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    Herc4 HECT and RLD domain containing E3 ubiquitin protein ligase 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 309758, updated on 2-May-2024

    Summary

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    Official Symbol
    Herc4provided by RGD
    Official Full Name
    HECT and RLD domain containing E3 ubiquitin protein ligase 4provided by RGD
    Primary source
    RGD:1310971
    See related
    Ensembl:ENSRNOG00000061040 AllianceGenome:RGD:1310971
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable ubiquitin-protein transferase activity. Predicted to be involved in negative regulation of smoothened signaling pathway and spermatogenesis. Predicted to be located in cytosol and fibrillar center. Orthologous to human HERC4 (HECT and RLD domain containing E3 ubiquitin protein ligase 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Liver (RPKM 195.2), Testes (RPKM 185.5) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Herc4 in Genome Data Viewer
    Location:
    20p11
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 20 NC_086038.1 (25329005..25403443, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 20 NC_051355.1 (25329972..25404657, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 20 NC_005119.4 (26755948..26831267)

    Chromosome 20 - NC_086038.1Genomic Context describing neighboring genes Neighboring gene DnaJ heat shock protein family (Hsp40) member C12 Neighboring gene transfer RNA alanine (anticodon AGC) 21 Neighboring gene sirtuin 1 Neighboring gene mitochondrial ribosomal protein S36, pseudogene 1 Neighboring gene myopalladin Neighboring gene U1 small nuclear ribonucleoprotein C pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Disruption of the ubiquitin ligase HERC4 causes defects in spermatozoon maturation and impaired fertility. Rodriguez CI, et al. Dev Biol, 2007 Dec 15. PMID 17967448
    2. HERC4 exerts an anti-tumor role through destabilizing the oncoprotein Smo. Sun X, et al. Biochem Biophys Res Commun, 2019 Jun 11. PMID 31010679
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Gerhard DS, et al. Genome Res, 2004 Oct. PMID 15489334, Free PMC Article
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ubiquitin protein ligase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin-protein transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of smoothened signaling pathway ISO
    Inferred from Sequence Orthology
    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 spermatogenesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in spermatogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in fibrillar center IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in fibrillar center ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable E3 ubiquitin-protein ligase HERC4
    Names
    HECT domain and RCC1-like domain-containing protein 4
    HECT-type E3 ubiquitin transferase HERC4
    hect domain and RLD 4
    NP_001012074.1
    XP_006256196.1
    XP_006256197.1
    XP_006256198.1
    XP_017457145.1
    XP_038954684.1
    XP_038954685.1
    XP_038954686.1
    XP_038954687.1
    XP_063135240.1
    XP_063135241.1
    XP_063135242.1

    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_001012074.1 → NP_001012074.1  probable E3 ubiquitin-protein ligase HERC4

      See identical proteins and their annotated locations for NP_001012074.1

      Status: PROVISIONAL

      Source sequence(s)
      BC087104
      UniProtKB/Swiss-Prot
      Q5PQN1
      Related
      ENSRNOP00000072219.1, ENSRNOT00000083017.2
      Conserved Domains (2) summary
      COG5184
      Location:2 → 344
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:709 → 1055
      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_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086038.1 Reference GRCr8

      Range
      25329005..25403443 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063279171.1 → XP_063135241.1  probable E3 ubiquitin-protein ligase HERC4 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZWE9, A6JKY7

    2. XM_006256135.5 → XP_006256197.1  probable E3 ubiquitin-protein ligase HERC4 isoform X2

      See identical proteins and their annotated locations for XP_006256197.1

      UniProtKB/TrEMBL
      A0A8I5ZWE9, A6JKY7
      Related
      ENSRNOP00000082108.1
      Conserved Domains (3) summary
      smart00119
      Location:727 → 1046
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:701 → 1047
      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:208 → 257
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    3. XM_039098757.2 → XP_038954685.1  probable E3 ubiquitin-protein ligase HERC4 isoform X5

      UniProtKB/TrEMBL
      A6JKY6
      Conserved Domains (2) summary
      COG5184
      Location:2 → 344
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:580 → 926
      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_039098756.2 → XP_038954684.1  probable E3 ubiquitin-protein ligase HERC4 isoform X4

      Conserved Domains (2) summary
      COG5184
      Location:2 → 344
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:588 → 934
      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_006256134.5 → XP_006256196.1  probable E3 ubiquitin-protein ligase HERC4 isoform X1

      See identical proteins and their annotated locations for XP_006256196.1

      UniProtKB/Swiss-Prot
      Q5PQN1
      Conserved Domains (2) summary
      COG5184
      Location:2 → 344
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:709 → 1055
      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_063279172.1 → XP_063135242.1  probable E3 ubiquitin-protein ligase HERC4 isoform X6

    7. XM_063279170.1 → XP_063135240.1  probable E3 ubiquitin-protein ligase HERC4 isoform X2

      UniProtKB/TrEMBL
      A0A8I5ZWE9, A6JKY7

    8. XM_017601656.3 → XP_017457145.1  probable E3 ubiquitin-protein ligase HERC4 isoform X1

      UniProtKB/Swiss-Prot
      Q5PQN1
      Conserved Domains (2) summary
      COG5184
      Location:2 → 344
      ATS1; Alpha-tubulin suppressor and related RCC1 domain-containing proteins [Cell cycle control, cell division, chromosome partitioning, Cytoskeleton]
      cd00078
      Location:709 → 1055
      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_006256136.5 → XP_006256198.1  probable E3 ubiquitin-protein ligase HERC4 isoform X3

      Conserved Domains (4) summary
      smart00119
      Location:665 → 984
      HECTc; Domain Homologous to E6-AP Carboxyl Terminus with
      cd00078
      Location:639 → 985
      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:138 → 187
      RCC1; Regulator of chromosome condensation (RCC1) repeat
      pfam13540
      Location:16 → 45
      RCC1_2; Regulator of chromosome condensation (RCC1) repeat

    10. XM_039098758.2 → XP_038954686.1  probable E3 ubiquitin-protein ligase HERC4 isoform X7

      Conserved Domains (2) summary
      cd00078
      Location:454 → 800
      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:5 → 53
      RCC1; Regulator of chromosome condensation (RCC1) repeat

    11. XM_039098759.2 → XP_038954687.1  probable E3 ubiquitin-protein ligase HERC4 isoform X8

      Conserved Domains (1) summary
      cd00078
      Location:291 → 637
      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_005497262.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5PQN1.1 GenPept UniProtKB/Swiss-Prot:Q5PQN1

    Gene LinkOut

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

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