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UBBP4 Gene

pseudogene   GIFtS: 18
GCID: GC17P022230

Ubiquitin B Pseudogene 4

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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
Ubiquitin B Pseudogene 41 2

External Ids:    HGNC: 124671   Entrez Gene: 236662   Ensembl: ENSG000002635637   UniProtKB: J3KSM44   UniProtKB: J3QL684   
UniProtKB: J3QLP74   UniProtKB: J3QRK54   UniProtKB: K7EMA84   

Export aliases for UBBP4 gene to outside databases

Previous GC identifers: GC17U990162 GC17P021581 GC17P021876 GC17P021654 GC17P021740


(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 UBBP4 Gene:
UBBP4 (ubiquitin B pseudogene 4) is a pseudogene. An important paralog of this gene is UBB.


(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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Regulatory elements:
   Search for regulatory transcription factor binding sites for UBBP4
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat UBBP4


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

Entrez Gene cytogenetic band: 17p11.2   Ensembl cytogenetic band:  17p11.2   HGNC cytogenetic band: 17p11.2

UBBP4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBBP4 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P022230:  view genomic region     (about GC identifiers)

Start:
21,729,601 bp from pter      End:
21,731,762 bp from pter
Size:
2,162 bases      Orientation:
plus 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, 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/TrEMBL: J3KSM4 (See protein sequence)
Recommended Name: Protein UBBP4  
Size: 98 amino acids; 11074 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: J3QL68 (See protein sequence)

Recommended Name: Protein UBBP4  
Size: 25 amino acids; 2878 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: J3QLP7 (See protein sequence)

Recommended Name: Protein UBBP4  
Size: 224 amino acids; 25154 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: J3QRK5 (See protein sequence)

Recommended Name: Protein UBBP4  
Size: 229 amino acids; 25797 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data

UniProtKB/TrEMBL: K7EMA8 (See protein sequence)

Recommended Name: Protein UBBP4  
Size: 53 amino acids; 5962 Da
Caution: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered
as preliminary data


ENSEMBL proteins: 
 ENSP00000462557   ENSP00000463647   ENSP00000463407   ENSP00000462326   ENSP00000464265  
 ENSP00000466427  

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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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3 InterPro protein domains:
 IPR019954 Ubiquitin_CS
 IPR000626 Ubiquitin_dom
 IPR019956 Ubiquitin

Graphical View of Domain Structure for InterPro Entry J3KSM4
Graphical View of Domain Structure for InterPro Entry J3QL68
Graphical View of Domain Structure for InterPro Entry J3QLP7
Graphical View of Domain Structure for InterPro Entry J3QRK5
Graphical View of Domain Structure for InterPro Entry K7EMA8

ProtoNet protein and cluster: J3KSM4


Find genes that share domains with UBBP4           About GenesLikeMe


(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): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding ----
     
Find genes that share ontologies with UBBP4           About GenesLikeMe


Animal Models:
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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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  --

(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 UBBP4

Gene Ontology (GO): Selected biological process terms (see all 8):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0007141male meiosis I ----
GO:0007144female meiosis I ----
GO:0008585female gonad development ----
GO:0010992ubiquitin homeostasis ----
GO:0021888hypothalamus gonadotrophin-releasing hormone neuron development ----

Find genes that share ontologies with UBBP4           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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Browse Tocris compounds for UBBP4



(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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6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000581769 ENST00000584755(uc002gyy.3) ENST00000583708 ENST00000584398
ENST00000578713 ENST00000581775
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24 AceView cDNA sequences:

BG203528 CD246678 BG199424 BG208889 BC070367 BG181223 CD049205 BU569242 
BU570205 AW881100 CA775048 AA488361 BG191718 BG200442 BI497069 AA745110 
AW881088 BQ775006 BF922457 F21047 AW075819 BM697114 BE826046 AA488492 

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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See probesets specificity/sensitivity at GeneAnnot
CGAP TAG: --

UBBP4 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --
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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)
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This gene was present in the common ancestor of animals and fungi.

Orthologs for UBBP4 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chicken
(Gallus gallus)
Aves UBB6
Polyubiquitin-B Ubiquitin
49(a)
1 → many
19(6584723-6586315)
lizard
(Anolis carolinensis)
Reptilia UBBP46
ubiquitin B pseudogene 4
71(a)
1 ↔ 1
AAWZ02039315(4814-5725)
zebrafish
(Danio rerio)
Actinopterygii ubb6
ubc6
ubiquitin C
89(a)
41(a)
many ↔ many
many ↔ many
5(43710809-43714913) ENSDARG00000093313
11(21577566-21580026) ENSDARG00000067755
fruit fly
(Drosophila melanogaster)
Insecta Ubi-p5E6
Ubiquitin-5E
40(a)
1 ↔ 1
X(6171010-6173305)
worm
(Caenorhabditis elegans)
Secernentea ubq-16
Protein UBQ-1, isoform a
25(a)
1 → many
III(5940244-5943838) WBGene00006727
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RPL40A6
RPL40B6
Fusion protein, identical to Rpl40Bp, that is clea...
Fusion protein, identical to Rpl40Ap, that is clea...
63(a)
63(a)
many ↔ many
many ↔ many
IX(68708-69528) YIL148W
XI(617996-618750) YKR094C
        Species with no ortholog for UBBP4

ENSEMBL Gene Tree for UBBP4 (if available)
TreeFam Gene Tree for UBBP4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for UBBP4 gene
UBB2  UBA522  UBC2  ZFAND42  
14 SIMAP similar genes for UBBP4 using alignment to 5 protein entries:     J3KSM4_HUMAN (see all proteins):
UBA52    UBB    UBC    RPS27A    DKFZp434K0435    UbC
NEDD8    NEDD8-MDP1    ZFAND4    FAU    PARK2    UBD
RAD23A    ISG15

Find genes that share paralogs with UBBP4           About GenesLikeMe



(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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Site Specific Mutation Identification with PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing UBBP4
DNA2.0 Custom Variant and Variant Library Synthesis for UBBP4

(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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  --

(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 UBBP4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with UBBP4)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human ubiquitin genes: one member of the UbB gene subfamily is a tetrameric non-processed pseudogene. (PubMed id 2834222)1, 3 Cowland J.B....Vuust J. (FEBS Lett. 1988)
  2. Localization of the human UbB polyubiquitin gene to chromosome band 17p11.1-17p12. (PubMed id 2154095)1 Webb G.C....Board P.G. (Am. J. Hum. Genet. 1990)

(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: 23666 HGNC: 12467 AceView: UBBP4 Ensembl:ENSG00000263563 euGenes: HUgn23666
ECgene: UBBP4 H-InvDB: UBBP4

(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 UBBP4 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 UBBP4 gene:
Search GeneIP for patents involving UBBP4

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
Advanced Cell Diagnostics, Animal models from genOway)
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