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NUP62CL Gene

protein-coding   GIFtS: 45
GCID: GC0XM106366

Nucleoporin 62kDa C-Terminal Like

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Nucleoporin 62kDa C-Terminal Like1 2
Nucleoporin-62 C-Terminal-Like Protein2
NUP62L3

External Ids:    HGNC: 259601   Entrez Gene: 548302   Ensembl: ENSG000001980887   UniProtKB: Q9H1M03   

Export aliases for NUP62CL gene to outside databases

Previous GC identifers: GC0XM106253 GC0XM095994


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for NUP62CL Gene:
This gene encodes a protein containing a domain found in nucleoporins which are glycoproteins found in nuclear
pore complexes. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Sep 2011)

GeneCards Summary for NUP62CL Gene:
NUP62CL (nucleoporin 62kDa C-terminal like) is a protein-coding gene. Diseases associated with NUP62CL include myelodysplastic syndromes. GO annotations related to this gene include structural constituent of nuclear pore. An important paralog of this gene is NUP62.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000023.11  NC_018934.2  NT_011651.18  
Regulatory elements:
   Regulatory transcription factor binding sites in the NUP62CL gene promoter:
         TBP   STAT5B   AML1a   E4BP4   Cdc5   YY1   E47   Hand1   Hlf   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidNUP62CL promoter sequence
   Search Chromatin IP Primers for NUP62CL

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat NUP62CL


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Xq22.3   Ensembl cytogenetic band:  Xq22.3   HGNC cytogenetic band: Xq22.3

NUP62CL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
NUP62CL gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM106366:  view genomic region     (about GC identifiers)

Start:
106,366,657 bp from pter      End:
106,449,670 bp from pter
Size:
83,014 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: N62CL_HUMAN, Q9H1M0 (See protein sequence)
Recommended Name: Nucleoporin-62 C-terminal-like protein  
Size: 184 amino acids; 20837 Da
Secondary accessions: D3DUX4 Q8WVL6 Q9NXP2
Alternative splicing: 2 isoforms:  Q9H1M0-1   Q9H1M0-2   

Explore the universe of human proteins at neXtProt for NUP62CL: NX_Q9H1M0

REFSEQ proteins: NP_060151.2  
ENSEMBL proteins: 
 ENSP00000361544   ENSP00000433269   ENSP00000408612   ENSP00000405906   ENSP00000361539  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR026010 NSP1/NUP62
 IPR007758 Nucleoporin_NSP1_C

Graphical View of Domain Structure for InterPro Entry Q9H1M0

ProtoNet protein and cluster: Q9H1M0

UniProtKB/Swiss-Prot: N62CL_HUMAN, Q9H1M0
Similarity: Belongs to the nucleoporin NSP1/NUP62 family


NUP62CL for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0017056structural constituent of nuclear pore IEA--
     
NUP62CL for ontologies           About GeneDecksing


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hsa-mir-335-5p (MIRT018851)

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5 qRT-PCR Assays for microRNAs that regulate NUP62CL:
hsa-miR-509-5p hsa-miR-708* hsa-miR-548b-3p hsa-miR-181a-2* hsa-miR-509-3-5p
SwitchGear 3'UTR luciferase reporter plasmidNUP62CL 3' UTR sequence
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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol3
mitochondrion3
nucleus2
extracellular1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005643nuclear pore IEA--

NUP62CL for ontologies           About GeneDecksing


(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for NUP62CL
Interactions:

    Search GeneGlobe Interaction Network for NUP62CL

STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

Selected Interacting proteins for NUP62CL (Q9H1M02, 3 ENSP000003615444) via UniProtKB, MINT, STRING, and/or I2D (see all 47)
InteractantInteraction Details
GeneCardExternal ID(s)
OGTO152943, ENSP000003628244I2D: score=4 STRING: ENSP00000362824
NUP214ENSP000003524004STRING: ENSP00000352400
NUP93ENSP000003106684STRING: ENSP00000310668
MCM3APENSP000002916884STRING: ENSP00000291688
NUP88ENSP000002256964STRING: ENSP00000225696
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0015031protein transport IEA--

NUP62CL for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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  Browse compounds at ApexBio 

Browse Tocris compounds for NUP62CL (N62CL)



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for NUP62CL gene: 
NM_017681.2  

Unigene Cluster for NUP62CL:

Nucleoporin 62kDa C-terminal like
Hs.163629  [show with all ESTs]
Unigene Representative Sequence: NM_017681
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000372466(uc004ena.3) ENST00000484614 ENST00000432145 ENST00000421752
ENST00000372461(uc004enb.3)
miRNA
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hsa-miR-509-5p hsa-miR-708* hsa-miR-548b-3p hsa-miR-181a-2* hsa-miR-509-3-5p
SwitchGear 3'UTR luciferase reporter plasmidNUP62CL 3' UTR sequence
Inhib. RNA
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  QuantiFast Probe-based Assays in human, mouse, rat NUP62CL

Additional mRNA sequence: 

AK000137.1 BC016327.1 NR_033676.1 

4 DOTS entries:

DT.70101593  DT.99997229  DT.95154426  DT.97810951 

20 AceView cDNA sequences:

BC016327 BP368021 CR605049 BC017799 AI393214 CA312712 CB112762 AK000137 
NM_017681 BX365434 BM844493 BX365433 BQ429014 BX340482 AI763282 H66935 
BG495310 H66934 H60787 AI702317 

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for NUP62CL    About this scheme

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9
SP1:                                                      
SP2:        -                 -                           


ECgene alternative splicing isoforms for NUP62CL

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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NUP62CL expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAATACTGAA
NUP62CL Expression
About this image

NUP62CL Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

SOURCE GeneReport for Unigene cluster: Hs.163629
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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for NUP62CL

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for NUP62CL gene from Selected species (see all 11)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Nup62cl5 nucleoporin 62 C-terminal like   --   X (61.35 cM) 140006805 
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
19(a)
1 → many
4(1874662-1883235)
lizard
(Anolis carolinensis)
Reptilia --
--
16(a)
1 → many
GL343376.1(1065644-1074319)
zebrafish
(Danio rerio)
Actinopterygii nup62l6
nucleoporin 62 like
18(a)
1 → many
14(10823540-10854840) ENSDARG00000020527
fruit fly
(Drosophila melanogaster)
Insecta Nup626
Nucleoporin 62
15(a)
1 → many
2R(12231882-12233333)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes NSP16
NUP16
Essential component of the nuclear pore complex, w...
Nuclear pore complex (NPC) subunit, involved in pr...
2(a)
1(a)
many ↔ many
many ↔ many
X(365784-368373) YJL041W
XV(507948-511178) YOR098C


ENSEMBL Gene Tree for NUP62CL (if available)
TreeFam Gene Tree for NUP62CL (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for NUP62CL gene
NUP622  
1 SIMAP similar gene for NUP62CL using alignment to 3 protein entries:     N62CL_HUMAN (see all proteins):
NUP62

NUP62CL for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for NUP62CL (see all 1023)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1868478171,2
C--106338009(+) GAAAAA/GATGTC 2 -- int10--------
rs1887465781,2
--106338466(+) GACTTA/CGGTGA 2 -- ut31 nc-transcript-variant0--------
rs2009544711,2
--106338547(+) CAAAC-/AAAAAA 2 -- ut31 nc-transcript-variant0--------
rs1815385091,2
--106338791(+) GACAAA/GCATTA 2 -- ut31 nc-transcript-variant0--------
rs12855821,2
C,F,A,H--106338832(+) TTGAGA/GAGAAG 2 -- ut31 nc-transcript-variantese3 trp330Minor allele frequency- G:0.36NA EA NS WA CSA 2836
rs557712121,2
C--106338932(+) GTACTA/GATGCC 2 -- ut31 nc-transcript-variant1Minor allele frequency- G:0.00NA 1
rs2003402551,2
--106339079(+) AAATG-/AAAAAA 2 -- ut31 nc-transcript-variant0--------
rs1864507911,2
--106339428(+) AACACA/GTAAGA 2 -- int10--------
rs1404351341,2
C--106339688(+) CATTTC/TTGTTC 2 -- int10--------
rs1908175111,2
--106339701(+) TTCCAA/GTAATG 2 -- int10--------

HapMap Linkage Disequilibrium report for NUP62CL (106366657 - 106449670 bp)

Structural Variations
     Database of Genomic Variants (DGV) 5 variations for NUP62CL:    About this table    
Variant IDTypeSubtypePubMed ID
esv2740376CNV Deletion23290073
nsv7027CNV Insertion18451855
esv1568973CNV Insertion17803354
esv2752312CNV Gain17911159
nsv519484CNV Gain19592680

Locus Specific Mutation Databases (LSDB): NUP62CL

Site Specific Mutation Identification with PCR Assays
SeqTarget long-range PCR primers for resequencing NUP62CL
DNA2.0 Custom Variant and Variant Library Synthesis for NUP62CL

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for NUP62CL:    
About MalaCards
myelodysplastic syndromes


NUP62CL for disorders           About GeneDecksing


Export disorders for NUP62CL gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for NUP62CL gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with NUP62CL)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The DNA sequence of the human X chromosome. (PubMed id 15772651)1, 2 Ross M.T.... Bentley D.R. (Nature 2005)
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  5. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
  6. Interactions of pathological hallmark proteins: tubulin polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (J. Biol. Chem. 2011)
  7. Systematic analysis of human protein complexes identifies chromosome segregation proteins. (PubMed id 20360068)1 Hutchins J.R.... Peters J.M. (Science 2010)
  8. Ubiquitin-mediated proteolysis of HuR by heat shock. (PubMed id 19322201)1 Abdelmohsen K....Gorospe M. (EMBO J. 2009)
  9. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (amp 2008)
  10. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 54830 HGNC: 25960 AceView: FLJ20130 Ensembl:ENSG00000198088 euGenes: HUgn54830
ECgene: NUP62CL H-InvDB: NUP62CL

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for NUP62CL Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for NUP62CL gene:
Search GeneIP for patents involving NUP62CL

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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