Human Gene NXF1 (ENST00000531709.6) from GENCODE V44
  Description: Homo sapiens nuclear RNA export factor 1 (NXF1), transcript variant 2, mRNA. (from RefSeq NM_001081491)
RefSeq Summary (NM_001081491): 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].
Gencode Transcript: ENST00000531709.6
Gencode Gene: ENSG00000162231.14
Transcript (Including UTRs)
   Position: hg38 chr11:62,792,123-62,805,470 Size: 13,348 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg38 chr11:62,800,322-62,805,356 Size: 5,035 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:62,792,123-62,805,470)mRNA (may differ from genome)Protein (356 aa)
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-  Comments and Description Text from UniProtKB
  ID: NXF1_HUMAN
DESCRIPTION: RecName: Full=Nuclear RNA export factor 1; AltName: Full=Tip-associated protein; AltName: Full=Tip-associating protein; AltName: Full=mRNA export factor TAP;
FUNCTION: Involved in the nuclear export of mRNA species bearing retroviral constitutive transport elements (CTE) and in the export of mRNA from the nucleus to the cytoplasm. The NXF1-NXT1 heterodimer is involved in the export of HSP70 mRNA in conjunction with ALYREF/THOC4 and THOC5.
SUBUNIT: Heterodimer with NXT1. Interacts (via NTF2 domain) with NXT1. The formation of NXF1/NXT1 heterodimers is required for the NXF1-mediated nuclear mRNA export. Interacts with NXT2, E1B-AP5, RAE1, ALYREF/THOC4 and with several nucleoporins. Is part of the exon junction complex (EJC) containing NCBP1, NCBP2, RNPS1, RBM8A, SRRM1, NXF1, UPF1, UPF2, UPF3A, UPF3B, ALYREF/THOC4 and/or REFBP2. Found in a mRNA complex with RENT3A and RENT3B. Interacts with FYTTD1/UIF, EIF4A3, NUPL2 and THOC5. Interacts with Saimiriine herpesvirus 2 TIP protein. Interacts with human herpes virus 1 (HHV-1) ICP27 protein; this interaction allows efficient export of HHV-1 early and late transcripts.
INTERACTION: P22575:- (xeno); NbExp=6; IntAct=EBI-398874, EBI-866709; O00571:DDX3X; NbExp=5; IntAct=EBI-398874, EBI-353779; Q08211:DHX9; NbExp=7; IntAct=EBI-398874, EBI-352022; Q9UKK6:NXT1; NbExp=2; IntAct=EBI-398874, EBI-301889; Q07955:SRSF1; NbExp=5; IntAct=EBI-398874, EBI-398920;
SUBCELLULAR LOCATION: Nucleus, nucleoplasm. Nucleus speckle. Cytoplasm. Note=Localized predominantly in the nucleoplasm and at both the nucleoplasmic and cytoplasmic faces of the nuclear pore complex. Shuttles between the nucleus and the cytoplasm. Travels to the cytoplasm as part of the exon junction complex (EJC) bound to mRNA.
TISSUE SPECIFICITY: Expressed ubiquitously.
DOMAIN: The minimal CTE binding domain consists of an RNP-type RNA binding domain (RBD) and leucine-rich repeats.
DOMAIN: The nucleoporin binding domain consists of a NTF2 domain (also called NTF2-like domain) and a TAP-C domain (also called UBA-like domain). It has 2 nucleoporin-FG-repeats binding sites (one in the NTF2 and the other in the TAP-C domain) which contribute to nucleoporin association and act synergistically to export cellular mRNAs.
DOMAIN: The NTF2 domain is functional only in the presence of NXT1 and is essential for the export of mRNA from the nucleus.
DOMAIN: The TAP-C domain mediates direct interactions with nucleoporin-FG-repeats and is necessary and sufficient for localization of NXF1 to the nuclear rim. The conserved loop 594- NWD-596 of the TAP-C domain has a critical role in the interaction with nucleoporins.
DOMAIN: The leucine-rich repeats are essential for the export of mRNA from the nucleus.
DOMAIN: The RNA-binding domain is a non-canonical RNP-type domain.
SIMILARITY: Belongs to the NXF family.
SIMILARITY: Contains 4 LRR (leucine-rich) repeats.
SIMILARITY: Contains 1 NTF2 domain.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.
SIMILARITY: Contains 1 TAP-C domain.

-  Primer design for this transcript
 

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-  MalaCards Disease Associations
  MalaCards Gene Search: NXF1
Diseases sorted by gene-association score: influenza (7)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 64.07 RPKM in Pituitary
Total median expression: 1623.39 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -42.30114-0.371 Picture PostScript Text
3' UTR -1075.002943-0.365 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001611 - Leu-rich_rpt
IPR002075 - NTF2
IPR018222 - Nuclear_transport_factor_2_euk
IPR012677 - Nucleotide-bd_a/b_plait
IPR005637 - TAP_C_dom
IPR015245 - Tap_RNA-bd
IPR003603 - U2A'_phosphoprotein32A_C
IPR009060 - UBA-like

Pfam Domains:
PF00560 - Leucine Rich Repeat
PF02136 - Nuclear transport factor 2 (NTF2) domain
PF09162 - Tap, RNA-binding
PF03943 - TAP C-terminal domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1FO1 - X-ray MuPIT 1FT8 - X-ray MuPIT 1GO5 - NMR MuPIT 1JKG - X-ray MuPIT 1JN5 - X-ray MuPIT 1KOH - X-ray MuPIT 1KOO - X-ray MuPIT 1OAI - X-ray 2Z5K - X-ray MuPIT 2Z5M - X-ray MuPIT 3RW6 - X-ray MuPIT 3RW7 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9UBU9
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
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Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0005515 protein binding

Biological Process:
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0016032 viral process
GO:0016973 poly(A)+ mRNA export from nucleus
GO:0051028 mRNA transport

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016607 nuclear speck
GO:0042405 nuclear inclusion body
GO:0000346 transcription export complex


-  Descriptions from all associated GenBank mRNAs
  CR749674 - Homo sapiens mRNA; cDNA DKFZp667O0311 (from clone DKFZp667O0311).
BC028041 - Homo sapiens nuclear RNA export factor 1, mRNA (cDNA clone MGC:40096 IMAGE:5248449), complete cds.
AB209915 - Homo sapiens mRNA for nuclear RNA export factor 1 variant protein.
AK027192 - Homo sapiens cDNA: FLJ23539 fis, clone LNG08101, highly similar to AF126246 Homo sapiens tip-associated protein TAP mRNA.
BC004904 - Homo sapiens nuclear RNA export factor 1, mRNA (cDNA clone MGC:4612 IMAGE:3504065), complete cds.
BC017421 - Homo sapiens nuclear RNA export factor 1, mRNA (cDNA clone IMAGE:4687823), with apparent retained intron.
JD164945 - Sequence 145969 from Patent EP1572962.
JD447939 - Sequence 428963 from Patent EP1572962.
JD548920 - Sequence 529944 from Patent EP1572962.
U80073 - Human tip associating protein (TAP) mRNA, complete cds.
AF112880 - Homo sapiens tip associating protein mRNA, complete cds.
AF126246 - Homo sapiens tip-associated protein TAP mRNA, complete cds.
AJ132712 - Homo sapiens mRNA for nuclear RNA export factor 1 (NXF1 gene).
KJ893058 - Synthetic construct Homo sapiens clone ccsbBroadEn_02452 NXF1 gene, encodes complete protein.
DQ892931 - Synthetic construct clone IMAGE:100005561; FLH190949.01X; RZPDo839F0976D nuclear RNA export factor 1 (NXF1) gene, encodes complete protein.
DQ896180 - Synthetic construct Homo sapiens clone IMAGE:100010640; FLH190947.01L; RZPDo839F0966D nuclear RNA export factor 1 (NXF1) gene, encodes complete protein.
AB528336 - Synthetic construct DNA, clone: pF1KB6112, Homo sapiens NXF1 gene for nuclear RNA export factor 1, without stop codon, in Flexi system.
AK307961 - Homo sapiens cDNA, FLJ97909.
AK307998 - Homo sapiens cDNA, FLJ97946.
AK304082 - Homo sapiens cDNA FLJ61053 complete cds, highly similar to Nuclear RNA export factor 1.
AK304743 - Homo sapiens cDNA FLJ57456 complete cds, highly similar to Nuclear RNA export factor 1.
AK304137 - Homo sapiens cDNA FLJ59010 complete cds, highly similar to Nuclear RNA export factor 1.
CU678798 - Synthetic construct Homo sapiens gateway clone IMAGE:100020341 5' read NXF1 mRNA.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9UBU9 (Reactome details) participates in the following event(s):

R-HSA-77587 Docking of Mature Replication Dependent Histone mRNA with the NPC
R-HSA-77594 Docking of the Mature intronless derived transcript derived mRNA, TAP and Aly/Ref at the NPC
R-HSA-111439 Docking of Mature Histone mRNA complex:TAP at the NPC
R-HSA-158447 Release of the Mature intronless derived mRNA, TAP, and Aly/Ref from the NPC
R-HSA-158484 Release of the SLBP independent Histone mRNA from the NPC
R-HSA-159050 Release of the Mature intronless transcript derived Histone mRNA:SLBP:eIF4E Complex
R-HSA-158441 Transport of the Mature intronless transcript derived mRNA:TAP:Aly/Ref Complex through the NPC
R-HSA-159046 Transport of the Mature IntronlessTranscript Derived Histone mRNA:SLBP:TAP:Aly/Ref complex through the NPC
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-75098 mRNP complex dissociates from cytosolic face of NPC
R-HSA-75096 Docking of the TAP:EJC Complex with the NPC
R-HSA-159230 Transport of the SLBP Dependant Mature mRNA
R-HSA-159231 Transport of Mature mRNA Derived from an Intronless Transcript
R-HSA-159227 Transport of the SLBP independent Mature mRNA
R-HSA-159234 Transport of Mature mRNAs Derived from Intronless Transcripts
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B4E269, ENST00000531709.1, ENST00000531709.2, ENST00000531709.3, ENST00000531709.4, ENST00000531709.5, NM_001081491, NXF1_HUMAN, Q99799, Q9UBU9, Q9UQL2, TAP, uc001nvg.1, uc001nvg.2
UCSC ID: ENST00000531709.6
RefSeq Accession: NM_001081491
Protein: Q9UBU9 (aka NXF1_HUMAN)
CCDS: CCDS44629.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.