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    ARK2C arkadia (RNF111) C-terminal like ring finger ubiquitin ligase 2C [ Homo sapiens (human) ]

    Gene ID: 494470, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ARK2Cprovided by HGNC
    Official Full Name
    arkadia (RNF111) C-terminal like ring finger ubiquitin ligase 2Cprovided by HGNC
    Primary source
    HGNC:HGNC:31696
    See related
    Ensembl:ENSG00000141622 AllianceGenome:HGNC:31696
    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
    Also known as
    ARKL2; RNF165; lncAMPC; RNF111L2
    Summary
    Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in motor neuron axon guidance and positive regulation of BMP signaling pathway. Predicted to act upstream of or within several processes, including forelimb morphogenesis; nervous system development; and protein polyubiquitination. Predicted to be part of protein-containing complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Biased expression in brain (RPKM 3.7), spleen (RPKM 1.6) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ARK2C in Genome Data Viewer
    Location:
    18q21.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (46334018..46463140)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (46524603..46653701)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (43913981..44043103)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene RNA, U6 small nuclear 1278, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr18:43735851-43736057 Neighboring gene HAUS augmin like complex subunit 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43744621-43745122 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43745123-43745622 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43747273-43748134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13272 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13273 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13274 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13275 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13276 Neighboring gene MPRA-validated peak3131 silencer Neighboring gene arkadia (RNF111) N-terminal like PKA signaling regulator 2N Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43829497-43830133 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:43830134-43830769 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43839023-43839587 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43839588-43840151 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:43841527-43842028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43874443-43874944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43891455-43892088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43912812-43913423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43913424-43914034 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13279 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43953278-43953778 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:43967128-43967628 Neighboring gene uncharacterized LOC105372095 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:43972627-43973160 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43991726-43992676 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:43994577-43995525 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44004729-44005693 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44007521-44008096 Neighboring gene uncharacterized LOC124904293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44015273-44015773 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44027257-44028040 Neighboring gene Sharpr-MPRA regulatory region 1203 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:44038097-44038886 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:44044737-44045236 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:44046140-44046972 Neighboring gene MPRA-validated peak3132 silencer Neighboring gene MPRA-validated peak3133 silencer Neighboring gene lipoxygenase homology PLAT domains 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:44237431-44238380 Neighboring gene uncharacterized LOC105372096

    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. Ubiquitin and a charged loop regulate the ubiquitin E3 ligase activity of Ark2C. Paluda A, et al. Nat Commun, 2022 Mar 4. PMID 35246518, Free PMC Article
    2. Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Wright JD, et al. Nat Struct Mol Biol, 2016 Jan. PMID 26656854
    3. Candidate psychiatric illness genes identified in patients with pericentric inversions of chromosome 18. Pickard BS, et al. Psychiatr Genet, 2005 Mar. PMID 15722956
    4. Rnf165/Ark2C enhances BMP-Smad signaling to mediate motor axon extension. Kelly CE, et al. PLoS Biol, 2013. PMID 23610558, Free PMC Article
    5. The UAS thioredoxin-like domain of UBXN7 regulates E3 ubiquitin ligase activity of RNF111/Arkadia. Amhaz S, et al. BMC Biol, 2023 Apr 7. PMID 37024974, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    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

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ34218

    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 zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in forelimb morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in innervation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in motor neuron axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in muscle structure development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of BMP signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein polyubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    E3 ubiquitin-protein ligase ARK2C
    Names
    E3 ubiquitin-protein ligase RNF165
    lncRNA activated in metastatic PCa
    ring finger protein 165
    NP_001243687.1
    NP_689683.2
    XP_011524318.1
    XP_016881277.1
    XP_024306959.1
    XP_054174648.1
    XP_054174649.1
    XP_054174650.1

    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_001256758.1 → NP_001243687.1  E3 ubiquitin-protein ligase ARK2C isoform 2

      See identical proteins and their annotated locations for NP_001243687.1

      Status: VALIDATED

      Source sequence(s)
      AC018931, AK122819
      Consensus CDS
      CCDS58621.1
      UniProtKB/Swiss-Prot
      Q6ZSG1
      Related
      ENSP00000444285.1, ENST00000543885.2
      Conserved Domains (1) summary
      cd16474
      Location:100 → 145
      RING-H2_RNF111_like; RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins

    2. NM_152470.3 → NP_689683.2  E3 ubiquitin-protein ligase ARK2C isoform 1

      See identical proteins and their annotated locations for NP_689683.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC015959, AC018931, AK122819, AK127467, AW160725, BM680948
      Consensus CDS
      CCDS32823.1
      UniProtKB/Swiss-Prot
      B3KVD1, Q6ZSG1
      UniProtKB/TrEMBL
      A0A059NXK6
      Related
      ENSP00000269439.6, ENST00000269439.12
      Conserved Domains (1) summary
      cd16474
      Location:292 → 337
      RING-H2_RNF111_like; RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins

    RNA

    1. NR_046357.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks several exons and uses an alternate 3' exon, compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
      Source sequence(s)
      AC015959, DA077941

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      46334018..46463140
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011526016.4 → XP_011524318.1  E3 ubiquitin-protein ligase ARK2C isoform X1

      See identical proteins and their annotated locations for XP_011524318.1

      Conserved Domains (1) summary
      cd16474
      Location:260 → 305
      RING-H2_RNF111_like; RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins

    2. XM_017025788.3 → XP_016881277.1  E3 ubiquitin-protein ligase ARK2C isoform X2

    3. XM_024451191.2 → XP_024306959.1  E3 ubiquitin-protein ligase ARK2C isoform X3

      Conserved Domains (1) summary
      cd16474
      Location:100 → 145
      RING-H2_RNF111_like; RING finger, H2 subclass, found in RING finger proteins RNF111, RNF165, and similar proteins

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      46524603..46653701
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054318673.1 → XP_054174648.1  E3 ubiquitin-protein ligase ARK2C isoform X1

    2. XM_054318674.1 → XP_054174649.1  E3 ubiquitin-protein ligase ARK2C isoform X2

    3. XM_054318675.1 → XP_054174650.1  E3 ubiquitin-protein ligase ARK2C isoform X3

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZSG1.1 GenPept UniProtKB/Swiss-Prot:Q6ZSG1

    Gene LinkOut

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

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