Human Gene UBE3B (ENST00000342494.8_4) from GENCODE V47lift37

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Description: ubiquitin protein ligase E3B, transcript variant 1 (from RefSeq NM_130466.4)
Gencode Transcript: ENST00000342494.8_4
Gencode Gene: ENSG00000151148.14_12
Transcript (Including UTRs)
Position: hg19 chr12:109,915,439-109,974,507 Size: 59,069 Total Exon Count: 28 Strand: +
Coding Region
Position: hg19 chr12:109,921,357-109,972,587 Size: 51,231 Coding Exon Count: 26

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	GeneReviews	Model Information
Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr12:109,915,439-109,974,507)			mRNA (may differ from genome)		Protein (1068 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: UBE3B_HUMAN DESCRIPTION: RecName: Full=Ubiquitin-protein ligase E3B; EC=6.3.2.-; FUNCTION: E3 ubiquitin-protein ligase which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme in the form of a thioester and then directly transfers the ubiquitin to targeted substrates (By similarity). PATHWAY: Protein modification; protein ubiquitination. TISSUE SPECIFICITY: Widely expressed. SIMILARITY: Contains 1 HECT (E6AP-type E3 ubiquitin-protein ligase) domain. SIMILARITY: Contains 1 IQ domain.

Primer design for this transcript

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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MalaCards Disease Associations


	MalaCards Gene Search: UBE3B Diseases sorted by gene-association score: kaufman oculocerebrofacial syndrome* (1690), moved to 244450* (350), blepharophimosis (17), ptosis (11), wilson-turner syndrome (10), spastic paraplegia 36, autosomal dominant (9), deafness, autosomal dominant 25 (8), syndromic x-linked intellectual disability (6), eyelid disease (5), intellectual disability (2) * = Manually curated disease association

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C009505 4,4'-diaminodiphenylmethane D000082 Acetaminophen D019327 Copper Sulfate D004997 Ethinyl Estradiol D008070 Lipopolysaccharides D011794 Quercetin D013749 Tetrachlorodibenzodioxin C006780 bisphenol A

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 9.34 RPKM in Bladder Total median expression: 343.13 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-247.30	603	-0.410	Picture	PostScript	Text
3' UTR	-609.00	1920	-0.317	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
IPR000569 - HECT
IPR000048 - IQ_motif_EF-hand-BS

Pfam Domains:
PF00612 - IQ calmodulin-binding motif
PF00632 - HECT-domain (ubiquitin-transferase)

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
56204 - Hect, E3 ligase catalytic domain

ModBase Predicted Comparative 3D Structure on Q7Z3V4


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	Genome Browser	No ortholog
Gene Details	Gene Details		Gene Details	Gene Details
Gene Sorter	Gene Sorter		Gene Sorter	Gene Sorter
	RGD	Ensembl		WormBase
				Protein Sequence
				Alignment

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0004842 ubiquitin-protein transferase activity GO:0016740 transferase activity GO:0061630 ubiquitin protein ligase activity Biological Process: GO:0016567 protein ubiquitination Cellular Component: GO:0005737 cytoplasm

Descriptions from all associated GenBank mRNAs


	KJ903534 - Synthetic construct Homo sapiens clone ccsbBroadEn_12928 UBE3B gene, encodes complete protein. BX537403 - Homo sapiens mRNA; cDNA DKFZp686A1051 (from clone DKFZp686A1051); complete cds. BC032301 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:5167597), partial cds. BC144684 - Homo sapiens cDNA clone IMAGE:9053218. BC150637 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone MGC:183547 IMAGE:9057007), complete cds. AL096740 - Homo sapiens mRNA; cDNA DKFZp586K2123 (from clone DKFZp586K2123). AF251046 - Homo sapiens UBE3B variant 1 (UBE3B) mRNA, complete cds. BC141880 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone MGC:150672 IMAGE:40124513), complete cds. KJ899890 - Synthetic construct Homo sapiens clone ccsbBroadEn_09284 UBE3B gene, encodes complete protein. AF130072 - Homo sapiens clone FLB9127 mRNA sequence. AK127227 - Homo sapiens cDNA FLJ45294 fis, clone BRHIP3003126, weakly similar to Homo sapiens ubiquitin-protein isopeptide ligase (E3). BC020348 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:3464523). AK301036 - Homo sapiens cDNA FLJ51547 complete cds, moderately similar to Homo sapiens ubiquitin protein ligase E3B (UBE3B), transcript variant 3, mRNA. AK304678 - Homo sapiens cDNA FLJ51548 complete cds, highly similar to Homo sapiens ubiquitin protein ligase E3B (UBE3B), transcript variant 3, mRNA. AK307385 - Homo sapiens cDNA, FLJ97333. BC108705 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:6022049), complete cds. BC051266 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:4640971), complete cds. BC068221 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:6573521), complete cds. JD227846 - Sequence 208870 from Patent EP1572962. JD191339 - Sequence 172363 from Patent EP1572962. JD396059 - Sequence 377083 from Patent EP1572962. JD321995 - Sequence 303019 from Patent EP1572962. JD498751 - Sequence 479775 from Patent EP1572962. JD445577 - Sequence 426601 from Patent EP1572962. JD073540 - Sequence 54564 from Patent EP1572962. JD231285 - Sequence 212309 from Patent EP1572962. JD262734 - Sequence 243758 from Patent EP1572962. JD166888 - Sequence 147912 from Patent EP1572962. JD520431 - Sequence 501455 from Patent EP1572962. JD129587 - Sequence 110611 from Patent EP1572962. JD522141 - Sequence 503165 from Patent EP1572962. JD313088 - Sequence 294112 from Patent EP1572962. JD039384 - Sequence 20408 from Patent EP1572962. BC040155 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:4386468), with apparent retained intron. JD078232 - Sequence 59256 from Patent EP1572962. HQ257990 - Synthetic construct Homo sapiens clone IMAGE:100072299 Unknown protein gene, encodes complete protein. AK022019 - Homo sapiens cDNA FLJ11957 fis, clone HEMBB1000913. DQ570810 - Homo sapiens piRNA piR-30922, complete sequence. AK056015 - Homo sapiens cDNA FLJ31453 fis, clone NT2NE2001048. JD528959 - Sequence 509983 from Patent EP1572962. JD167226 - Sequence 148250 from Patent EP1572962. JD240923 - Sequence 221947 from Patent EP1572962. JD325237 - Sequence 306261 from Patent EP1572962. JD383614 - Sequence 364638 from Patent EP1572962. JD104756 - Sequence 85780 from Patent EP1572962. JD192686 - Sequence 173710 from Patent EP1572962. JD392820 - Sequence 373844 from Patent EP1572962. JD399726 - Sequence 380750 from Patent EP1572962. JD479722 - Sequence 460746 from Patent EP1572962. JD276241 - Sequence 257265 from Patent EP1572962. JD418720 - Sequence 399744 from Patent EP1572962. JD524086 - Sequence 505110 from Patent EP1572962. JD377475 - Sequence 358499 from Patent EP1572962. JD078985 - Sequence 60009 from Patent EP1572962. JD451125 - Sequence 432149 from Patent EP1572962. JD380002 - Sequence 361026 from Patent EP1572962. JD206209 - Sequence 187233 from Patent EP1572962. BC013182 - Homo sapiens ubiquitin protein ligase E3B, mRNA (cDNA clone IMAGE:4345655), with apparent retained intron. JD251603 - Sequence 232627 from Patent EP1572962. JD252270 - Sequence 233294 from Patent EP1572962. JD423962 - Sequence 404986 from Patent EP1572962. JD226998 - Sequence 208022 from Patent EP1572962. JD403933 - Sequence 384957 from Patent EP1572962. JD499454 - Sequence 480478 from Patent EP1572962. JD085929 - Sequence 66953 from Patent EP1572962. JD157206 - Sequence 138230 from Patent EP1572962. JD019312 - Sequence 336 from Patent EP1572962. JD317403 - Sequence 298427 from Patent EP1572962. JD501305 - Sequence 482329 from Patent EP1572962. JD419625 - Sequence 400649 from Patent EP1572962. JD271898 - Sequence 252922 from Patent EP1572962. JD521422 - Sequence 502446 from Patent EP1572962. JD530222 - Sequence 511246 from Patent EP1572962. JD215105 - Sequence 196129 from Patent EP1572962. JD318331 - Sequence 299355 from Patent EP1572962. JD082729 - Sequence 63753 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q7Z3V4 (Reactome details) participates in the following event(s): R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex R-HSA-983147 Release of E3 from polyubiquitinated substrate R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2 R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation R-HSA-983169 Class I MHC mediated antigen processing & presentation R-HSA-1280218 Adaptive Immune System R-HSA-168256 Immune System

Other Names for This Gene


	Alternate Gene Symbols: A5D8Z3, ENST00000342494.1, ENST00000342494.2, ENST00000342494.3, ENST00000342494.4, ENST00000342494.5, ENST00000342494.6, ENST00000342494.7, NM_130466, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4, UBE3B_HUMAN, uc317wjd.1, uc317wjd.2 UCSC ID: ENST00000342494.8_4 RefSeq Accession: NM_130466.4 Protein: Q7Z3V4 (aka UBE3B_HUMAN)

GeneReviews for This Gene


	GeneReviews article(s) related to gene UBE3B: kos (Kaufman Oculocerebrofacial Syndrome)

Gene Model Information


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Methods, Credits, and Use Restrictions


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