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    Nfia nuclear factor I/A [ Rattus norvegicus (Norway rat) ]

    Gene ID: 25492, updated on 4-Jan-2025

    Summary

    Official Symbol
    Nfiaprovided by RGD
    Official Full Name
    nuclear factor I/Aprovided by RGD
    Primary source
    RGD:3170
    See related
    EnsemblRapid:ENSRNOG00000006966 AllianceGenome:RGD:3170
    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
    Enables DNA binding activity. Involved in positive regulation of DNA-templated transcription and response to organic cyclic compound. Predicted to be located in cell junction and nucleoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in NFIA-related disorder. Orthologous to human NFIA (nuclear factor I A). [provided by Alliance of Genome Resources, Jan 2025]
    Expression
    Biased expression in Heart (RPKM 292.9), Lung (RPKM 205.8) and 9 other tissues See more
    Orthologs
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    Genomic context

    See Nfia in Genome Data Viewer
    Location:
    5q33
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 5 NC_086023.1 (117359006..117897391)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 5 NC_051340.1 (112436655..112781878)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 5 NC_005104.4 (116421895..116750381)

    Chromosome 5 - NC_086023.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA48 Neighboring gene large ribosomal subunit protein P1-like Neighboring gene uncharacterized LOC102553524 Neighboring gene uncharacterized LOC120103115 Neighboring gene uncharacterized LOC120103114 Neighboring gene uncharacterized LOC108351005 Neighboring gene small nucleolar RNA, H/ACA box 9

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    General gene information

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding PubMed 
    enables DNA binding  
    enables DNA binding  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor activity  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific  
    enables DNA-binding transcription factor binding  
    enables DNA-binding transcription factor binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding  
    enables chromatin binding  
    enables chromatin binding  
    enables protein binding PubMed 
    Items 1 - 25 of 39
    Process Evidence Code Pubs
    involved_in BMP signaling pathway  
    involved_in BMP signaling pathway  
    involved_in DNA replication  
    involved_in cartilage development  
    involved_in cartilage development  
    involved_in cell morphogenesis  
    involved_in cell morphogenesis  
    involved_in exit from mitosis  
    acts_upstream_of_or_within exit from mitosis  
    involved_in gene expression  
    acts_upstream_of_or_within gene expression  
    involved_in gene expression  
    acts_upstream_of_or_within generation of neurons  
    involved_in glial cell fate specification  
    acts_upstream_of_or_within glial cell fate specification  
    involved_in glial cell proliferation  
    acts_upstream_of_or_within glial cell proliferation  
    involved_in limb morphogenesis  
    involved_in limb morphogenesis  
    involved_in neural precursor cell proliferation  
    acts_upstream_of_or_within neural precursor cell proliferation  
    acts_upstream_of_or_within neurogenesis  
    involved_in neuron fate specification  
    acts_upstream_of_or_within neuron fate specification  
    involved_in positive regulation of DNA-templated transcription PubMed 
    involved_in positive regulation of DNA-templated transcription  
    involved_in positive regulation of transcription by RNA polymerase II  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II  
    involved_in positive regulation of transcription by RNA polymerase II  
    involved_in regulation of transcription by RNA polymerase II  
    involved_in response to organic cyclic compound PubMed 
    involved_in response to wounding  
    acts_upstream_of_or_within response to wounding  
    involved_in retina development in camera-type eye  
    acts_upstream_of_or_within retina development in camera-type eye  
    involved_in synapse maturation  
    acts_upstream_of_or_within synapse maturation  
    involved_in ureter development  
    acts_upstream_of_or_within ureter development  
    Items 1 - 25 of 39
    Component Evidence Code Pubs
    located_in cell junction  
    located_in cell junction  
    located_in nucleoplasm  
    located_in nucleoplasm  
    is_active_in nucleus  
    located_in nucleus  
    located_in nucleus  

    General protein information

    Preferred Names
    nuclear factor 1 A-type
    Names
    CCAAT-box-binding transcription factor
    CTF
    NF-I/A
    NF1-A
    NFI-A
    TGGCA-binding protein
    nuclear factor 1/A

    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_012988.2NP_037120.1  nuclear factor 1 A-type

      See identical proteins and their annotated locations for NP_037120.1

      Status: PROVISIONAL

      Source sequence(s)
      D78017
      UniProtKB/Swiss-Prot
      P09414, Q54A99, Q63782
      UniProtKB/TrEMBL
      A0A8I6G968
      Related
      ENSRNOP00000073066.3, ENSRNOT00000086628.3
      Conserved Domains (3) summary
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:214508
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain

    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_086023.1 Reference GRCr8

      Range
      117359006..117897391
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063287182.1XP_063143252.1  nuclear factor 1 A-type isoform X2

      UniProtKB/TrEMBL
      A0A8I6G968, A6JRJ7
    2. XM_063287181.1XP_063143251.1  nuclear factor 1 A-type isoform X1

      UniProtKB/TrEMBL
      A0A8I6G968, Q9QY90
      Related
      ENSRNOP00000004017.9, ENSRNOT00000004017.9
    3. XM_063287183.1XP_063143253.1  nuclear factor 1 A-type isoform X3

      UniProtKB/TrEMBL
      A0A8I6G968, A6JRJ9
    4. XM_039109300.2XP_038965228.1  nuclear factor 1 A-type isoform X4

      UniProtKB/TrEMBL
      A0A8I6AR84, A0A8I6G968
      Related
      ENSRNOP00000097022.1, ENSRNOT00000117135.2
      Conserved Domains (3) summary
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:206500
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam03165
      Location:60164
      MH1; MH1 domain
    5. XM_063287184.1XP_063143254.1  nuclear factor 1 A-type isoform X6

      UniProtKB/TrEMBL
      A0A8I6G968
    6. XM_063287185.1XP_063143255.1  nuclear factor 1 A-type isoform X7

      UniProtKB/TrEMBL
      A0A8I6G968, F1LRV0, Q63783
      Related
      ENSRNOP00000082237.2, ENSRNOT00000106921.2
    7. XM_039109301.2XP_038965229.1  nuclear factor 1 A-type isoform X5

      UniProtKB/TrEMBL
      A0A0G2K5I9, A0A8I6G968, Q63573
      Related
      ENSRNOP00000073444.2, ENSRNOT00000087089.3
      Conserved Domains (3) summary
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:214473
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain
    8. XM_039109303.2XP_038965231.1  nuclear factor 1 A-type isoform X9

      UniProtKB/TrEMBL
      Q63785
      Conserved Domains (1) summary
      pfam00859
      Location:60354
      CTF_NFI; CTF/NF-I family transcription modulation region
    9. XM_039109302.2XP_038965230.1  nuclear factor 1 A-type isoform X8

      Conserved Domains (1) summary
      pfam00859
      Location:72366
      CTF_NFI; CTF/NF-I family transcription modulation region
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