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    Nfia nuclear factor I/A [ Mus musculus (house mouse) ]

    Gene ID: 18027, updated on 9-Dec-2024

    Summary

    Official Symbol
    Nfiaprovided by MGI
    Official Full Name
    nuclear factor I/Aprovided by MGI
    Primary source
    MGI:MGI:108056
    See related
    Ensembl:ENSMUSG00000028565 AllianceGenome:MGI:108056
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    CTF; NF1A; NF1-A; 1110047K16Rik; 9430022M17Rik
    Summary
    Enables DNA binding activity and chromatin binding activity. Involved in several processes, including BMP signaling pathway; limb morphogenesis; and positive regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including exit from mitosis; nervous system development; and ureter development. Located in nucleus. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. 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, Dec 2024]
    Expression
    Ubiquitous expression in limb E14.5 (RPKM 8.7), CNS E14 (RPKM 7.7) and 27 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Nfia in Genome Data Viewer
    Location:
    4 C5- C6; 4 45.52 cM
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 4 NC_000070.7 (97469534..98007113)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 4 NC_000070.6 (97578066..98118876)

    Chromosome 4 - NC_000070.7Genomic Context describing neighboring genes Neighboring gene RIKEN cDNA E130114P18 gene Neighboring gene predicted gene 12696 Neighboring gene STARR-seq mESC enhancer starr_10836 Neighboring gene U2 small nuclear ribonucleoprotein B pseudogene Neighboring gene STARR-seq mESC enhancer starr_10837 Neighboring gene predicted gene, 54242 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:97417857-97418058 Neighboring gene STARR-positive B cell enhancer ABC_E339 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:97439041-97439228 Neighboring gene STARR-positive B cell enhancer ABC_E1033 Neighboring gene predicted gene, 38709 Neighboring gene STARR-seq mESC enhancer starr_10839 Neighboring gene STARR-seq mESC enhancer starr_10840 Neighboring gene predicted gene, 19417 Neighboring gene predicted gene, 40208 Neighboring gene predicted gene, 34218 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:97758089-97758198 Neighboring gene CapStarr-seq enhancer MGSCv37_chr4:97767981-97768168 Neighboring gene predicted gene, 34784 Neighboring gene predicted gene 12691 Neighboring gene STARR-seq mESC enhancer starr_10841 Neighboring gene ras homolog gene family, member G pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Targeted (4)  1 citation

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in BMP signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA replication IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within cell quiescence IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within exit from mitosis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in gene expression IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    acts_upstream_of_or_within gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within generation of neurons IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within glial cell fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within glial cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in limb morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neural precursor cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neurogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within neuron fate specification IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
     
    acts_upstream_of_or_within response to wounding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within synapse maturation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within ureter development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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
    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_001122952.1NP_001116424.1  nuclear factor 1 A-type isoform 1

      See identical proteins and their annotated locations for NP_001116424.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK052204, AK139357, AL670260, AW122288
      UniProtKB/Swiss-Prot
      P70250, P70251, Q02780, Q3UUZ2, Q61960, Q8VBT5, Q9R1G5
      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      cl00055
      Location:91195
      MH1; N-terminal Mad Homology 1 (MH1) domain
      pfam00859
      Location:237531
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:3269
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    2. NM_001122953.1NP_001116425.1  nuclear factor 1 A-type isoform 3

      See identical proteins and their annotated locations for NP_001116425.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) has an alternate 5' exon and lacks an internal coding exon, which does not affect the reading frame, as compared to variant 1. The resulting isoform (2) has a different and shorter N-terminus and lacks an internal segment, as compared to isoform 1.
      Source sequence(s)
      AL670195, AL670260, AL671238, AW122288, BC122878, BC122880
      Consensus CDS
      CCDS51234.1
      UniProtKB/TrEMBL
      B1AUB9
      Related
      ENSMUSP00000130032.2, ENSMUST00000092532.13
      Conserved Domains (3) summary
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain
      pfam00859
      Location:214465
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:846
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    3. NM_010905.3NP_035035.1  nuclear factor 1 A-type isoform 2

      See identical proteins and their annotated locations for NP_035035.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 5' exon, as compared to variant 1. The resulting isoform (2) has a different and shorter N-terminus, as compared to isoform 1.
      Source sequence(s)
      AF326553, AL670195, AL670260, AL671238, AW122288
      Consensus CDS
      CCDS18373.1
      UniProtKB/TrEMBL
      B1AUB9
      Related
      ENSMUSP00000074899.7, ENSMUST00000075448.13
      Conserved Domains (3) summary
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain
      pfam00859
      Location:214508
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:846
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000070.7 Reference GRCm39 C57BL/6J

      Range
      97469534..98007113
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006502841.5XP_006502904.1  nuclear factor 1 A-type isoform X1

      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      pfam00859
      Location:237496
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:3369
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      cl00055
      Location:91195
      MH1; N-terminal Mad Homology 1 (MH1) domain
    2. XM_006502844.5XP_006502907.1  nuclear factor 1 A-type isoform X5

      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      pfam00859
      Location:237488
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam03165
      Location:91195
      MH1; MH1 domain
      pfam10524
      Location:3369
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    3. XM_036163811.1XP_036019704.1  nuclear factor 1 A-type isoform X6

      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      pfam10524
      Location:3369
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:237453
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:91195
      MH1; N-terminal Mad Homology 1 (MH1) domain
    4. XM_030253303.2XP_030109163.1  nuclear factor 1 A-type isoform X2

      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      pfam00859
      Location:206500
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam03165
      Location:60164
      MH1; MH1 domain
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    5. XM_036163810.1XP_036019703.1  nuclear factor 1 A-type isoform X4

      UniProtKB/TrEMBL
      Q69ZJ5
      Conserved Domains (3) summary
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:206465
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:60164
      MH1; N-terminal Mad Homology 1 (MH1) domain
    6. XM_006502842.4XP_006502905.1  nuclear factor 1 A-type isoform X2

      See identical proteins and their annotated locations for XP_006502905.1

      UniProtKB/TrEMBL
      Q3UTK6
      Conserved Domains (3) summary
      pfam00859
      Location:206500
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam03165
      Location:60164
      MH1; MH1 domain
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    7. XM_006502843.4XP_006502906.1  nuclear factor 1 A-type isoform X3

      UniProtKB/TrEMBL
      B1AUB9, B1AUC0
      Related
      ENSMUSP00000102677.3, ENSMUST00000107062.9
      Conserved Domains (3) summary
      pfam00859
      Location:214473
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain
    8. XM_006502845.4XP_006502908.1  nuclear factor 1 A-type isoform X7

      See identical proteins and their annotated locations for XP_006502908.1

      UniProtKB/TrEMBL
      B1AUB9, Q05B39
      Conserved Domains (3) summary
      pfam00859
      Location:214430
      CTF_NFI; CTF/NF-I family transcription modulation region
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      cl00055
      Location:68172
      MH1; N-terminal Mad Homology 1 (MH1) domain