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

    Gene ID: 309728, updated on 6-Jun-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
    Ensembl: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
    • 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-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, ENSRNOT00000000787.9
      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

      UniProtKB/TrEMBL
      A0A8I6AEL5

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

      UniProtKB/TrEMBL
      A0A8I6AEL5

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

      UniProtKB/TrEMBL
      A0A8I6AEL5

    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
      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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