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nfixb nuclear factor I/Xb [ Danio rerio (zebrafish) ]

Gene ID: 678521, updated on 4-Jan-2025

Summary

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Official Symbol
nfixbprovided by ZNC
Official Full Name
nuclear factor I/Xbprovided by ZNC
Primary source
ZFIN:ZDB-GENE-060421-5000
See related
Ensembl:ENSDARG00000061836 AllianceGenome:ZFIN:ZDB-GENE-060421-5000
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
zgc:136878
Summary
Predicted to enable DNA binding activity and DNA-binding transcription factor activity. Predicted to be involved in positive regulation of DNA-templated transcription. Predicted to act upstream of or within DNA replication and regulation of DNA-templated transcription. Predicted to be located in nucleus. Is expressed in dorsal telencephalon; midbrain; muscle; and telencephalon. Human ortholog(s) of this gene implicated in Marshall-Smith syndrome and Sotos syndrome 2. Orthologous to human NFIX (nuclear factor I X). [provided by Alliance of Genome Resources, Jan 2025]
Orthologs
human mouse all
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Genomic context

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See nfixb in Genome Data Viewer
Location:
chromosome: 3
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (14749593..15064157)
105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (14617789..14914357)

Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene zgc:158403 Neighboring gene growth arrest and DNA-damage-inducible, gamma interacting protein 1 Neighboring gene uncharacterized LOC110439336 Neighboring gene NME/NM23 nucleoside diphosphate kinase 4 Neighboring gene exportin 6 Neighboring gene adenine nucleotide translocase lysine methyltransferase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Enhancers reside in a unique epigenetic environment during early zebrafish development. Kaaij LJ, et al. Genome Biol, 2016 Jul 5. PMID 27381023, Free PMC Article
  2. Conserved and divergent functions of Nfix in skeletal muscle development during vertebrate evolution. Pistocchi A, et al. Development, 2013 Apr. PMID 23482488
  3. Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos. Armant O, et al. Dev Biol, 2013 Aug 15. PMID 23684812, Free PMC Article
  4. Comprehensive expression map of transcription regulators in the adult zebrafish telencephalon reveals distinct neurogenic niches. Diotel N, et al. J Comp Neurol, 2015 Jun 1. PMID 25556858, Free PMC Article
  5. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article

See all (9) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Clone Names

  • MGC136878

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA replication IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within regulation of DNA-templated transcription IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
nuclear factor I/Xb

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_001040248.1 → NP_001035338.1  nuclear factor I/Xb

    See identical proteins and their annotated locations for NP_001035338.1

    Status: PROVISIONAL

    Source sequence(s)
    BC115305
    UniProtKB/TrEMBL
    A0A8M1N8M6, A0A8M3B0T9, Q1RLS5
    Related
    ENSDARP00000084668.3, ENSDART00000090235.5
    Conserved Domains (3) summary
    cl00055
    Location:88 → 192
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:233 → 417
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:30 → 66
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007114.7 Reference GRCz11 Primary Assembly

    Range
    14749593..15064157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_068217605.1 → XP_068073706.1  nuclear factor I/Xb isoform X2

    UniProtKB/TrEMBL
    A0A8M3AQD4

  2. XM_068217604.1 → XP_068073705.1  nuclear factor I/Xb isoform X1

    UniProtKB/TrEMBL
    A0A8M3AQD4

  3. XM_068217609.1 → XP_068073710.1  nuclear factor I/Xb isoform X5

    UniProtKB/TrEMBL
    A0A8M3AXV2

  4. XM_068217618.1 → XP_068073719.1  nuclear factor I/Xb isoform X15

    UniProtKB/TrEMBL
    A0A8M3AQR5

  5. XM_068217607.1 → XP_068073708.1  nuclear factor I/Xb isoform X3

    UniProtKB/TrEMBL
    A0A8M3B860

  6. XM_068217608.1 → XP_068073709.1  nuclear factor I/Xb isoform X4

    UniProtKB/TrEMBL
    A0A8M3B0T6

  7. XM_068217610.1 → XP_068073711.1  nuclear factor I/Xb isoform X6

    UniProtKB/TrEMBL
    A0A8M3AXV2

  8. XM_068217612.1 → XP_068073713.1  nuclear factor I/Xb isoform X8

    UniProtKB/TrEMBL
    A0A8M3B863

  9. XM_068217611.1 → XP_068073712.1  nuclear factor I/Xb isoform X7

    UniProtKB/TrEMBL
    A0A8M3AQD9

  10. XM_068217619.1 → XP_068073720.1  nuclear factor I/Xb isoform X16

    UniProtKB/TrEMBL
    A0A8M3B0T9

  11. XM_068217617.1 → XP_068073718.1  nuclear factor I/Xb isoform X14

    UniProtKB/TrEMBL
    A0A8M3B0T9

  12. XM_068217616.1 → XP_068073717.1  nuclear factor I/Xb isoform X13

    UniProtKB/TrEMBL
    A0A8M3B0T9

  13. XM_009299287.4 → XP_009297562.1  nuclear factor I/Xb isoform X10

    UniProtKB/TrEMBL
    A0A8M3AQD4, A0A8M3AQR1
    Conserved Domains (3) summary
    cl00055
    Location:88 → 192
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:233 → 556
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:30 → 66
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

  14. XM_005163820.5 → XP_005163877.1  nuclear factor I/Xb isoform X11

    UniProtKB/TrEMBL
    A0A8M2BBB5, A0A8M3AQD4
    Conserved Domains (3) summary
    cl00055
    Location:68 → 172
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:213 → 536
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:8 → 46
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

  15. XM_005163822.5 → XP_005163879.1  nuclear factor I/Xb isoform X12

    UniProtKB/TrEMBL
    A0A8M2BAY5, A0A8M3AQD4
    Conserved Domains (3) summary
    cl00055
    Location:60 → 164
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:205 → 528
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:1 → 38
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus

  16. XM_009299284.4 → XP_009297559.1  nuclear factor I/Xb isoform X9

    UniProtKB/TrEMBL
    A0A8M3AQD4, A0A8M3AXU6
    Conserved Domains (3) summary
    cl00055
    Location:106 → 210
    MH1; N-terminal Mad Homology 1 (MH1) domain
    pfam00859
    Location:251 → 574
    CTF_NFI; CTF/NF-I family transcription modulation region
    pfam10524
    Location:47 → 84
    NfI_DNAbd_pre-N; Nuclear factor I protein pre-N-terminus
Nucleotide Protein Strain
Heading Accession and Version

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