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UBE2DNL Gene

pseudogene   GIFtS: 29
GCID: GC0XP084197

Ubiquitin-Conjugating Enzyme E2D N-Terminal Like (Pseudogene)

(Previous names: ubiquitin-conjugating enzyme E2D N-terminal like, ubiquitin-conjugating...)
  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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Ubiquitin-Conjugating Enzyme E2D N-Terminal Like (Pseudogene)1 2     Ubiquitin Carrier Protein D2-Like3
Ubiquitin-Conjugating Enzyme E2D N-Terminal Like1     Ubiquitin-Conjugating Enzyme E2D N-Terminal-Like3
Ubiquitin-Conjugating Enzyme E2D N-Terminal Like Pseudogene1     Ubiquitin-Protein Ligase D2-Like3
UBE2D2L3     

External Ids:    HGNC: 286561   Entrez Gene: 1001318162   Ensembl: ENSG000002295477   UniProtKB: Q8IWF73   
ORGUL members:         

Export aliases for UBE2DNL gene to outside databases

Previous GC identifers: GC0XU900848 GC0XP084077 GC0XP084190 GC0XP084191 GC0XP084193 GC0XP084195


(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 UBE2DNL Gene:
UBE2DNL (ubiquitin-conjugating enzyme E2D N-terminal like (pseudogene)) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with UBE2DNL include pulmonary function. GO annotations related to this gene include acid-amino acid ligase activity.


(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 UBE2DNL gene promoter:
         AhR   POU2F1   AML1a   POU2F1a   Nkx2-5   Arnt   
         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 UBE2DNL


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

Entrez Gene cytogenetic band: Xq21.1   Ensembl cytogenetic band:  Xq21.1   HGNC cytogenetic band: Xq21.1

UBE2DNL Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
UBE2DNL gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XP084197:  view genomic region     (about GC identifiers)

Start:
84,189,157 bp from pter      End:
84,189,896 bp from pter
Size:
740 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, 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: U2D2L_HUMAN, Q8IWF7 (See protein sequence)
Recommended Name: Putative ubiquitin-conjugating enzyme E2 D2-like protein  
Size: 75 amino acids; 8761 Da
Caution: Could be the product of a pseudogene. Probably inactive as a ubiquitin-conjugating enzyme since it lacks
the essential active site cysteine

Explore the universe of human proteins at neXtProt for UBE2DNL: NX_Q8IWF7

Explore proteomics data for UBE2DNL at MOPED


See UBE2DNL Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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:
 IPR000608 UBQ-conjugat_E2
 IPR016135 UBQ-conjugating_enzyme/RWD

Graphical View of Domain Structure for InterPro Entry Q8IWF7

ProtoNet protein and cluster: Q8IWF7

1 Blocks protein domain: IPB000608 Ubiquitin-conjugating enzymes

UniProtKB/Swiss-Prot: U2D2L_HUMAN, Q8IWF7
Similarity: Belongs to the ubiquitin-conjugating enzyme family


UBE2DNL 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:0016881acid-amino acid ligase activity IEA--
     
UBE2DNL for ontologies           About GeneDecksing


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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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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for UBE2DNL
Interactions:

    Search GeneGlobe Interaction Network for UBE2DNL

Selected Interacting proteins for UBE2DNL (Q8IWF73) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
InteractantInteraction Details
GeneCardExternal ID(s)
DNM1Q051933I2D: score=1 
DTX3Q8N9I93I2D: score=1 
EIF3FO003033I2D: score=1 
FTLP027923I2D: score=1 
MSTO1Q9BUK63I2D: score=1 
About this table

(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 drugs & compounds from Enzo Life Sciences
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Browse Tocris compounds for UBE2DNL (U2D2L)



(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 UBE2DNL gene: 
NM_178567.2  

Unigene Cluster for UBE2DNL:

Ubiquitin-conjugating enzyme E2D N-terminal like (pseudogene)
Hs.460809  [show with all ESTs]
Unigene Representative Sequence: BG717914
4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000602536 ENST00000442533 ENST00000451386 ENST00000474922(uc011mqw.2)

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Additional mRNA sequence: 

BC040290.1 NR_024062.1 

1 DOTS entry:

DT.40218494 

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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UBE2DNL expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: TAATTTCAAA
UBE2DNL Expression
About this image

UBE2DNL Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

UBE2DNL Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.460809
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In Situ
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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 human and mouse.

Orthologs for UBE2DNL gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Ube2dnl15 ubiquitin-conjugating enzyme E2D N-terminal like   --   X (49.47 cM) 114905012 


ENSEMBL Gene Tree for UBE2DNL (if available)
TreeFam Gene Tree for UBE2DNL (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for UBE2DNL gene
13 SIMAP similar genes for UBE2DNL using alignment to 1 protein entry:     U2D2L_HUMAN:
UBE2D3    UBE2D2    UBE2D1    UBE2D4    UBE2E3    UBE2G2
UBE2J2    UBE2E1    UBE2N    UBE2Z    UBE2B    UBE2U
UBE2S

UBE2DNL 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 UBE2DNL (see all 40)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1834235301,2
--84187185(+) TATTTA/TAAAAG 1 -- us2k10--------
rs1883758401,2
--84187192(+) AAAGTA/CAAAAA 1 -- us2k10--------
rs1926657891,2
--84187229(+) GAGAAA/GGGAAC 1 -- us2k10--------
rs360382811,2
C--84187604(+) AAACC-/AAAAAC 1 -- us2k10--------
rs1113810561,2
F--84187629(+) TATAAA/GTAGGA 1 -- us2k11Minor allele frequency- G:0.00CSA 1
rs7687361,2
C,F,O,A,H--84187962(+) CTCCCA/GGGAAG 1 -- us2k125Minor allele frequency- G:0.27MN NS EA NA WA 2727
rs1867380071,2
--84188076(+) CTTCTC/GTGGTA 1 -- us2k10--------
rs2004556301,2
--84188107(+) GGGAA-/AGTTCC
TTTCAATT
AGTTA
1 -- us2k10--------
rs1911052071,2
--84188286(+) ATCCAG/TTATCT 1 -- us2k10--------
rs1423784081,2
--84188437(+) TTTACA/CTTCCC 1 -- us2k10--------

HapMap Linkage Disequilibrium report for UBE2DNL (84189157 - 84189896 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for UBE2DNL: --
Site Specific Mutation Identification with PCR Assays
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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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1 disease for UBE2DNL:    
About MalaCards
pulmonary function


UBE2DNL for disorders           About GeneDecksing

Genetic Association Database (GAD): UBE2DNL

Export disorders for UBE2DNL 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 UBE2DNL gene integrated from 10 sources:
(articles sorted by number of sources associating them with UBE2DNL)
    Utopia: connect your pdf to the dynamic
world of online information

  1. 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)
  2. 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)
  3. 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)
  4. Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network. (PubMed id 19549727)1 Markson G....Sanderson C.M. (Genome Res. 2009)
  5. Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study. (PubMed id 17903294)4 Yang Q....O'Donnell C.J. (BMC Med. Genet. 2007)
  6. Framingham Heart Study genome-wide association: results for pulmonary function measures. (PubMed id 17903307)4 Wilk J.B....O'Connor G.T. (BMC Med. Genet. 2007)

(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: 100131816 HGNC: 28656 Ensembl:ENSG00000229547 euGenes: HUgn100131816 ECgene: UBE2DNL
H-InvDB: UBE2DNL

(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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(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for UBE2DNL gene:
Search GeneIP for patents involving UBE2DNL

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
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GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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