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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

TUBBP5 Gene

pseudogene   GIFtS: 26
GCID: GC09P141044

Tubulin, Beta Pseudogene 5

(Previous names: tubulin, beta polypeptide pseudogene 5)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Tubulin, Beta Pseudogene 51 2
Tubulin, Beta Polypeptide Pseudogene 51

External Ids:    HGNC: 236741   Entrez Gene: 6432242   Ensembl: ENSG000001592477   
ORGUL members:         
NONCODE14:n346217 n407687      

Export aliases for TUBBP5 gene to outside databases

Previous GC identifers: GC09U900291 GC09P140186 GC09P110512


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for TUBBP5 Gene: 
TUBBP5 (tubulin, beta pseudogene 5) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with TUBBP5 include distal hereditary motor neuropathy, and facioscapulohumeral muscular dystrophy. GO annotations related to this gene include structural molecule activity and GTP binding.


(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000009.11  NC_018920.2  NT_024000.16  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for TUBBP5
         Other transcription factors

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Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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 UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB: --


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
  --

(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,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

     Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003924GTPase activity IEA--
GO:0005200structural constituent of cytoskeleton IEA--
GO:0005525GTP binding IEA--
     
TUBBP5 for ontologies           About GeneDecksing


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(Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for TUBBP5

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

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

TUBBP5 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
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Search CenterWatch for drugs/clinical trials and news about TUBBP5

(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,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

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
miRNA
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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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

TUBBP5 expression in normal human tissues (normalized intensities)      TUBBP5 embryonic expression: see
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 
 5/3 selected tissues (see all 3) fully expand
 
 Epithelium (Respiratory System)    fully expand to see all 2 entries
         bronchial epithelial cells   
 
 Ovary (Reproductive System)
         Secondary Oocyte Antral Follicle
 
 Gonad
         Secondary Oocyte Antral Follicle

Genevestigator expression for TUBBP5

SOURCE GeneReport for Unigene cluster: Hs.551805
    SABiosciences Custom PCR Arrays for TUBBP5
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In Situ
Assay Products:
 

 
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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)
About This Section
  --

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)
About This Section
  --

(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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/1069 SNPs in TUBBP5 are shown (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) 10/14 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, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
4 diseases for TUBBP5:    About MalaCards
distal hereditary motor neuropathy    facioscapulohumeral muscular dystrophy    muscular dystrophy    neuropathy

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

TUBBP5 for disorders           About GeneDecksing


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)
About This Section

PubMed articles for TUBBP5 gene integrated from 9 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. (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. (2013)
  3. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section
 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)
About This Section
Entrez Gene: 643224 HGNC: 23674 Ensembl:ENSG00000159247 euGenes: HUgn643224 ECgene: TUBBP5
H-InvDB: TUBBP5

(According to HUGE)
About This Section
  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
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.)
About This Section
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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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