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

Gene ID: 18027, updated on 12-May-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 positive regulation of transcription by RNA polymerase II. Acts upstream of or within synapse maturation 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, Apr 2022]
Expression
Ubiquitous expression in limb E14.5 (RPKM 8.7), CNS E14 (RPKM 7.7) and 27 other tissues See more
Orthologs
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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 
acts_upstream_of_or_within 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 DNA-templated transcription IEA
Inferred from Electronic Annotation
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 ISO
Inferred from Sequence Orthology
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)

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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_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