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NXF1 nuclear RNA export factor 1 [ Homo sapiens (human) ]

Gene ID: 10482, updated on 6-Jan-2019

Summary

Official Symbol
NXF1provided by HGNC
Official Full Name
nuclear RNA export factor 1provided by HGNC
Primary source
HGNC:HGNC:8071
See related
Ensembl:ENSG00000162231 MIM:602647
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
TAP; MEX67
Summary
This gene is one member of a family of nuclear RNA export factor genes. Common domain features of this family are a noncanonical RNP-type RNA-binding domain (RBD), 4 leucine-rich repeats (LRRs), a nuclear transport factor 2 (NTF2)-like domain that allows heterodimerization with NTF2-related export protein-1 (NXT1), and a ubiquitin-associated domain that mediates interactions with nucleoporins. The LRRs and NTF2-like domains are required for export activity. Alternative splicing seems to be a common mechanism in this gene family. The encoded protein of this gene shuttles between the nucleus and the cytoplasm and binds in vivo to poly(A)+ RNA. It is the vertebrate homologue of the yeast protein Mex67p. The encoded protein overcomes the mRNA export block caused by the presence of saturating amounts of CTE (constitutive transport element) RNA of type D retroviruses. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 39.4), spleen (RPKM 22.8) and 25 other tissues See more
Orthologs

Genomic context

See NXF1 in Genome Data Viewer
Location:
11q12.3
Exon count:
21
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 11 NC_000011.10 (62792125..62805492, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (62559597..62572964, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene transmembrane protein 179B Neighboring gene microRNA 6748 Neighboring gene transmembrane protein 223 Neighboring gene microRNA 6514 Neighboring gene syntaxin 5 Neighboring gene RNA, U6 small nuclear 118, pseudogene Neighboring gene uncharacterized LOC105369332 Neighboring gene WD repeat domain 74

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 FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of nuclear RNA export factor 1 (NXF1) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Pr55(Gag) gag NXF1 upregulates the RBM15-mediated Gag expression from pNLgag-RTE, suggesting cooperation between RBM15 and NXF1 PubMed
gag NXF1 upregulates the OTT3-mediated Gag expression from pNLgag-RTE, suggesting cooperation between OTT3 and NXF1 PubMed
gag Disruption of NXF1 expression downregulates MPMV CTE-mediated HIV-1 Gag expression PubMed
Rev rev HIV-1 Rev specifically inhibits the association of TAP with spliced RRE-containing RNA and the TAP-dependent pathway reduces singly spliced and unspliced HIV-1 RNA levels PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Herpes simplex infection, organism-specific biosystem (from KEGG)
    Herpes simplex infection, organism-specific biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Herpes simplex infection, conserved biosystem (from KEGG)
    Herpes simplex infection, conserved biosystemHerpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishme...
  • Influenza A, organism-specific biosystem (from KEGG)
    Influenza A, organism-specific biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Influenza A, conserved biosystem (from KEGG)
    Influenza A, conserved biosystemInfluenza is a contagious respiratory disease caused by influenza virus infection. Influenza A virus is responsible for both annual seasonal epidemics and periodic worldwide pandemics. Novel strains ...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RNA transport, organism-specific biosystem (from KEGG)
    RNA transport, organism-specific biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • RNA transport, conserved biosystem (from KEGG)
    RNA transport, conserved biosystemRNA transport from the nucleus to the cytoplasm is fundamental for gene expression. The different RNA species that are produced in the nucleus are exported through the nuclear pore complexes (NPCs) ...
  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Transport of Mature Transcript to Cytoplasm, organism-specific biosystem (from REACTOME)
    Transport of Mature Transcript to Cytoplasm, organism-specific biosystemTransport of mRNA through the Nuclear Pore Complex (NPC) is a dynamic process involving distinct machinery and receptor subsets. The separation of the two compartments and the regulation of this tran...
  • Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA Derived from an Intronless Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing.
  • Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNA derived from an Intron-Containing Transcript, organism-specific biosystemTransport of mRNA from the nucleus to the cytoplasm, where it is translated into protein, is highly selective and closely coupled to correct RNA processing. This coupling is achieved by the nuclear p...
  • Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystem (from REACTOME)
    Transport of Mature mRNAs Derived from Intronless Transcripts, organism-specific biosystemTransport of mature mRNAs derived from intronless transcripts require some of the same protein complexes as mRNAs derived from intron containing complexes, including TAP and Aly/Ref. However a number...
  • Transport of the SLBP Dependant Mature mRNA, organism-specific biosystem (from REACTOME)
    Transport of the SLBP Dependant Mature mRNA, organism-specific biosystemTransport of U7 snRNP and stem-loop binding protein (SLBP) processed mRNA.
  • Transport of the SLBP independent Mature mRNA, organism-specific biosystem (from REACTOME)
    Transport of the SLBP independent Mature mRNA, organism-specific biosystemTransport of the SLBP independent Mature mRNA through the nuclear pore.
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA surveillance pathway, organism-specific biosystem (from KEGG)
    mRNA surveillance pathway, organism-specific biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...
  • mRNA surveillance pathway, conserved biosystem (from KEGG)
    mRNA surveillance pathway, conserved biosystemThe mRNA surveillance pathway is a quality control mechanism that detects and degrades abnormal mRNAs. These pathways include nonsense-mediated mRNA decay (NMD), nonstop mRNA decay (NSD), and no-go ...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • DKFZp667O0311

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA export from nucleus TAS
Traceable Author Statement
more info
 
mRNA export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
mRNA export from nucleus TAS
Traceable Author Statement
more info
 
poly(A)+ mRNA export from nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
nuclear inclusion body IEA
Inferred from Electronic Annotation
more info
 
nuclear pore IEA
Inferred from Electronic Annotation
more info
 
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with transcription export complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
nuclear RNA export factor 1
Names
mRNA export factor TAP
tip associating protein
tip-associated 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.

mRNA and Protein(s)

  1. NM_001081491.1NP_001074960.1  nuclear RNA export factor 1 isoform 2

    See identical proteins and their annotated locations for NP_001074960.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate segment, compared to variant 1, resulting in a shorter protein (isoform 2) that has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AB209915, AV750251, DB141140
    Consensus CDS
    CCDS44629.1
    UniProtKB/Swiss-Prot
    Q9UBU9
    UniProtKB/TrEMBL
    Q59E96
    Related
    ENSP00000453885.1, ENST00000531709.6
    Conserved Domains (3) summary
    sd00035
    Location:224266
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam09162
    Location:116198
    Tap-RNA_bind; Tap, RNA-binding
    pfam13855
    Location:265327
    LRR_8; Leucine rich repeat
  2. NM_006362.5NP_006353.2  nuclear RNA export factor 1 isoform 1

    See identical proteins and their annotated locations for NP_006353.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AP001160, BC004904, BC028041
    Consensus CDS
    CCDS8037.1
    UniProtKB/Swiss-Prot
    Q9UBU9
    Related
    ENSP00000294172.2, ENST00000294172.6
    Conserved Domains (5) summary
    smart00804
    Location:556618
    TAP_C; C-terminal domain of vertebrate Tap protein
    cd00780
    Location:382538
    NTF2; Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many ...
    sd00035
    Location:224266
    LRR_NTF; leucine-rich repeat [structural motif]
    pfam09162
    Location:116198
    Tap-RNA_bind; Tap, RNA-binding
    pfam13855
    Location:265327
    LRR_8; Leucine rich repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p12 Primary Assembly

    Range
    62792125..62805492 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001747724.2 RNA Sequence

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