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    Herc3 hect domain and RLD 3 [ Mus musculus (house mouse) ]

    Gene ID: 73998, updated on 12-May-2024

    Summary

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    Official Symbol
    Herc3provided by MGI
    Official Full Name
    hect domain and RLD 3provided by MGI
    Primary source
    MGI:MGI:1921248
    See related
    Ensembl:ENSMUSG00000029804 AllianceGenome:MGI:1921248
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    mKIAA0032; 5730409F18Rik
    Summary
    Predicted to be located in cytosol. Is expressed in embryo mesenchyme; esophagus; lung; nervous system; and sensory organ. Orthologous to human HERC3 (HECT and RLD domain containing E3 ubiquitin protein ligase 3). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in cortex adult (RPKM 14.6), frontal lobe adult (RPKM 10.7) and 24 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Herc3 in Genome Data Viewer
    Location:
    6 B3; 6 27.82 cM
    Exon count:
    34
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (58808440..58897383)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (58831455..58920398)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene ATP binding cassette subfamily G member 2 (Junior blood group) Neighboring gene STARR-seq mESC enhancer starr_16022 Neighboring gene STARR-seq mESC enhancer starr_16023 Neighboring gene predicted gene, 38822 Neighboring gene STARR-seq mESC enhancer starr_16024 Neighboring gene STARR-seq mESC enhancer starr_16025 Neighboring gene STARR-seq mESC enhancer starr_16026 Neighboring gene STARR-seq mESC enhancer starr_16027 Neighboring gene STARR-seq mESC enhancer starr_16029 Neighboring gene nucleosome assembly protein 1-like 5 Neighboring gene RIKEN cDNA 8430415O14 gene Neighboring gene family with sequence similarity 13, member A Neighboring gene TPX2, microtubule-associated protein homolog pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration. Li X, et al. Life Sci, 2023 May 1. PMID 36878279
    2. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Cowley M, et al. Nucleic Acids Res, 2012 Oct. PMID 22790983, Free PMC Article
    3. Optimising experimental design for high-throughput phenotyping in mice: a case study. Karp NA, et al. Mamm Genome, 2010 Oct. PMID 20799038, Free PMC Article
    4. Novel skin phenotypes revealed by a genome-wide mouse reverse genetic screen. Liakath-Ali K, et al. Nat Commun, 2014 Apr 11. PMID 24721909, Free PMC Article
    5. Prediction of the coding sequences of mouse homologues of KIAA gene: II. The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Feb 28. PMID 12693553

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. E3 ubiquitin ligase Herc3 deficiency leads to accumulation of subretinal microglia and retinal neurodegeneration.
      Title: E3 ubiquitin ligase Herc3 deficiency leads to accumulation of subretinal microglia and retinal neurodegeneration.
    2. Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration.
      Title: Accumulation of NCOA1 dependent on HERC3 deficiency transactivates matrix metallopeptidases and promotes extracellular matrix degradation in intervertebral disc degeneration.
    3. Allele-specific polyadenylation occurs at the imprinted Herc3/Nap1l5 locus.
      Title: Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Targeted (1) 

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC30404

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in protein ubiquitination IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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    Preferred Names
    probable E3 ubiquitin-protein ligase HERC3
    NP_001348895.1
    NP_001348896.1
    NP_082981.3
    XP_006506759.1
    XP_006506760.1
    XP_006506761.1
    XP_006506764.1
    XP_011239792.1
    XP_030111494.1
    XP_030111495.1
    XP_036008252.1
    XP_036008253.1

    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_001361966.1 → NP_001348895.1  probable E3 ubiquitin-protein ligase HERC3 isoform a

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AC115881, AC166819
      Consensus CDS
      CCDS20196.1
      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    2. NM_001361967.1 → NP_001348896.1  probable E3 ubiquitin-protein ligase HERC3 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, 3' UTR, and 3' coding sequence compared to variant 1. The resulting isoform (b) has a shorter and distinct C-terminus compared to isoform a.
      Source sequence(s)
      AC115881, AC166819, AK017531
      Consensus CDS
      CCDS90054.1
      UniProtKB/TrEMBL
      G5E876, Q9CYM1
      Related
      ENSMUSP00000031823.6, ENSMUST00000031823.12
      Conserved Domains (3) summary
      pfam00415
      Location:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      cl27008
      Location:702 → 887
      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 ...
      cl27697
      Location:2 → 331
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    3. NM_028705.3 → NP_082981.3  probable E3 ubiquitin-protein ligase HERC3 isoform a

      See identical proteins and their annotated locations for NP_082981.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      BC042574, BC145980
      Consensus CDS
      CCDS20196.1
      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Related
      ENSMUSP00000040025.9, ENSMUST00000041401.11
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      58808440..58897383
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006506696.3 → XP_006506759.1  probable E3 ubiquitin-protein ligase HERC3 isoform X1

      See identical proteins and their annotated locations for XP_006506759.1

      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    2. XM_006506701.5 → XP_006506764.1  probable E3 ubiquitin-protein ligase HERC3 isoform X3

      Conserved Domains (2) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      pfam00415
      Location:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    3. XM_006506698.5 → XP_006506761.1  probable E3 ubiquitin-protein ligase HERC3 isoform X1

      See identical proteins and their annotated locations for XP_006506761.1

      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    4. XM_030255635.2 → XP_030111495.1  probable E3 ubiquitin-protein ligase HERC3 isoform X2

      Conserved Domains (1) summary
      cd00078
      Location:320 → 666
      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_030255634.2 → XP_030111494.1  probable E3 ubiquitin-protein ligase HERC3 isoform X1

      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    6. XM_006506697.5 → XP_006506760.1  probable E3 ubiquitin-protein ligase HERC3 isoform X1

      See identical proteins and their annotated locations for XP_006506760.1

      UniProtKB/TrEMBL
      A6H6S0, Q8CFQ0
      Conserved Domains (3) summary
      COG5184
      Location:2 → 331
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:702 → 1048
      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:313 → 377
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    7. XM_036152359.1 → XP_036008252.1  probable E3 ubiquitin-protein ligase HERC3 isoform X2

      Conserved Domains (1) summary
      cd00078
      Location:320 → 666
      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_036152360.1 → XP_036008253.1  probable E3 ubiquitin-protein ligase HERC3 isoform X4

      Conserved Domains (1) summary
      cd00078
      Location:280 → 626
      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 ...

    9. XM_011241490.3 → XP_011239792.1  probable E3 ubiquitin-protein ligase HERC3 isoform X5

      Conserved Domains (1) summary
      cd00078
      Location:191 → 537
      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 ...

    RNA

    1. XR_003956257.1 RNA Sequence

    2. XR_377496.4 RNA Sequence

    3. XR_377495.4 RNA Sequence

    4. XR_001785176.3 RNA Sequence

    5. XR_001785177.3 RNA Sequence

    6. XR_001785178.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version

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