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

Gene ID: 4784, updated on 10-Dec-2024

Summary

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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; AllianceGenome:HGNC:7788
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; MALNS; 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
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Genomic context

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See NFIX in Genome Data Viewer
Location:
19p13.13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12995475..13098796)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13120686..13224010)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (13106289..13209610)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:13063321-13064520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14100 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13067513-13068385 Neighboring gene GADD45G interacting protein 1 Neighboring gene RAD23 homolog A, nucleotide excision repair protein Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14101 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14102 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13079936-13080539 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13080540-13081142 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13085246-13085752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10187 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13095227-13095752 Neighboring gene DAN domain BMP antagonist family member 5 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10188 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13106570-13107158 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13121583-13122126 Neighboring gene uncharacterized LOC107985286 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14103 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13134224-13134736 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13135703-13136522 Neighboring gene VISTA enhancer hs1900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13168092-13168678 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13170695-13171596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13171597-13172496 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13187265-13188200 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:13206733-13207596 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14104 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:13210189-13211052 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14106 Neighboring gene CRISPRi-FlowFISH-validated CALR, DNASE2 and KLF1 regulatory element Neighboring gene Sharpr-MPRA regulatory region 14065 Neighboring gene uncharacterized LOC105372282 Neighboring gene LYL1 basic helix-loop-helix family member

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Nuclear factor IA is expressed in astrocytomas and is associated with improved survival. Song HR, et al. Neuro Oncol, 2010 Feb. PMID 20150379, Free PMC Article
  2. Two nuclear localization signals are required for nuclear translocation of nuclear factor 1-A. Imagawa M, et al. FEBS Lett, 2000 Nov 3. PMID 11068044
  3. Parental gonadal but not somatic mosaicism leading to de novo NFIX variants shared by two brothers with Malan syndrome. Hancarova M, et al. Am J Med Genet A, 2019 Oct. PMID 31369202
  4. NFIX downregulation independently predicts poor prognosis in lung adenocarcinoma, but not in squamous cell carcinoma. Ge J, et al. Future Oncol, 2018 Dec. PMID 30418046
  5. Nuclear Factor One X in Development and Disease. Piper M, et al. Trends Cell Biol, 2019 Jan. PMID 30287093

See all (85) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Circular RNA NFIX Functions as an Oncogene in Non-Small Cell Lung Cancer by Modulating the miR-214-3p/TRIAP1 Axis.
    Title: Circular RNA NFIX Functions as an Oncogene in Non-Small Cell Lung Cancer by Modulating the miR-214-3p/TRIAP1 Axis.
  2. [NFIX gene mutation causes Marshall-Smith syndrome in a pair of identical twins and literature review].
    Title: [NFIX gene mutation causes Marshall-Smith syndrome in a pair of identical twins and literature review].
  3. m6A-modified circNFIX promotes ovarian cancer progression and immune escape via activating IL-6R/JAK1/STAT3 signaling by sponging miR-647.
    Title: m6A-modified circNFIX promotes ovarian cancer progression and immune escape via activating IL-6R/JAK1/STAT3 signaling by sponging miR-647.
  4. A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome.
    Title: A rare cause of intellectual disability: Novel mutations of NFIX gene in two patients with clinical features of Marshall-Smith syndrome and Malan syndrome.
  5. NFIXing Cancer: The Role of NFIX in Oxidative Stress Response and Cell Fate.
    Title: NFIXing Cancer: The Role of NFIX in Oxidative Stress Response and Cell Fate.
  6. CircNFIX stimulates the proliferation, invasion, and stemness properties of ovarian cancer cells by enhancing SH3RF3 mRNA stability via binding LIN28B.
    Title: CircNFIX stimulates the proliferation, invasion, and stemness properties of ovarian cancer cells by enhancing SH3RF3 mRNA stability via binding LIN28B.
  7. A Novel Tumor-Promoting Role for Nuclear Factor IX in Glioblastoma Is Mediated through Transcriptional Activation of GINS1.
    Title: A Novel Tumor-Promoting Role for Nuclear Factor IX in Glioblastoma Is Mediated through Transcriptional Activation of GINS1.
  8. CircNFIX regulates chondrogenesis and cartilage homeostasis by targeting the miR758-3p/KDM6A axis.
    Title: CircNFIX regulates chondrogenesis and cartilage homeostasis by targeting the miR758-3p/KDM6A axis.
  9. A novel miRNA-762/NFIX pathway modulates LPS-induced acute lung injury.
    Title: A novel miRNA-762/NFIX pathway modulates LPS-induced acute lung injury.
  10. Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism.
    Title: Pathogenic variant in NFIX gene affecting three sisters due to paternal mosaicism.
Submit: New GeneRIF Correction See all GeneRIFs (39)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Malan overgrowth syndrome
MedGen: C3553660 OMIM: 614753 GeneReviews: NFIX-Related Malan Syndrome
Compare labs
Marshall-Smith syndrome
MedGen: C0265211 OMIM: 602535 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2022-04-12)

ClinGen Genome Curation PagePubMed
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated 2022-04-12)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
A genome-wide association study of seasonal pattern mania identifies NF1A as a possible susceptibility gene for bipolar disorder.
EBI GWAS Catalog
Clozapine-induced agranulocytosis is associated with rare HLA-DQB1 and HLA-B alleles.
EBI GWAS Catalog
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity TAS
Traceable Author Statement
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific double-stranded DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA replication IEA
Inferred from Electronic Annotation
more info
  
involved_in negative 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 regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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

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.

Genomic

  1. NG_032925.2 RefSeqGene

    Range
    4706..108027
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001271043.2 → NP_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
    Consensus CDS
    CCDS92532.1
    UniProtKB/TrEMBL
    B4DHW2
    Related
    ENSP00000502554.1, ENST00000676441.1
    Conserved Domains (3) summary
    pfam10524
    Location:18 → 54
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:221 → 510
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:76 → 178
    MH1; N-terminal Mad Homology 1 (MH1) domain

  2. NM_001271044.3 → NP_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/TrEMBL
    Q7Z3K7
    Related
    ENSP00000466389.1, ENST00000587760.5
    Conserved Domains (3) summary
    pfam10524
    Location:2 → 38
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:205 → 410
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:60 → 162
    MH1; N-terminal Mad Homology 1 (MH1) domain

  3. NM_001365902.3 → NP_001352831.1  nuclear factor 1 X-type isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Consensus CDS
    CCDS92530.1
    UniProtKB/Swiss-Prot
    B4DM25, O60413, Q0VG09, Q12859, Q13050, Q13052, Q14938, Q5U094, Q9UPH1, Q9Y6R8
    Related
    ENSP00000467512.1, ENST00000592199.6
    Conserved Domains (3) summary
    pfam10524
    Location:9 → 46
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:213 → 502
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:68 → 170
    MH1; N-terminal Mad Homology 1 (MH1) domain

  4. NM_001365982.2 → NP_001352911.1  nuclear factor 1 X-type isoform 5

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    UniProtKB/TrEMBL
    Q7Z3K7
    Related
    ENSP00000353219.4, ENST00000360105.8
    Conserved Domains (3) summary
    pfam10524
    Location:9 → 46
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:213 → 377
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:68 → 170
    MH1; N-terminal Mad Homology 1 (MH1) domain

  5. NM_001365983.2 → NP_001352912.1  nuclear factor 1 X-type isoform 6

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    UniProtKB/TrEMBL
    Q7Z3K7
    Conserved Domains (2) summary
    pfam00859
    Location:166 → 371
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:21 → 123
    MH1; N-terminal Mad Homology 1 (MH1) domain

  6. NM_001365984.2 → NP_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
    pfam10524
    Location:8 → 45
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:212 → 501
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:67 → 169
    MH1; N-terminal Mad Homology 1 (MH1) domain

  7. NM_001365985.2 → NP_001352914.1  nuclear factor 1 X-type isoform 8

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Consensus CDS
    CCDS92533.1
    UniProtKB/TrEMBL
    Q7Z3K7
    Related
    ENSP00000467785.1, ENST00000587260.1
    Conserved Domains (3) summary
    pfam10524
    Location:8 → 45
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:212 → 417
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:67 → 169
    MH1; N-terminal Mad Homology 1 (MH1) domain

  8. NM_001378404.1 → NP_001365333.1  nuclear factor 1 X-type isoform 9

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Consensus CDS
    CCDS92531.1
    UniProtKB/TrEMBL
    D2DXM9
    Related
    ENSP00000468794.1, ENST00000585575.5
    Conserved Domains (3) summary
    pfam10524
    Location:2 → 38
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:205 → 494
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:60 → 162
    MH1; N-terminal Mad Homology 1 (MH1) domain

  9. NM_001378405.1 → NP_001365334.1  nuclear factor 1 X-type isoform 10

    Status: REVIEWED

    Source sequence(s)
    AC007787, AC138474, KF456509
    Conserved Domains (3) summary
    pfam10524
    Location:26 → 62
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:229 → 518
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:84 → 186
    MH1; N-terminal Mad Homology 1 (MH1) domain

  10. NM_002501.4 → NP_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/TrEMBL
    Q7Z3K7
    Related
    ENSP00000380781.2, ENST00000397661.6
    Conserved Domains (3) summary
    pfam10524
    Location:9 → 46
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
    pfam00859
    Location:213 → 418
    CTF_NFI; CTF/NF-I family transcription modulation region
    cl00055
    Location:68 → 170
    MH1; N-terminal Mad Homology 1 (MH1) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

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

mRNA and Protein(s)

  1. XM_047438864.1 → XP_047294820.1  nuclear factor 1 X-type isoform X3

    UniProtKB/TrEMBL
    Q7Z3K7

  2. XM_047438865.1 → XP_047294821.1  nuclear factor 1 X-type isoform X4

    UniProtKB/TrEMBL
    Q7Z3K7

  3. XM_005259917.5 → XP_005259974.2  nuclear factor 1 X-type isoform X1

    Related
    ENSP00000351354.5, ENST00000358552.8

  4. XM_047438863.1 → XP_047294819.1  nuclear factor 1 X-type isoform X2

    UniProtKB/TrEMBL
    Q7Z3K7

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    13120686..13224010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321074.1 → XP_054177049.1  nuclear factor 1 X-type isoform X3

    UniProtKB/TrEMBL
    Q7Z3K7

  2. XM_054321075.1 → XP_054177050.1  nuclear factor 1 X-type isoform X4

    UniProtKB/TrEMBL
    Q7Z3K7

  3. XM_054321072.1 → XP_054177047.1  nuclear factor 1 X-type isoform X1

  4. XM_054321073.1 → XP_054177048.1  nuclear factor 1 X-type isoform X2

    UniProtKB/TrEMBL
    Q7Z3K7
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q14938.2 GenPept UniProtKB/Swiss-Prot:Q14938

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