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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 2-Nov-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
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Genomic context

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See HERC6 in Genome Data Viewer
Location:
4q22.1
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (88378852..88443097)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (91709824..91774756)
RS_2024_09 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 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, Free PMC Article
  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_2024_08

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

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