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NFIA nuclear factor I A [ Homo sapiens (human) ]

Gene ID: 4774, updated on 1-Aug-2020

Summary

Official Symbol
NFIAprovided by HGNC
Official Full Name
nuclear factor I Aprovided by HGNC
Primary source
HGNC:HGNC:7784
See related
Ensembl:ENSG00000162599 MIM:600727
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CTF; NF1-A; NFI-A; NFI-L; BRMUTD; NF-I/A
Summary
This gene encodes a member of the NF1 (nuclear factor 1) family of transcription factors. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]
Expression
Ubiquitous expression in fat (RPKM 9.2), thyroid (RPKM 8.8) and 25 other tissues See more
Orthologs

Genomic context

See NFIA in Genome Data Viewer
Location:
1p31.3
Exon count:
15
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (61077227..61462788)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (61542946..61928460)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378764 Neighboring gene NFIA antisense RNA 2 Neighboring gene NFE2L2 motif-containing MPRA enhancer 286 Neighboring gene NFIA antisense RNA 1 Neighboring gene VISTA enhancer hs1309 Neighboring gene uncharacterized LOC105378766 Neighboring gene VISTA enhancer hs1484

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Brain malformations and urinary tract defects
MedGen: C4478940 OMIM: 613735 GeneReviews: NFIA-Related Disorder
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2017-01-12)

ClinGen Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2017-01-12)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
NHGRI GWA Catalog
A meta-analysis of thyroid-related traits reveals novel loci and gender-specific differences in the regulation of thyroid function.
NHGRI GWA Catalog
Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
NHGRI GWA Catalog
Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk.
NHGRI GWA Catalog
Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ39164, KIAA1439, DKFZp434L0422, DKFZp686J23256

Gene Ontology Provided by GOA

Process Evidence Code Pubs
DNA replication IEA
Inferred from Electronic Annotation
more info
 
negative regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription, DNA-templated NAS
Non-traceable Author Statement
more info
PubMed 
synapse maturation IEA
Inferred from Electronic Annotation
more info
 
ureter development IEA
Inferred from Electronic Annotation
more info
 
viral genome replication NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cell junction IDA
Inferred from Direct Assay
more info
 
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
nuclear factor 1 A-type
Names
CCAAT-box-binding transcription factor
TGGCA-binding protein

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_011787.2 RefSeqGene

    Range
    4954..390515
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001134673.4NP_001128145.1  nuclear factor 1 A-type isoform 1

    See identical proteins and their annotated locations for NP_001128145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform 1.
    Source sequence(s)
    AA974652, AB037860, AL096888
    Consensus CDS
    CCDS44156.1
    UniProtKB/Swiss-Prot
    Q12857
    Related
    ENSP00000384523.3, ENST00000403491.8
    Conserved Domains (3) summary
    pfam00859
    Location:214508
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam03165
    Location:68172
    MH1; MH1 domain
    pfam10524
    Location:946
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  2. NM_001145511.2NP_001138983.1  nuclear factor 1 A-type isoform 3

    See identical proteins and their annotated locations for NP_001138983.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 3) has a shorter and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA974652, AB037860, AC096534, AK024964, AK299289, AL096888, AW014151, BC022264, CA398137, CN372139, DB544485
    Consensus CDS
    CCDS53321.1
    UniProtKB/Swiss-Prot
    Q12857
    Related
    ENSP00000384680.2, ENST00000407417.7
    Conserved Domains (3) summary
    pfam00859
    Location:206500
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam03165
    Location:60164
    MH1; MH1 domain
    pfam10524
    Location:138
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  3. NM_001145512.2NP_001138984.1  nuclear factor 1 A-type isoform 4

    See identical proteins and their annotated locations for NP_001138984.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR and coding region compared to variant 1. The resulting protein (isoform 4) has a longer and distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AA974652, AB037860, AC096534, AK024964, AK299579, AL096888, AW014151, BC022264, CA398137, CN372139, DB544485
    Consensus CDS
    CCDS53322.1
    UniProtKB/Swiss-Prot
    Q12857
    Related
    ENSP00000360231.3, ENST00000371189.8
    Conserved Domains (3) summary
    pfam00859
    Location:259553
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:5491
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    cl00055
    Location:113217
    MH1; N-terminal Mad Homology 1 (MH1) domain
  4. NM_005595.5NP_005586.1  nuclear factor 1 A-type isoform 2

    See identical proteins and their annotated locations for NP_005586.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate segment in the 3' UTR, which shifts the reading frame, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus when it is compared to isoform 1.
    Source sequence(s)
    AA974652, AC096534, AL096888, BC022264
    Consensus CDS
    CCDS615.1
    UniProtKB/Swiss-Prot
    Q12857
    Related
    ENSP00000360229.3, ENST00000371187.7
    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

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    61077227..61462788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011541514.3XP_011539816.1  nuclear factor 1 A-type isoform X2

    Conserved Domains (3) summary
    pfam03165
    Location:60164
    MH1; MH1 domain
    pfam00859
    Location:206518
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:138
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  2. XM_017001362.2XP_016856851.1  nuclear factor 1 A-type isoform X4

    Related
    ENSP00000360233.1, ENST00000371191.5
    Conserved Domains (3) summary
    cl00055
    Location:60164
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:206465
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:138
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  3. XM_011541512.3XP_011539814.1  nuclear factor 1 A-type isoform X1

    Conserved Domains (3) summary
    cl00055
    Location:68172
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:214526
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:846
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  4. XM_011541515.3XP_011539817.1  nuclear factor 1 A-type isoform X3

    Conserved Domains (3) summary
    cl00055
    Location:68172
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:214491
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:846
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  5. XM_017001363.1XP_016856852.1  nuclear factor 1 A-type isoform X5

    Related
    ENSP00000499693.1, ENST00000657234.1
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