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NFIX nuclear factor I X [ Homo sapiens (human) ]

Gene ID: 4784, updated on 1-Jun-2020

Summary

Official Symbol
NFIXprovided by HGNC
Official Full Name
nuclear factor I Xprovided by HGNC
Primary source
HGNC:HGNC:7788
See related
Ensembl:ENSG00000008441 MIM:164005
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; NF1A; NF1-X; MRSHSS; NF-I/X; SOTOS2
Summary
The protein encoded by this gene is a transcription factor that binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3 in viral and cellular promoters. The encoded protein can also stimulate adenovirus replication in vitro. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2012]
Expression
Ubiquitous expression in brain (RPKM 36.5), fat (RPKM 32.4) and 23 other tissues See more
Orthologs

Genomic context

See NFIX in Genome Data Viewer
Location:
19p13.13
Exon count:
13
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (12995475..13098796)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13106584..13209610)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene GADD45G interacting protein 1 Neighboring gene RAD23 homolog A, nucleotide excision repair protein Neighboring gene DAN domain BMP antagonist family member 5 Neighboring gene uncharacterized LOC107985286 Neighboring gene VISTA enhancer hs1900 Neighboring gene CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element Neighboring gene uncharacterized LOC105372282 Neighboring gene Sharpr-MPRA regulatory region 14065 Neighboring gene LYL1 basic helix-loop-helix family member Neighboring gene tRNA methyltransferase 1

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
Marshall-Smith syndrome
MedGen: C0265211 OMIM: 602535 GeneReviews: Not available
Compare labs
Sotos syndrome 2
MedGen: C3553660 OMIM: 614753 GeneReviews: Not available
Compare labs

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
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
NHGRI GWA Catalog
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
 
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
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 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
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 
transcription by RNA polymerase II TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
nuclear chromatin ISA
Inferred from Sequence Alignment
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

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

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_032925.2 RefSeqGene

    Range
    4706..108018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271043.2NP_001257972.1  nuclear factor 1 X-type isoform 1

    See identical proteins and their annotated locations for NP_001257972.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC007787, AK295290, KF456509
    UniProtKB/TrEMBL
    B4DHW2
    Conserved Domains (3) summary
    pfam00859
    Location:221510
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:1854
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    cl00055
    Location:76178
    MH1; N-terminal Mad Homology 1 (MH1) domain
  2. NM_001271044.3NP_001257973.1  nuclear factor 1 X-type isoform 3

    See identical proteins and their annotated locations for NP_001257973.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks an alternate 3' exon compared to variant 1, that causes a frameshift. The resulting isoform (3) has shorter and distinct N- and C-termini compared to isoform 1.
    Source sequence(s)
    AC007787, BP228658, KF456509, U18759
    Consensus CDS
    CCDS59359.1
    UniProtKB/Swiss-Prot
    Q14938
    Related
    ENSP00000466389.1, ENST00000587760.5
    Conserved Domains (3) summary
    pfam00859
    Location:205410
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:138
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    cl00055
    Location:60162
    MH1; N-terminal Mad Homology 1 (MH1) domain
  3. NM_001365902.3NP_001352831.1  nuclear factor 1 X-type isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Related
    ENSP00000467512.1, ENST00000592199.5
    Conserved Domains (3) summary
    pfam00859
    Location:213502
    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:68170
    MH1; N-terminal Mad Homology 1 (MH1) domain
  4. NM_001365982.2NP_001352911.1  nuclear factor 1 X-type isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Conserved Domains (3) summary
    pfam00859
    Location:213377
    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:68170
    MH1; N-terminal Mad Homology 1 (MH1) domain
  5. NM_001365983.2NP_001352912.1  nuclear factor 1 X-type isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Conserved Domains (2) summary
    pfam00859
    Location:166371
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:21123
    MH1; N-terminal Mad Homology 1 (MH1) domain
  6. NM_001365984.2NP_001352913.1  nuclear factor 1 X-type isoform 7

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Related
    ENSP00000466735.1, ENST00000588228.5
    Conserved Domains (3) summary
    pfam00859
    Location:212501
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:845
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    cl00055
    Location:67169
    MH1; N-terminal Mad Homology 1 (MH1) domain
  7. NM_001365985.2NP_001352914.1  nuclear factor 1 X-type isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Related
    ENSP00000467785.1, ENST00000587260.1
    Conserved Domains (3) summary
    pfam00859
    Location:212417
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:845
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    cl00055
    Location:67169
    MH1; N-terminal Mad Homology 1 (MH1) domain
  8. NM_001378404.1NP_001365333.1  nuclear factor 1 X-type isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Related
    ENSP00000468794.1, ENST00000585575.5
  9. NM_001378405.1NP_001365334.1  nuclear factor 1 X-type isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
  10. NM_002501.4NP_002492.2  nuclear factor 1 X-type isoform 2

    See identical proteins and their annotated locations for NP_002492.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence and lacks an alternate 3' exon compared to variant 1, that causes a frameshift. The resulting isoform (2) has shorter and distinct N- and C-termini compared to isoform 1.
    Source sequence(s)
    AC007787, AC138474, BF115883, KF456509, U18759
    Consensus CDS
    CCDS45996.1
    UniProtKB/Swiss-Prot
    Q14938
    Related
    ENSP00000380781.2, ENST00000397661.6
    Conserved Domains (3) summary
    pfam00859
    Location:213418
    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:68170
    MH1; N-terminal Mad Homology 1 (MH1) domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    12995475..13098796
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259917.4XP_005259974.1  nuclear factor 1 X-type isoform X1

    See identical proteins and their annotated locations for XP_005259974.1

    Conserved Domains (3) summary
    cl00055
    Location:127229
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:272520
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:66105
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
  2. XM_006722760.2XP_006722823.1  nuclear factor 1 X-type isoform X6

    See identical proteins and their annotated locations for XP_006722823.1

    Related
    ENSP00000353219.4, ENST00000360105.8
    Conserved Domains (3) summary
    cl00055
    Location:127229
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:272436
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:66105
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
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