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

    Gene ID: 25492, updated on 2-Nov-2024

    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, Nov 2024]
    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 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

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
     
    enables DNA-binding transcription factor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables DNA-binding transcription factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA-binding transcription factor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in BMP signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in exit from mitosis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within exit from mitosis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within generation of neurons ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in glial cell fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within glial cell fate specification ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in glial cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within glial cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in limb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in limb morphogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neural precursor cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within neural precursor cell proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within neurogenesis ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in neuron fate specification IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within neuron fate specification ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II 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
     
    involved_in response to organic cyclic compound IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in response to wounding IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within response to wounding ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within retina development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in synapse maturation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within synapse maturation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in ureter development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within ureter development ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cell junction ISO
    Inferred from Sequence Orthology
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     

    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)

    NEW Try the new Transcript table

    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
      A6JRJ7
    2. XM_063287181.1XP_063143251.1  nuclear factor 1 A-type isoform X1

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

      UniProtKB/TrEMBL
      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

    6. XM_063287185.1XP_063143255.1  nuclear factor 1 A-type isoform X7

      UniProtKB/TrEMBL
      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