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TUBBP5 Gene

pseudogene   GIFtS: 25
GCID: GC09P141044

Tubulin, Beta Pseudogene 5

(Previous names: tubulin, beta polypeptide pseudogene 5)
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(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
Tubulin, Beta Pseudogene 51 2
Tubulin, Beta Polypeptide Pseudogene 51

External Ids:    HGNC: 236741   Entrez Gene: 6432242   Ensembl: ENSG000001592477   

Export aliases for TUBBP5 gene to outside databases

Previous GC identifers: GC09U900291 GC09P140186 GC09P110512


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for TUBBP5 Gene:
TUBBP5 (tubulin, beta pseudogene 5) is a pseudogene. GO annotations related to this gene include GTP binding and structural constituent of cytoskeleton.


(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 at NCBI GenBank:
NC_000009.11  NC_018920.2  NT_008470.20  
Regulatory elements:
   Search for regulatory transcription factor binding sites for TUBBP5
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat TUBBP5


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

Entrez Gene cytogenetic band: 9q34.3   Ensembl cytogenetic band:  9q34.3   HGNC cytogenetic band: 9q34.3

TUBBP5 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
TUBBP5 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P141044:  view genomic region     (about GC identifiers)

Start:
141,044,565 bp from pter      End:
141,071,885 bp from pter
Size:
27,321 bases      Orientation:
plus strand
ORGUL member locations:
Legend (see complete legend)

ORGUL Member Locations for TUBBP5

(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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003924GTPase activity IEA--
GO:0005200structural constituent of cytoskeleton IEA--
GO:0005525GTP binding IEA--
     
Find genes that share ontologies with TUBBP5           About GenesLikeMe


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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
cytoskeleton3
cytosol3
extracellular1
mitochondrion1
nucleus1
peroxisome1

Gene Ontology (GO): 2 cellular component terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005737cytoplasm IEA--
GO:0005874microtubule IEA--

Find genes that share ontologies with TUBBP5           About GenesLikeMe


(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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Interactions:

    Search GeneGlobe Interaction Network for TUBBP5

Gene Ontology (GO): 2 biological process terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007017microtubule-based process IEA--
GO:0051258protein polymerization IEA--

Find genes that share ontologies with TUBBP5           About GenesLikeMe



(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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(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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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Unigene Cluster for TUBBP5:

Tubulin, beta pseudogene 5
Hs.551805  [show with all ESTs]
Unigene Representative Sequence: NR_027156
3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000503395(uc010ncq.3) ENST00000290377 ENST00000508529
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Additional mRNA sequence: 

AK308459.1 NR_027156.1 

4 DOTS entries:

DT.121200856  DT.121200855  DT.121185994  DT.91732871 

GeneLoc Exon Structure


(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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TUBBP5 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
TUBBP5 Expression
About this image


TUBBP5 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database
 selected tissues (see all 2) fully expand
 
 Ovary (Reproductive System)
         Secondary Oocyte Antral Follicle
 
 Gonad
         Secondary Oocyte Antral Follicle
TUBBP5 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

TUBBP5 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.551805
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(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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  --

ENSEMBL Gene Tree for TUBBP5 (if available)
TreeFam Gene Tree for TUBBP5 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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  --

(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 TUBBP5 (see all 1069)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 9 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs714850431,2
C--141042644(+) CACAGC/GCTGAG 1 -- us2k13Minor allele frequency- G:0.00NA CSA 5
rs713878911,2
C--141042706(+) TTTTT-/T/TT  
        
GAGAC
1 -- us2k12NA 4
rs94101721,2
C,F,A,H--141042774(+) CCTCCG/ACCTCC 1 -- us2k15Minor allele frequency- A:0.27NA CSA 11
rs1112545541,2
F--141042843(+) CCATCC/TCACCT 1 -- us2k11Minor allele frequency- T:0.50CSA 2
rs1510855241,2
C--141043000(+) AAAGA-/AAAT  
        
AAATA
1 -- us2k10--------
rs1169748621,2
F--141043015(+) AGTTTC/TGTCTA 1 -- us2k11Minor allele frequency- T:0.06NA 120
rs123807911,2
C,F,A--141043023(+) CTACTG/AGCTAT 1 -- us2k16Minor allele frequency- A:0.38NA WA EA 364
rs713878921,2
C--141043051(+) TTTTT-/TCTTTT 1 -- us2k11Minor allele frequency- T:0.00NA 2
rs1139572621,2
C--141043151(+) CCTCCA/CGGGTT 1 -- us2k10--------
rs3768295231,2
C--141043251(+) ATGGGA/GTTCCT 1 -- us2k10--------

HapMap Linkage Disequilibrium report for TUBBP5 (141044565 - 141071885 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for TUBBP5 (see all 14):    About this table    
Variant IDTypeSubtypePubMed ID
esv1004105CNV Deletion20482838
esv1773938CNV Deletion17803354
esv1243673CNV Insertion17803354
esv997327CNV Insertion20482838
nsv482947CNV Loss15286789
nsv831764CNV Loss17160897
nsv894682CNV Gain21882294
nsv894683CNV Gain21882294
nsv894686CNV Gain21882294
dgv8465n71CNV Gain21882294

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(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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2 diseases from the University of Copenhagen DISEASES database for TUBBP5:
Facioscapulohumeral muscular dystrophy     Distal hereditary motor neuropathy

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Export disorders for TUBBP5 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 TUBBP5 gene integrated from 10 sources:
(articles sorted by number of sources associating them with TUBBP5)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A cascade of complex subtelomeric duplications during the evolution of the hominoid and Old World monkey genomes. (PubMed id 11731935)1, 3 van Geel M.... de Jong P.J. (Am. J. Hum. Genet. 2002)
  2. A newly uncovered group of distantly related lysine methyltransferases preferentially interact with molecular chaperones to regulate their activity. (PubMed id 23349634)1 Cloutier P.... Coulombe B. (PLoS Genet. 2013)
  3. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)

(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: 643224 HGNC: 23674 Ensembl:ENSG00000159247 euGenes: HUgn643224 ECgene: TUBBP5
H-InvDB: TUBBP5

(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 TUBBP5 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 TUBBP5 gene:
Search GeneIP for patents involving TUBBP5

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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