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    Rai1 retinoic acid induced 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 303188, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Rai1provided by RGD
    Official Full Name
    retinoic acid induced 1provided by RGD
    Primary source
    RGD:1308500
    See related
    EnsemblRapid:ENSRNOG00000060615 AllianceGenome:RGD:1308500
    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 metal ion binding activity. Predicted to be involved in circadian regulation of gene expression and positive regulation of DNA-templated transcription. Predicted to act upstream of or within regulation of growth; regulation of transcription by RNA polymerase II; and skeletal system development. Predicted to be located in nucleoplasm. Human ortholog(s) of this gene implicated in Smith-Magenis syndrome. Orthologous to human RAI1 (retinoic acid induced 1). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 78.3), Adrenal (RPKM 57.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Rai1 in Genome Data Viewer
    Location:
    10q22
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (45412748..45507747)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (44913231..45008232)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (46511271..46571591)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member A1, pseudogene 3 Neighboring gene phosphatidylethanolamine N-methyltransferase Neighboring gene uncharacterized LOC102549418 Neighboring gene sterol regulatory element binding transcription factor 1 Neighboring gene target of myb1 like 2 membrane trafficking protein Neighboring gene dynein regulatory complex subunit 3 Neighboring gene ATP synthase mitochondrial F1 complex assembly factor 2 Neighboring gene GID complex subunit 4

    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. Inactivation of Rai1 in mice recapitulates phenotypes observed in chromosome engineered mouse models for Smith-Magenis syndrome. Bi W, et al. Hum Mol Genet, 2005 Apr 15. PMID 15746153
    2. Mutations in RAI1 associated with Smith-Magenis syndrome. Slager RE, et al. Nat Genet, 2003 Apr. PMID 12652298
    3. Smith-Magenis syndrome results in disruption of CLOCK gene transcription and reveals an integral role for RAI1 in the maintenance of circadian rhythmicity. Williams SR, et al. Am J Hum Genet, 2012 Jun 8. PMID 22578325, Free PMC Article
    4. Penetrance of craniofacial anomalies in mouse models of Smith-Magenis syndrome is modified by genomic sequence surrounding Rai1: not all null alleles are alike. Yan J, et al. Am J Hum Genet, 2007 Mar. PMID 17273973, Free PMC Article
    5. Gene and alternative splicing annotation with AIR. Florea L, et al. Genome Res, 2005 Jan. PMID 15632090, Free PMC Article

    See all (7) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in biological_process ND
    No biological Data available
    more info
    		  
    involved_in circadian regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of multicellular organism growth ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription 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 regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within skeletal system development 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
    		  

    General protein information

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    Preferred Names
    retinoic acid-induced protein 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)

    1. NM_001271207.1 → NP_001258136.1  retinoic acid-induced protein 1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6
      Related
      ENSRNOP00000073029.1, ENSRNOT00000080828.3
      Conserved Domains (2) summary
      PHA03247
      Location:941 → 1200
      PHA03247; large tegument protein UL36; Provisional
      cl22851
      Location:1653 → 1882
      PHD_SF; PHD finger 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

    1. NC_086028.1 Reference GRCr8

      Range
      45412748..45507747
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063269004.1 → XP_063125074.1  retinoic acid-induced protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6

    2. XM_039085953.2 → XP_038941881.1  retinoic acid-induced protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6
      Conserved Domains (2) summary
      PHA03247
      Location:941 → 1200
      PHA03247; large tegument protein UL36; Provisional
      cl22851
      Location:1653 → 1882
      PHD_SF; PHD finger superfamily

    3. XM_039085955.2 → XP_038941883.1  retinoic acid-induced protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6
      Conserved Domains (2) summary
      PHA03247
      Location:941 → 1200
      PHA03247; large tegument protein UL36; Provisional
      cl22851
      Location:1653 → 1882
      PHD_SF; PHD finger superfamily

    4. XM_063269005.1 → XP_063125075.1  retinoic acid-induced protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6

    5. XM_008767819.4 → XP_008766041.2  retinoic acid-induced protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A0G2K4G0, A0A8I6GEB6
      Conserved Domains (2) summary
      PHA03247
      Location:941 → 1200
      PHA03247; large tegument protein UL36; Provisional
      cl22851
      Location:1653 → 1882
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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