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

    Gene ID: 89910, updated on 27-Nov-2024

    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; AllianceGenome:HGNC:13478
    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See UBE3B in Genome Data Viewer
    Location:
    12q24.11
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (109477634..109547829)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (109452543..109519796)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (109915439..109974507)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene myosin IH Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6985 Neighboring gene long intergenic non-protein coding RNA 1486 Neighboring gene MPRA-validated peak1943 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109871570-109872074 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109896331-109897136 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109897944-109898749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109898750-109899556 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109900363-109901169 Neighboring gene potassium channel tetramerization domain containing 10 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:109914018-109914753 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6986 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109976965-109977466 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:109978915-109979477 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109995443-109995944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:109999353-109999852 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:110001138-110001638 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110010699-110011200 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:110011201-110011700 Neighboring gene RNA, U4 small nuclear 32, pseudogene Neighboring gene metabolism of cobalamin associated B 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
    Oculocerebrofacial syndrome, Kaufman type not available

    EBI GWAS Catalog

    Description
    Genetic variants influencing circulating lipid levels and risk of coronary artery disease.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ45294, MGC78388, MGC131858, DKFZp586K2123, DKFZp686A1051

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ubiquitin protein ligase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in protein polyubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in regulation of postsynapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in ubiquitin-dependent protein catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in postsynaptic density IEA
    Inferred from Electronic Annotation
    more info
     

    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_016875685.1
    XP_047285800.1
    XP_047285801.1
    XP_047285802.1
    XP_047285803.1
    XP_047285804.1
    XP_047285805.1
    XP_047285806.1
    XP_047285807.1
    XP_047285808.1
    XP_047285809.1
    XP_047285810.1
    XP_054229740.1
    XP_054229741.1
    XP_054229742.1
    XP_054229743.1
    XP_054229744.1
    XP_054229745.1
    XP_054229746.1
    XP_054229747.1
    XP_054229748.1
    XP_054229749.1
    XP_054229750.1
    XP_054229751.1
    XP_054229752.1
    XP_054229753.1
    XP_054229754.1
    XP_054229755.1
    XP_054229756.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_033898.2 RefSeqGene

      Range
      5002..64070
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001270449.2NP_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/TrEMBL
      F5H6D6
      Related
      ENSP00000342614.5, ENST00000340074.9
    2. NM_001270450.2NP_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/TrEMBL
      F5H6D6
      Related
      ENSP00000440585.1, ENST00000536398.5
      Conserved Domains (1) summary
      cl15479
      Location:3050
      IQ; IQ calmodulin-binding motif
    3. NM_001270451.2NP_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/TrEMBL
      F5H6D6
      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
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Related
      ENSP00000340596.3, ENST00000342494.8
      Conserved Domains (1) summary
      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
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Related
      ENSP00000391529.2, ENST00000434735.6
      Conserved Domains (1) summary
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      109477634..109547829
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011538961.2XP_011537263.1  ubiquitin-protein ligase E3B isoform X5

      UniProtKB/TrEMBL
      B9EK57
      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_047429852.1XP_047285808.1  ubiquitin-protein ligase E3B isoform X5

    3. XM_047429851.1XP_047285807.1  ubiquitin-protein ligase E3B isoform X5

    4. XM_047429853.1XP_047285809.1  ubiquitin-protein ligase E3B isoform X6

      Related
      ENSP00000443131.1, ENST00000539599.5
    5. XM_047429844.1XP_047285800.1  ubiquitin-protein ligase E3B isoform X2

    6. XM_006719681.4XP_006719744.1  ubiquitin-protein ligase E3B isoform X3

      UniProtKB/TrEMBL
      B9EK57
      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 ...
    7. XM_006719682.3XP_006719745.1  ubiquitin-protein ligase E3B isoform X4

      UniProtKB/TrEMBL
      B9EK57
      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 ...
    8. XM_047429847.1XP_047285803.1  ubiquitin-protein ligase E3B isoform X3

    9. XM_005253987.3XP_005254044.1  ubiquitin-protein ligase E3B isoform X1

      See identical proteins and their annotated locations for XP_005254044.1

      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      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 ...
    10. XM_047429845.1XP_047285801.1  ubiquitin-protein ligase E3B isoform X2

    11. XM_047429846.1XP_047285802.1  ubiquitin-protein ligase E3B isoform X3

    12. XM_047429849.1XP_047285805.1  ubiquitin-protein ligase E3B isoform X4

    13. XM_047429848.1XP_047285804.1  ubiquitin-protein ligase E3B isoform X3

    14. XM_047429850.1XP_047285806.1  ubiquitin-protein ligase E3B isoform X4

    15. XM_011538959.3XP_011537261.1  ubiquitin-protein ligase E3B isoform X1

      See identical proteins and their annotated locations for XP_011537261.1

      UniProtKB/Swiss-Prot
      A5D8Z3, Q05BX9, Q659F7, Q7Z3V4, Q7Z7Q1, Q9BXZ4
      UniProtKB/TrEMBL
      B9EK57
      Conserved Domains (1) summary
      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 ...
    16. XM_047429854.1XP_047285810.1  ubiquitin-protein ligase E3B isoform X7

    17. XM_017020196.2XP_016875685.1  ubiquitin-protein ligase E3B isoform X8

      UniProtKB/TrEMBL
      F5H6D6

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      109452543..109519796
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373776.1XP_054229751.1  ubiquitin-protein ligase E3B isoform X5

    2. XM_054373778.1XP_054229753.1  ubiquitin-protein ligase E3B isoform X5

    3. XM_054373777.1XP_054229752.1  ubiquitin-protein ligase E3B isoform X5

    4. XM_054373779.1XP_054229754.1  ubiquitin-protein ligase E3B isoform X6

    5. XM_054373767.1XP_054229742.1  ubiquitin-protein ligase E3B isoform X2

    6. XM_054373769.1XP_054229744.1  ubiquitin-protein ligase E3B isoform X3

    7. XM_054373773.1XP_054229748.1  ubiquitin-protein ligase E3B isoform X4

    8. XM_054373771.1XP_054229746.1  ubiquitin-protein ligase E3B isoform X3

    9. XM_054373765.1XP_054229740.1  ubiquitin-protein ligase E3B isoform X1

    10. XM_054373768.1XP_054229743.1  ubiquitin-protein ligase E3B isoform X2

    11. XM_054373770.1XP_054229745.1  ubiquitin-protein ligase E3B isoform X3

    12. XM_054373774.1XP_054229749.1  ubiquitin-protein ligase E3B isoform X4

    13. XM_054373772.1XP_054229747.1  ubiquitin-protein ligase E3B isoform X3

    14. XM_054373775.1XP_054229750.1  ubiquitin-protein ligase E3B isoform X4

    15. XM_054373766.1XP_054229741.1  ubiquitin-protein ligase E3B isoform X1

    16. XM_054373780.1XP_054229755.1  ubiquitin-protein ligase E3B isoform X7

    17. XM_054373781.1XP_054229756.1  ubiquitin-protein ligase E3B isoform X8

    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.