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

    Gene ID: 4784, updated on 5-Feb-2024

    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NFIX in Genome Data Viewer
    Location:
    19p13.13
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (12995475..13098796)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (13120686..13224010)
    105.20220307 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

    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
    Malan overgrowth syndrome
    MedGen: C3553660 OMIM: 614753 GeneReviews: Not available
    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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)

    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.

    Genomic

    1. NG_032925.2 RefSeqGene

      Range
      4706..108027
      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
      Consensus CDS
      CCDS92532.1
      UniProtKB/TrEMBL
      B4DHW2
      Related
      ENSP00000502554.1, ENST00000676441.1
      Conserved Domains (3) summary
      pfam10524
      Location:1854
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:221510
      CTF_NFI; CTF/NF-I family transcription modulation region
      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/TrEMBL
      Q7Z3K7
      Related
      ENSP00000466389.1, ENST00000587760.5
      Conserved Domains (3) summary
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:205410
      CTF_NFI; CTF/NF-I family transcription modulation region
      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
      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:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213502
      CTF_NFI; CTF/NF-I family transcription modulation region
      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
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000353219.4, ENST00000360105.8
      Conserved Domains (3) summary
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213377
      CTF_NFI; CTF/NF-I family transcription modulation region
      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
      UniProtKB/TrEMBL
      Q7Z3K7
      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
      pfam10524
      Location:845
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:212501
      CTF_NFI; CTF/NF-I family transcription modulation region
      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
      Consensus CDS
      CCDS92533.1
      UniProtKB/TrEMBL
      Q7Z3K7
      Related
      ENSP00000467785.1, ENST00000587260.1
      Conserved Domains (3) summary
      pfam10524
      Location:845
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:212417
      CTF_NFI; CTF/NF-I family transcription modulation region
      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
      Consensus CDS
      CCDS92531.1
      UniProtKB/TrEMBL
      D2DXM9
      Related
      ENSP00000468794.1, ENST00000585575.5
      Conserved Domains (3) summary
      pfam10524
      Location:238
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:205494
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:60162
      MH1; N-terminal Mad Homology 1 (MH1) domain
    9. NM_001378405.1NP_001365334.1  nuclear factor 1 X-type isoform 10

      Status: REVIEWED

      Source sequence(s)
      AC007787, AC138474, KF456509
      Conserved Domains (3) summary
      pfam10524
      Location:2662
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:229518
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:84186
      MH1; N-terminal Mad Homology 1 (MH1) domain
    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/TrEMBL
      Q7Z3K7
      Related
      ENSP00000380781.2, ENST00000397661.6
      Conserved Domains (3) summary
      pfam10524
      Location:946
      NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
      pfam00859
      Location:213418
      CTF_NFI; CTF/NF-I family transcription modulation region
      cl00055
      Location:68170
      MH1; N-terminal Mad Homology 1 (MH1) domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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_047438864.1XP_047294820.1  nuclear factor 1 X-type isoform X3

      UniProtKB/TrEMBL
      Q7Z3K7
    2. XM_047438865.1XP_047294821.1  nuclear factor 1 X-type isoform X4

      UniProtKB/TrEMBL
      Q7Z3K7
    3. XM_005259917.5XP_005259974.2  nuclear factor 1 X-type isoform X1

      Related
      ENSP00000351354.5, ENST00000358552.8
    4. XM_047438863.1XP_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_054321074.1XP_054177049.1  nuclear factor 1 X-type isoform X3

      UniProtKB/TrEMBL
      Q7Z3K7
    2. XM_054321075.1XP_054177050.1  nuclear factor 1 X-type isoform X4

      UniProtKB/TrEMBL
      Q7Z3K7
    3. XM_054321072.1XP_054177047.1  nuclear factor 1 X-type isoform X1

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

      UniProtKB/TrEMBL
      Q7Z3K7