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UBAP1 Gene

protein-coding   GIFtS: 51

GC09P034169
ubiquitin associated protein 1
(Previous name: ubiquitin associated protein )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: UBAP)
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
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Aliases
MGC119669 2
MGC8710 2
NAG20 2
OTTHUMP00000000480 2
OTTHUMP00000000481 2
UAP 2
UBAP 2, 3, 5
Descriptions
Nasopharyngeal carcinoma-associated gene 20 protein 3
ubiquitin associated protein 1
ubiquitin associated protein 1 2
External Ids
HGNC: 124611
Entrez Gene: 512712
UniProtKB: Q9NZ093
Ensembl: ENSG000001650067
Search outside databases for aliases for UBAP1 gene

Previous GC identifers: GC09P034491 GC09P034348 GC09P034026

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for UBAP1:
This gene is a member of the UBA domain family, whose members include proteins having connections
to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a
non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular
protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of
heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location,
this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal
carcinomas. [provided by RefSeq]

Gene Wiki entry for UBAP1
(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:
UCSC Golden Path with GeneCards custom track

 Transcription factor binding sites upstream to the UBAP1 gene  

Entrez Gene cytogenetic band: 9p13.3   Ensembl cytogenetic band:  9p13.3   HGNC cytogenetic band: 9p13.3

UBAP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P034169:     (about GC identifiers)

Start:
34,169,011 bp from pter
End:
34,242,521 bp from pter
Size:
73,511 bases
Orientation:
plus strand
RefSeq DNA sequence:
NC_000009.10  NT_008413.17  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: UBAP1_HUMAN, Q9NZ09 (See protein sequence)
Recommended Name: Ubiquitin-associated protein 1  
Size: 502 amino acids; 55084 Da
PDB structures from and Proteopedia :
1WGN (3D)    
Secondary accessions: Q4V759 Q53FP7 Q5T7B3 Q6FI75 Q8NC52 Q8NCG6 Q8NCH9
Alternative splicing: 2 isoforms:  Q9NZ09-1   Q9NZ09-2   

REFSEQ proteins: NP_057609.2  

ENSEMBL proteins: 
ENSP00000352541 ENSP00000297661 ENSP00000368484 


Human Recombinant Proteins 
Browse Drug Discovery Central at Invitrogen for human recombinant proteins
Browse Purified and Recombinant Proteins at Millipore
Browse Human Recombinant Proteins at Sigma-Aldrich  
Browse R&D Systems for human recombinant proteins
Browse recombinant and purified proteins available from Enzo Life Sciences
Browse Abcam for Recombinant Proteins
Human Recombinant Proteins from Abnova (UBAP1)
                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

1 Gene Ontology (GO) cellular component term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005737 cytoplasm IDA11256614
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Antibodies for UBAP1: 
Browse Antibodies Central at Invitrogen
Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
Sigma-Aldrich Antibodies for UBAP1
Browse R&D Systems for Antibodies
Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
Monoclonal and Polyclonal Antibodies from Abnova (UBAP1)
Novus Biologicals Antibody for UBAP1

Assays for UBAP1: 
Browse Invitrogen for biochemical assays
Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro domain/family:
 IPR015940 UBA/transl_elong_EF1B_N_euk


   GeneDecks  UBAP1 for the domains selected above  
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Graphical View of Domain Structure for InterPro Entry Q9NZ09

ProtoNet protein and cluster: Q9NZ09

1 Blocks protein family: IPB000449 Ubiquitin-associated domain

UniProtKB/Swiss-Prot: UBAP1_HUMAN, Q9NZ09
Similarity: Contains 2 UBA domains

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (UBAP1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016525

              Applied Biosystems Silencer® siRNAs for UBAP1

              Sigma-Aldrich siRNA and siRNA Panels for UBAP1  
                     Sigma-Aldrich shRNA for UBAP1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Invitrogen Clones for UBAP1
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_016525
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_016525
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_016525 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_016525

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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2 Interacting proteins for UBAP1 (ENSP000003525413) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
CRPENSP000002550303STRING (score=.734)
TNNT2ENSP000003562863STRING (score=.728)
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for UBAP1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (UBAP1)
Browse for Gene Knock-down Tools from Millipore
Browse Abnova for Chimera RNAi Products
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016525

              Sigma-Aldrich siRNA and siRNA Panels for UBAP1  
                     Sigma-Aldrich shRNA for UBAP1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_016525  

REFSEQ mRNAs for UBAP1 gene: 

NM_016525.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_016525  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_016525
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_016525
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_016525 

Additional cDNA sequence: 

AF130079.1 AF222043.2 AK074426.1 AK074724.1 AK074745.1 AK074812.1 AK074969.1 AK074995.1 
AK223235.1 AK295482.1 AK303711.1 AK309329.1 AL136733.1 BC020950.1 BC098141.1 BC098316.1 
BC099726.1 BC100668.1 CR533551.1 CR620852.1 CR621006.1 CR624683.1 

21 DOTS entries:

DT.99954471  DT.100811475  DT.85105562  DT.100811480  DT.40190940  DT.100811478  DT.121202525  DT.91751636 
DT.95199215  DT.95364726  DT.99981033  DT.95153446  DT.95199211  DT.100663602  DT.101982850  DT.121202511 
DT.121202542  DT.40228494  DT.91770670  DT.121202518  DT.87014157 

24/209 AceView cDNA sequences (see all 209 ):

BU731774 BI766247 BU166893 BP360371 AW593698 CB156898 CD369110 BQ059715 
BM473450 AA908859 AU279488 BQ049210 D62515 AA938430 NM_016525 BE301381 
BP340766 AA705563 BQ642063 BC020950 CR624683 BG818050 AI354695 AI445067 

highest scoring ESTs for UBAP1:

AI679180 AA025100 AA025206 AA056988 AA149434 AA176548 AA190830 AA443759 AA648447 AA693356 

Unigene Cluster for UBAP1:

Ubiquitin associated protein 1
Hs.268963  [show with all ESTs]
Unigene Representative Sequence: AK074969


GeneLoc Exon Structure

5/7 Alternative Splicing Database (ASD) splice patterns (SP) for UBAP1 (see all 7 )

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c · 6d · 6e · 6f ^ 7 ^ 8 ^ 9
SP1:              -     -           -                                                               
SP2:              -                 -                                                               
SP3:                    -           -                                                               
SP4:              -     -     -     -                                                               
SP5:              -     -           -     -                                                         

About this scheme

ECgene alternative splicing isoforms for UBAP1

3 Ensembl transcripts including schematic representations:
ENST00000359544  ENST00000297661  ENST00000379186  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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UBAP1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for UBAP1

1 / 2 / 3

6 probe-sets matching UBAP1 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

46270_at2, 3 U133-B 1 1.00 1.00 0.82 1.14 AL039447 0.80 0.80 0.80 1
45376_s_at2, 3 U95-B 1 1.00 1.00 0.97 0.86 AI679180 1.00 1.00 1.00 1

46270_at2, 3 U133-A 1 1.00 1.00 -- -- AL039447 0.80 0.80 0.80 1

221490_at2, 3 U133-A 1 1.00 1.00 -- -- AL136733 0.80 1.00 0.91 1

46270_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --

221490_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
GeneDecks  UBAP1 for binary patterns associated with the probe-sets selected above  
About GeneDecksing
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.268963

UniProtKB/Swiss-Prot: UBAP1_HUMAN, Q9NZ09
Tissue specificity: Ubiquitous. Highly expressed in heart, brain, placenta, lung, liver, skeletal
muscle and pancreas

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for UBAP1 gene from 5/9 species (see all 9 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
dog
(Canis familiaris)
UBAP11   -- ubiquitin associated protein 1 94.02(n)
95.22(a)
474745  XM_847340.1  XP_852433.1 
chimpanzee
(Pan troglodytes)
UBAP11   -- ubiquitin associated protein 1 99.73(n)
99.39(a)
747117  XM_001155943.1  XP_001155943.1 
cow
(Bos taurus)
UBAP11   -- ubiquitin associated protein 1 92.1(n)
92.03(a)
517788  XM_001251128.1  XP_001251129.1 
rat
(Rattus norvegicus)
Ubap11   -- ubiquitin-associated protein 1 91.17(n)
91.24(a)
362502  NM_001012190.1  NP_001012190.1 
mouse
(Mus musculus)
Ubap11, 5 45
ubiquitin-associated protein 11, 5 90.36(n)1
89.75(a)1
671231  NM_023305.21  NP_075794.21 
 AF2755495  AK0095965  (see all 22)
About this table        Species with no ortholog for UBAP1

ENSEMBL Gene Tree for UBAP1
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --
(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
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10/412 NCBI SNPs in UBAP1 are shown (see all 412 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 87)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 9 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs169354571,2
C,F,H34232094(+) CCAAAT/AACTGG 1 K/N mis1 ese312Minor allele frequency- A:0.06NA EU EA WA 1052
rs96507051,2
C,F,H34168974(+) GGTCCG/AGGCGT 1 -- ng518Minor allele frequency- A:0.07EU EA WA 838
--
rs15482901,2
A,C34167891(+) gcccaG/AgctCA 1 -- ng513Minor allele frequency- A:0.01NA 140
--
rs70380441,2
A,C34167071(+) cctccA/Tcctct 1 -- ng51 trp30--------
rs125513451,2
C,H34231760(+) AAAGAT/CGTCAC 1 T/M mis1 ese34Minor allele frequency- C:0.00EU EA WA 420
rs10412511,2
A,C,F,H,O34177354(-) TCTAAG/AAAGTC 1 -- int19Minor allele frequency- A:0.27MN EU EA WA NA 964
rs15372181,2
A,C,F,H,O34201524(+) GAAGCG/ATTTTT 1 -- int16Minor allele frequency- A:0.27EA WA NA 440
rs23809261,2
A,C,F,H,O34239354(+) AATGAC/TGCCTC 1 -- int112Minor allele frequency- T:0.25EU EA WA NA 1054
--
rs108140781,2
A,C,F,H34184053(+) AATTAC/TGAACC 1 -- int14Minor allele frequency- T:0.45EU EA WA 418
rs48797581,2
A,C,F,H34178403(+) TGAATA/GCTAAA 1 -- int14Minor allele frequency- G:0.45EU EA WA 418
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HapMap Linkage Disequilibrium images for UBAP1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 609787

(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
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10/16 PubMed articles for UBAP1 gene (see all 16 ):
(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, and/or H-InvDB)
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Entrez Gene: 51271 HGNC: 12461 AceView: UBAP1 Ensembl:ENSG00000165006 euGenes: HUgn51271
ECgene: UBAP1 H-InvDB: UBAP1
(According to HUGE)
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  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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NameDescription
ATLAS Chromosomes in Cancer entry for UBAP1 Genetics and Cytogenetics in Oncology and Haematology
(Available from WIS Yeda, Salk, Tufts)
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  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for UBAP1:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



  Invitrogen iPath Pathways  Invitrogen BLOCK-iT™ RNAi
  Invitrogen Antibodies  Invitrogen Assays
  Invitrogen Clones  Invitrogen Q-PCR Products
  Invitrogen Human Recombinant Kinases  Invitrogen Custom Antibody and Peptide Service
  Invitrogen Proteins / Assays / Screening Services  Search Invitrogen catalog for UBAP1-related products

 Millipore Custom Antibody & Bulk Services
 Millipore Preclinical / Clinical Development Services
 Millipore Immunoassay Services
 Millipore Target Screening & Profiling Services


 Predesigned and custom siRNAs for UBAP1 Antibodies for UBAP1
 Explore super-pooled esiRNAs Browse proteins at Sigma-Aldrich
 Lentivirus-delivered shRNAs for UBAP1 Browse small molecules at Sigma-Aldrich
 "Your Favorite Gene" Pathwaysfeedback


  
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 Antibodies for UBAP1

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