Human Gene SNUPN (uc002bas.3) Description and Page Index
  Description: Homo sapiens snurportin 1 (SNUPN), transcript variant 3, mRNA.
RefSeq Summary (NM_001042588): The nuclear import of the spliceosomal snRNPs U1, U2, U4 and U5, is dependent on the presence of a complex nuclear localization signal. The latter is composed of the 5'-2,2,7-terminal trimethylguanosine (m3G) cap structure of the U snRNA and the Sm core domain. The protein encoded by this gene interacts specifically with m3G-cap and functions as an snRNP-specific nuclear import receptor. Alternatively spliced transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr15:75,890,424-75,918,719 Size: 28,296 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg19 chr15:75,890,699-75,913,392 Size: 22,694 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:75,890,424-75,918,719)mRNA (may differ from genome)Protein (360 aa)
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SPN1_HUMAN
DESCRIPTION: RecName: Full=Snurportin-1; AltName: Full=RNA U transporter 1;
FUNCTION: Functions as an U snRNP-specific nuclear import adapter. Involved in the trimethylguanosine (m3G)-cap-dependent nuclear import of U snRNPs. Binds specifically to the terminal m3G-cap U snRNAs.
SUBUNIT: Component of an import snRNP complex composed of KPNB1, SNUPN, SMN1 and ZNF259. Component of a nuclear export receptor complex composed of KPNB1, Ran, SNUPN and XPO1. Found in a trimeric export complex with SNUPN, Ran and XPO1. Interacts with DDX20, IPO7, KPNB1, SMN1, SNRPB and XPO1. Interacts directly with XPO1. Its interaction with XPO1 and binding to m3G-cap U snRNPs appears to be mutually exclusive.
SUBCELLULAR LOCATION: Nucleus. Cytoplasm. Note=Nucleoplasmic shuttling protein. Its nuclear import involves the nucleocytoplasmic transport receptor importin beta. It is re- exported to the cytoplasm by the XPO1-dependent nuclear export receptor pathway.
SIMILARITY: Belongs to the snurportin family.
SIMILARITY: Contains 1 IBB domain.

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 16.15 RPKM in Testis
Total median expression: 282.45 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -47.29145-0.326 Picture PostScript Text
3' UTR -76.70275-0.279 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
IPR002652 - Importin-a_IBB
IPR017336 - Snurportin-1
IPR024721 - Snurportin-1_N

Pfam Domains:
PF11538 - Snurportin1

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1XK5
- X-ray MuPIT

2P8Q
- X-ray MuPIT

2Q5D
- X-ray MuPIT
To conserve bandwidth, only the images from the first 3 structures are shown.
2QNA - X-ray MuPIT 3GB8 - X-ray MuPIT 3GJX - X-ray MuPIT
3LWW - X-ray MuPIT 3NBY - X-ray MuPIT 3NBZ - X-ray MuPIT
3NC0 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on O95149
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000339 RNA cap binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0061608 nuclear import signal receptor activity

Biological Process:
GO:0000387 spliceosomal snRNP assembly
GO:0006606 protein import into nucleus
GO:0051170 nuclear import
GO:0061015 snRNA import into nucleus

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  BC004203 - Homo sapiens snurportin 1, mRNA (cDNA clone MGC:3769 IMAGE:3605328), complete cds.
LF384553 - JP 2014500723-A/192056: Polycomb-Associated Non-Coding RNAs.
AF039029 - Homo sapiens snurportin1 mRNA, complete cds.
AK054641 - Homo sapiens cDNA FLJ30079 fis, clone BGGI12000544, highly similar to Snurportin-1 (RNA U transporter 1).
AK289475 - Homo sapiens cDNA FLJ75948 complete cds, highly similar to Homo sapiens RNA, U transporter 1 (RNUT1), mRNA.
JD310351 - Sequence 291375 from Patent EP1572962.
JD354298 - Sequence 335322 from Patent EP1572962.
MA620130 - JP 2018138019-A/192056: Polycomb-Associated Non-Coding RNAs.
JD074060 - Sequence 55084 from Patent EP1572962.
JD055827 - Sequence 36851 from Patent EP1572962.
CR456811 - Homo sapiens full open reading frame cDNA clone RZPDo834E0118D for gene RNUT1, RNA, U transporter 1; complete cds, incl. stopcodon.
DQ893088 - Synthetic construct clone IMAGE:100005718; FLH193630.01X; RZPDo839A0579D snurportin 1 (SNUPN) gene, encodes complete protein.
KJ892910 - Synthetic construct Homo sapiens clone ccsbBroadEn_02304 SNUPN gene, encodes complete protein.
DQ896360 - Synthetic construct Homo sapiens clone IMAGE:100010820; FLH193626.01L; RZPDo839A0569D snurportin 1 (SNUPN) gene, encodes complete protein.
CU678612 - Synthetic construct Homo sapiens gateway clone IMAGE:100019088 5' read SNUPN mRNA.
LF377188 - JP 2014500723-A/184691: Polycomb-Associated Non-Coding RNAs.
LF377187 - JP 2014500723-A/184690: Polycomb-Associated Non-Coding RNAs.
LF377185 - JP 2014500723-A/184688: Polycomb-Associated Non-Coding RNAs.
JD026827 - Sequence 7851 from Patent EP1572962.
JD029915 - Sequence 10939 from Patent EP1572962.
MA612765 - JP 2018138019-A/184691: Polycomb-Associated Non-Coding RNAs.
MA612764 - JP 2018138019-A/184690: Polycomb-Associated Non-Coding RNAs.
MA612762 - JP 2018138019-A/184688: Polycomb-Associated Non-Coding RNAs.

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

Protein O95149 (Reactome details) participates in the following event(s):

R-HSA-191763 snRNP:Snurportin complex formation
R-HSA-191830 snRNP nuclear import and release
R-HSA-191859 snRNP Assembly
R-HSA-194441 Metabolism of non-coding RNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A6NE34, A8K0B0, D3DW76, NM_001042588, NP_005692, O95149, RNUT1, SPN1, SPN1_HUMAN
UCSC ID: uc002bas.3
RefSeq Accession: NM_001042588
Protein: O95149 (aka SPN1_HUMAN)
CCDS: CCDS10281.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001042588.1
exon count: 9CDS single in 3' UTR: no RNA size: 1503
ORF size: 1083CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1586.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

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