Human Gene UBE2A (uc004erl.3) Description and Page Index
  Description: Homo sapiens ubiquitin-conjugating enzyme E2A (UBE2A), transcript variant 1, mRNA.
RefSeq Summary (NM_003336): The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, ubiquitin-conjugating enzymes, and ubiquitin-protein ligases. This gene encodes a member of the E2 ubiquitin-conjugating enzyme family. This enzyme is required for post-replicative DNA damage repair, and may play a role in transcriptional regulation. Mutations in this gene are associated with cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013].
Transcript (Including UTRs)
   Position: hg19 chrX:118,708,499-118,718,379 Size: 9,881 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chrX:118,708,675-118,717,218 Size: 8,544 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chrX:118,708,499-118,718,379)mRNA (may differ from genome)Protein (152 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: UBE2A_HUMAN
DESCRIPTION: RecName: Full=Ubiquitin-conjugating enzyme E2 A; EC=6.3.2.19; AltName: Full=RAD6 homolog A; Short=HR6A; Short=hHR6A; AltName: Full=Ubiquitin carrier protein A; AltName: Full=Ubiquitin-protein ligase A;
FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In association with the E3 enzyme BRE1 (RNF20 and/or RNF40), it plays a role in transcription regulation by catalyzing the monoubiquitination of histone H2B at 'Lys-120' to form H2BK120ub1. H2BK120ub1 gives a specific tag for epigenetic transcriptional activation, elongation by RNA polymerase II, telomeric silencing, and is also a prerequisite for H3K4me and H3K79me formation. In vitro catalyzes 'Lys-11', as well as 'Lys-48'-linked polyubiquitination. Required for postreplication repair of UV-damaged DNA.
CATALYTIC ACTIVITY: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Interacts with RAD18 and WAC.
DISEASE: Defects in UBE2A are the cause of mental retardation syndromic X-linked Nascimento-type (MRXSN) [MIM:300860]. Mental retardation is characterized by significantly below average general intellectual functioning associated with impairments in adaptative behavior and manifested during the developmental period. MRXSN features include dysmorphic facies, hirsutism, skin and nails abnormalities, obesity, speech anomalies and seizures.
SIMILARITY: Belongs to the ubiquitin-conjugating enzyme family.
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/ube2a/";

-  MalaCards Disease Associations
  MalaCards Gene Search: UBE2A
Diseases sorted by gene-association score: mental retardation, x-linked syndromic, nascimento-type* (1680)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.45 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 835.21 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -64.50176-0.366 Picture PostScript Text
3' UTR -282.531161-0.243 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000608 - UBQ-conjugat_E2
IPR023313 - UBQ-conjugating_AS
IPR016135 - UBQ-conjugating_enzyme/RWD

Pfam Domains:
PF00179 - Ubiquitin-conjugating enzyme

SCOP Domains:
54495 - UBC-like

ModBase Predicted Comparative 3D Structure on P49459
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016740 transferase activity
GO:0031625 ubiquitin protein ligase binding
GO:0043130 ubiquitin binding
GO:0061630 ubiquitin protein ligase activity
GO:0061631 ubiquitin conjugating enzyme activity

Biological Process:
GO:0000209 protein polyubiquitination
GO:0001701 in utero embryonic development
GO:0006281 DNA repair
GO:0006301 postreplication repair
GO:0006325 chromatin organization
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 cellular response to DNA damage stimulus
GO:0008284 positive regulation of cell proliferation
GO:0009411 response to UV
GO:0016567 protein ubiquitination
GO:0033522 histone H2A ubiquitination
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0051865 protein autoubiquitination
GO:0060135 maternal process involved in female pregnancy
GO:0070936 protein K48-linked ubiquitination
GO:0070979 protein K11-linked ubiquitination

Cellular Component:
GO:0000785 chromatin
GO:0000790 nuclear chromatin
GO:0001741 XY body
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0033503 HULC complex


-  Descriptions from all associated GenBank mRNAs
  AK301675 - Homo sapiens cDNA FLJ51703 complete cds, highly similar to Ubiquitin-conjugating enzyme E2 A (EC 6.3.2.19).
D28459 - Homo sapiens mRNA for ubiquitin-conjugating enzyme E2-17kDa, 5'UTR region.
AK313092 - Homo sapiens cDNA, FLJ93575, highly similar to Homo sapiens ubiquitin-conjugating enzyme E2A (RAD6 homolog) (UBE2A), mRNA.
AK297696 - Homo sapiens cDNA FLJ50812 complete cds, highly similar to Homo sapiens ubiquitin-conjugating enzyme E2A (UBE2A), transcript variant 2, mRNA.
AK223045 - Homo sapiens mRNA for ubiquitin-conjugating enzyme E2A isoform 1 variant, clone: JTH14565.
AK223064 - Homo sapiens mRNA for ubiquitin-conjugating enzyme E2A isoform 1 variant, clone: KAT01535.
BC010175 - Homo sapiens ubiquitin-conjugating enzyme E2A (RAD6 homolog), mRNA (cDNA clone MGC:20175 IMAGE:3051041), complete cds.
M74524 - Human HHR6A (yeast RAD 6 homologue) mRNA, complete cds.
JD253741 - Sequence 234765 from Patent EP1572962.
JD273533 - Sequence 254557 from Patent EP1572962.
JD273534 - Sequence 254558 from Patent EP1572962.
JD193479 - Sequence 174503 from Patent EP1572962.
JD190586 - Sequence 171610 from Patent EP1572962.
JD460599 - Sequence 441623 from Patent EP1572962.
AB590387 - Synthetic construct DNA, clone: pFN21AE1357, Homo sapiens UBE2A gene for ubiquitin-conjugating enzyme E2A, without stop codon, in Flexi system.
DQ893386 - Synthetic construct clone IMAGE:100006016; FLH199458.01X; RZPDo839B0282D ubiquitin-conjugating enzyme E2A (RAD6 homolog) (UBE2A) gene, encodes complete protein.
DQ896706 - Synthetic construct Homo sapiens clone IMAGE:100011166; FLH199364.01L; RZPDo839B0281D ubiquitin-conjugating enzyme E2A (RAD6 homolog) (UBE2A) gene, encodes complete protein.
KJ904582 - Synthetic construct Homo sapiens clone ccsbBroadEn_13976 UBE2A gene, encodes complete protein.
BC042021 - Homo sapiens cDNA clone IMAGE:5312200.
JD235183 - Sequence 216207 from Patent EP1572962.
JD551154 - Sequence 532178 from Patent EP1572962.
JD246457 - Sequence 227481 from Patent EP1572962.
JD297789 - Sequence 278813 from Patent EP1572962.
JD530430 - Sequence 511454 from Patent EP1572962.
JD475776 - Sequence 456800 from Patent EP1572962.
JD208350 - Sequence 189374 from Patent EP1572962.
JD514361 - Sequence 495385 from Patent EP1572962.
JD272299 - Sequence 253323 from Patent EP1572962.
JD314784 - Sequence 295808 from Patent EP1572962.
JD502069 - Sequence 483093 from Patent EP1572962.
JD412217 - Sequence 393241 from Patent EP1572962.
JD156607 - Sequence 137631 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04120 - Ubiquitin mediated proteolysis

Reactome (by CSHL, EBI, and GO)

Protein P49459 (Reactome details) participates in the following event(s):

R-HSA-983152 Transfer of ubiquitin from E1 to E2
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-8852130 UBA1 conjugates ubiquitin to nuclear E2 enzymes
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-8942099 RNF20:RNF40 binds PAF complex, Ubiquitin:UBE2A,B (Ubiquitin:RAD6), WAC and Histone H2B
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-HSA-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-8852135 Protein ubiquitination
R-HSA-1280218 Adaptive Immune System
R-HSA-597592 Post-translational protein modification
R-HSA-168256 Immune System
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A6NFE9, A6NGR2, A6NMF5, B2R7R9, D3DWI1, NM_003336, NP_861442, P49459, Q4TTG1, Q96FX4, RAD6A, UBE2A_HUMAN
UCSC ID: uc004erl.3
RefSeq Accession: NM_003336
Protein: P49459 (aka UBE2A_HUMAN or UBCA_HUMAN)
CCDS: CCDS14580.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003336.2
exon count: 6CDS single in 3' UTR: no RNA size: 1799
ORF size: 459CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1110.50frame shift in genome: no % Coverage: 99.83
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.