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UBE3B ubiquitin protein ligase E3B [ Homo sapiens (human) ]

Gene ID: 89910, updated on 1-Jun-2020

Summary

Official Symbol
UBE3Bprovided by HGNC
Official Full Name
ubiquitin protein ligase E3Bprovided by HGNC
Primary source
HGNC:HGNC:13478
See related
Ensembl:ENSG00000151148 MIM:608047
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KOS; BPIDS
Summary
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: E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes, and E3 ubiquitin-protein ligases. This gene encodes a member of the E3 ubiquitin-conjugating enzyme family which accepts ubiquitin from an E2 ubiquitin-conjugating enzyme and transfers the ubiquitin to the targeted substrates. A HECT (homology to E6-AP C-terminus) domain in the C-terminus of the longer isoform of this protein is the catalytic site of ubiquitin transfer and forms a complex with E2 conjugases. Shorter isoforms of this protein which lack the C-terminal HECT domain are therefore unlikely to bind E2 enzymes. Alternatively spliced transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2012]
Expression
Ubiquitous expression in thyroid (RPKM 7.7), testis (RPKM 7.5) and 25 other tissues See more
Orthologs

Genomic context

See UBE3B in Genome Data Viewer
Location:
12q24.11
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 12 NC_000012.12 (109477410..109543628)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109915215..109974510)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene myosin IH Neighboring gene potassium channel tetramerization domain containing 10 Neighboring gene metabolism of cobalamin associated B Neighboring gene RNA, U4 small nuclear 32, pseudogene Neighboring gene mevalonate kinase

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Kaufman oculocerebrofacial syndrome Compare labs

NHGRI GWAS Catalog

Description
Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ45294, MGC78388, MGC131858, DKFZp586K2123, DKFZp686A1051

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ubiquitin conjugating enzyme activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
protein polyubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ubiquitin-dependent protein catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ubiquitin-protein ligase E3B
Names
HECT-type ubiquitin transferase E3B
NP_001257378.1
NP_001257379.1
NP_001257380.1
NP_569733.2
NP_904324.1
XP_005254044.1
XP_006719744.1
XP_006719745.1
XP_011537261.1
XP_011537263.1
XP_016875684.1
XP_016875685.1
XP_024305037.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033898.1 RefSeqGene

    Range
    5012..64080
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001270449.1NP_001257378.1  ubiquitin-protein ligase E3B isoform 3

    See identical proteins and their annotated locations for NP_001257378.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) contains an alternate 3' exon, compared to variant 1. This difference results in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
    Source sequence(s)
    BC051266, DA771082
    Consensus CDS
    CCDS58277.1
    UniProtKB/Swiss-Prot
    Q7Z3V4
    Related
    ENSP00000342614.5, ENST00000340074.9
  2. NM_001270450.1NP_001257379.1  ubiquitin-protein ligase E3B isoform 3

    See identical proteins and their annotated locations for NP_001257379.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) uses an alternate splice site in the 5' UTR and contains an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
    Source sequence(s)
    BC108705, DA771082
    Consensus CDS
    CCDS58277.1
    UniProtKB/Swiss-Prot
    Q7Z3V4
    Related
    ENSP00000440585.1, ENST00000536398.5
    Conserved Domains (1) summary
    cl15479
    Location:3050
    IQ; IQ calmodulin-binding motif
  3. NM_001270451.1NP_001257380.1  ubiquitin-protein ligase E3B isoform 3

    See identical proteins and their annotated locations for NP_001257380.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) uses an alternate splice site in the 5' UTR and contains an alternate 3' exon, compared to variant 1. These differences result in a distinct 3' UTR and 3' coding region and a protein (isoform 3) with a shorter and distinct C-terminus, compared to isoform 1. Variants 4-6 encode the same protein (isoform 3).
    Source sequence(s)
    BC068221, BC108705, DA771082
    Consensus CDS
    CCDS58277.1
    UniProtKB/Swiss-Prot
    Q7Z3V4
    Related
    ENSP00000443565.1, ENST00000540230.5
    Conserved Domains (1) summary
    cl15479
    Location:3050
    IQ; IQ calmodulin-binding motif
  4. NM_130466.4NP_569733.2  ubiquitin-protein ligase E3B isoform 1

    See identical proteins and their annotated locations for NP_569733.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript, and encodes the longer protein (isoform 1). Variants 1 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AF251046, BC032301, BC144684, BQ889238, DA771082, DR760197
    Consensus CDS
    CCDS9129.1
    UniProtKB/Swiss-Prot
    Q7Z3V4
    UniProtKB/TrEMBL
    A0A024RBI2
    Related
    ENSP00000340596.3, ENST00000342494.8
    Conserved Domains (2) summary
    smart00119
    Location:7071065
    HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
    cd00078
    Location:6821066
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  5. NM_183415.3NP_904324.1  ubiquitin-protein ligase E3B isoform 1

    See identical proteins and their annotated locations for NP_904324.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' UTR, as compared to variant 1. Variants 1 and 3 encode the same protein (isoform 1).
    Source sequence(s)
    AF251046, BC032301, BQ889238, DA771082, DR760197
    Consensus CDS
    CCDS9129.1
    UniProtKB/Swiss-Prot
    Q7Z3V4
    UniProtKB/TrEMBL
    A0A024RBI2
    Related
    ENSP00000391529.2, ENST00000434735.6
    Conserved Domains (2) summary
    smart00119
    Location:7071065
    HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
    cd00078
    Location:6821066
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p13 Primary Assembly

    Range
    109477410..109543628
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538961.1XP_011537263.1  ubiquitin-protein ligase E3B isoform X4

    Related
    ENSP00000443131.1, ENST00000539599.5
    Conserved Domains (1) summary
    cd00078
    Location:6821007
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  2. XM_006719681.3XP_006719744.1  ubiquitin-protein ligase E3B isoform X2

    Conserved Domains (1) summary
    cd00078
    Location:6821004
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  3. XM_006719682.2XP_006719745.1  ubiquitin-protein ligase E3B isoform X3

    Conserved Domains (1) summary
    cd00078
    Location:6821004
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  4. XM_024449269.1XP_024305037.1  ubiquitin-protein ligase E3B isoform X5

    Conserved Domains (1) summary
    cd00078
    Location:489873
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  5. XM_005253987.2XP_005254044.1  ubiquitin-protein ligase E3B isoform X1

    See identical proteins and their annotated locations for XP_005254044.1

    UniProtKB/Swiss-Prot
    Q7Z3V4
    UniProtKB/TrEMBL
    A0A024RBI2
    Conserved Domains (2) summary
    smart00119
    Location:7071065
    HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
    cd00078
    Location:6821066
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  6. XM_017020195.1XP_016875684.1  ubiquitin-protein ligase E3B isoform X5

    Conserved Domains (1) summary
    cd00078
    Location:489873
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  7. XM_011538959.2XP_011537261.1  ubiquitin-protein ligase E3B isoform X1

    See identical proteins and their annotated locations for XP_011537261.1

    UniProtKB/Swiss-Prot
    Q7Z3V4
    UniProtKB/TrEMBL
    A0A024RBI2
    Conserved Domains (2) summary
    smart00119
    Location:7071065
    HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
    cd00078
    Location:6821066
    HECTc; HECT domain; C-terminal catalytic domain of a subclass of Ubiquitin-protein ligase (E3). It binds specific ubiquitin-conjugating enzymes (E2), accepts ubiquitin from E2, transfers ubiquitin to substrate lysine side chains, and transfers additional ...
  8. XM_017020196.1XP_016875685.1  ubiquitin-protein ligase E3B isoform X6

    UniProtKB/Swiss-Prot
    Q7Z3V4

RNA

  1. XR_429118.3 RNA Sequence

    Related
    ENST00000449510.6
  2. XR_429119.4 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_183414.1: Suppressed sequence

    Description
    NM_183414.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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