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

Gene ID: 309728, updated on 10-Oct-2024

Summary

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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 animal organ development; cellular response to leukemia inhibitory factor; and face morphogenesis. Orthologous to human ARID5B (AT-rich interaction domain 5B). [provided by Alliance of Genome Resources, Apr 2022]
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

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See Arid5b in Genome Data Viewer
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_086038.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134483790 Neighboring gene transfer RNA alanine (anticodon AGC) 57 Neighboring gene uncharacterized LOC134483791 Neighboring gene uncharacterized LOC108349057 Neighboring gene uncharacterized LOC102550601 Neighboring gene rhotekin 2 Neighboring gene uncharacterized LOC120098810

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Modulator recognition factor-2 is required for adipogenesis in mouse embryo fibroblasts and 3T3-L1 cells. Yamakawa T, et al. Mol Endocrinol, 2008 Feb. PMID 17962384, Free PMC Article
  2. Neonatal mortality and leanness in mice lacking the ARID transcription factor Mrf-2. Whitson RH, et al. Biochem Biophys Res Commun, 2003 Dec 26. PMID 14651970
  3. The novel Mrf-2 DNA-binding domain recognizes a five-base core sequence through major and minor-groove contacts. Whitson RH, et al. Biochem Biophys Res Commun, 1999 May 10. PMID 10329386
  4. Gene expression of type II collagen is regulated by direct interaction with Kruppel-like factor 4 and AT-rich interactive domain 5B. Zhang X, et al. Gene, 2021 Mar 20. PMID 33383116
  5. Role of modulator recognition factor 2 in adipogenesis and leptin expression in 3T3-L1 cells. Dong J, et al. Biochem Biophys Res Commun, 2008 Feb 8. PMID 18070594

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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

Homology

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 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
  
involved_in positive regulation of DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
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
  
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
located_in nucleus IEA
Inferred from Electronic Annotation
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)

  1. 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

  1. NC_086038.1 Reference GRCr8

    Range
    20305693..20489689
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

    Related
    ENSRNOP00000103812.1, ENSRNOT00000164224.1

  3. XM_039098746.2 → XP_038954674.2  AT-rich interactive domain-containing protein 5B isoform X2

  4. 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

  5. XM_063279168.1 → XP_063135238.1  AT-rich interactive domain-containing protein 5B isoform X6

  6. 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
Nucleotide Protein Strain
Heading Accession and Version

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