKB/TrEMBL

A0A8I6AEL5
XM_039098745.2 → XP_038954673.2 AT-rich interactive domain-containing protein 5B isoform X1

UniProtKB/TrEMBL

A0A8I6AEL5

Related

ENSRNOP00000103812.1, ENSRNOT00000164224.1
XM_039098746.2 → XP_038954674.2 AT-rich interactive domain-containing protein 5B isoform X2

UniProtKB/TrEMBL

A0A8I6AEL5
XM_039098747.2 → XP_038954675.1 AT-rich interactive domain-containing protein 5B isoform X4

UniProtKB/TrEMBL

A0A8I6AEL5

Conserved Domains (2) summary

PTZ00121
Location:222 → 347

PTZ00121; MAEBL; Provisional

cd16885
Location:132 → 226

ARID_ARID5B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins
XM_063279168.1 → XP_063135238.1 AT-rich interactive domain-containing protein 5B isoform X6
XM_039098749.2 → XP_038954677.1 AT-rich interactive domain-containing protein 5B isoform X5

UniProtKB/TrEMBL

A0A8I6GGM4, A6JKU8

Related

ENSRNOP00000088828.1, ENSRNOT00000105517.2

Conserved Domains (2) summary

PTZ00121
Location:168 → 293

PTZ00121; MAEBL; Provisional

cd16885
Location:78 → 172

ARID_ARID5B; ARID/BRIGHT DNA binding domain of AT-rich interactive domain-containing protein 5B (ARID5B) and similar proteins