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    HERC6 HECT and RLD domain containing E3 ubiquitin protein ligase family member 6 [ Homo sapiens (human) ]

    Gene ID: 55008, updated on 3-Apr-2024

    Summary

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    Official Symbol
    HERC6provided by HGNC
    Official Full Name
    HECT and RLD domain containing E3 ubiquitin protein ligase family member 6provided by HGNC
    Primary source
    HGNC:HGNC:26072
    See related
    Ensembl:ENSG00000138642 MIM:609249; AllianceGenome:HGNC:26072
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    HERC6 belongs to the HERC family of ubiquitin ligases, all of which contain a HECT domain and at least 1 RCC1 (MIM 179710)-like domain (RLD). The 350-amino acid HECT domain is predicted to catalyze the formation of a thioester with ubiquitin before transferring it to a substrate, and the RLD is predicted to act as a guanine nucleotide exchange factor for small G proteins (Hochrainer et al., 2005 [PubMed 15676274]).[supplied by OMIM, Mar 2008]
    Expression
    Ubiquitous expression in esophagus (RPKM 12.4), gall bladder (RPKM 7.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4q22.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (88378852..88443097)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (91709824..91774756)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (89300004..89364249)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124900731 Neighboring gene uncharacterized LOC105377326 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15563 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21713 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21714 Neighboring gene uncharacterized LOC102723458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21715 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase 5 Neighboring gene ReSE screen-validated silencer GRCh37_chr4:89403116-89403280 Neighboring gene nuclear receptor coactivator 4 pseudogene 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects. Hochrainer K, et al. Genomics, 2005 Feb. PMID 15676274
    2. Highly homologous HERC proteins localize to endosomes and exhibit specific interactions with hPLIC and Nm23B. Hochrainer K, et al. Cell Mol Life Sci, 2008 Jul. PMID 18535780
    3. System-Wide Modulation of HECT E3 Ligases with Selective Ubiquitin Variant Probes. Zhang W, et al. Mol Cell, 2016 Apr 7. PMID 26949039, Free PMC Article
    4. The essential player in adipogenesis GRP78 is a novel KCTD15 interactor. Smaldone G, et al. Int J Biol Macromol, 2018 Aug. PMID 29665387
    5. Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis. Inouye M, et al. PLoS Genet, 2012. PMID 22916037, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. HERC6 ancestor emerged in nematodes and that the family expanded throughout evolution. The mRNA expression pattern was found to be diverse in selected tissues and cells
      Title: The human HERC family of ubiquitin ligases: novel members, genomic organization, expression profiling, and evolutionary aspects.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Novel Loci for metabolic networks and multi-tissue expression studies reveal genes for atherosclerosis.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of HECT and RLD domain containing E3 ubiquitin protein ligase family member 6 (HERC6) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ20637

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in hematopoietic progenitor cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in response to bacterium 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
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    probable E3 ubiquitin-protein ligase HERC6
    Names
    HECT domain and RCC1-like domain-containing protein 6
    HECT-type E3 ubiquitin transferase HERC6
    hect domain and RLD 6
    potential ubiquitin ligase
    NP_001158608.1
    NP_060382.3
    XP_005263140.1
    XP_011530355.1
    XP_047271822.1
    XP_047271823.1
    XP_054206290.1
    XP_054206291.1
    XP_054206292.1
    XP_054206293.1

    NCBI Reference Sequences (RefSeq)

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    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.

    mRNA and Protein(s)

    1. NM_001165136.2 → NP_001158608.1  probable E3 ubiquitin-protein ligase HERC6 isoform 2

      See identical proteins and their annotated locations for NP_001158608.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
      Source sequence(s)
      AC083829, FJ695209
      Consensus CDS
      CCDS54777.1
      UniProtKB/Swiss-Prot
      Q8IVU3
      Related
      ENSP00000369617.5, ENST00000380265.9
      Conserved Domains (4) summary
      smart00119
      Location:663 → 978
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:636 → 978
      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 ...
      pfam00415
      Location:93 → 143
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      pfam13540
      Location:238 → 267
      RCC1_2; Regulator of chromosome condensation (RCC1) repeat

    2. NM_017912.4 → NP_060382.3  probable E3 ubiquitin-protein ligase HERC6 isoform 1

      See identical proteins and their annotated locations for NP_060382.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC083829, FJ695209
      Consensus CDS
      CCDS47098.1
      UniProtKB/Swiss-Prot
      B4DIY5, Q5GC90, Q5GRH3, Q5HYM6, Q5JPB6, Q6PIF4, Q8IVU3, Q8NAN3, Q9NWS4
      Related
      ENSP00000264346.8, ENST00000264346.12
      Conserved Domains (4) summary
      smart00119
      Location:699 → 1014
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:672 → 1014
      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 ...
      pfam00415
      Location:93 → 143
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      pfam13540
      Location:238 → 267
      RCC1_2; Regulator of chromosome condensation (RCC1) repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      88378852..88443097
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005263083.5 → XP_005263140.1  probable E3 ubiquitin-protein ligase HERC6 isoform X1

      Conserved Domains (4) summary
      smart00119
      Location:711 → 1026
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:684 → 1026
      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 ...
      pfam00415
      Location:105 → 155
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      pfam13540
      Location:250 → 279
      RCC1_2; Regulator of chromosome condensation (RCC1) repeat

    2. XM_011532053.4 → XP_011530355.1  probable E3 ubiquitin-protein ligase HERC6 isoform X2

      Conserved Domains (4) summary
      smart00119
      Location:675 → 990
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:648 → 990
      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 ...
      pfam00415
      Location:105 → 155
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      pfam13540
      Location:250 → 279
      RCC1_2; Regulator of chromosome condensation (RCC1) repeat

    3. XM_047415867.1 → XP_047271823.1  probable E3 ubiquitin-protein ligase HERC6 isoform X4

    4. XM_047415866.1 → XP_047271822.1  probable E3 ubiquitin-protein ligase HERC6 isoform X3

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      91709824..91774756
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350315.1 → XP_054206290.1  probable E3 ubiquitin-protein ligase HERC6 isoform X1

    2. XM_054350316.1 → XP_054206291.1  probable E3 ubiquitin-protein ligase HERC6 isoform X2

    3. XM_054350318.1 → XP_054206293.1  probable E3 ubiquitin-protein ligase HERC6 isoform X4

    4. XM_054350317.1 → XP_054206292.1  probable E3 ubiquitin-protein ligase HERC6 isoform X3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001013000.1: Suppressed sequence

      Description
      NM_001013000.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

    2. NM_001013002.1: Suppressed sequence

      Description
      NM_001013002.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.

    3. NM_001013005.1: Suppressed sequence

      Description
      NM_001013005.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8IVU3.2 GenPept UniProtKB/Swiss-Prot:Q8IVU3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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