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

Gene ID: 494470, updated on 2-Nov-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, Nov 2024]
Expression
Biased expression in brain (RPKM 3.7), spleen (RPKM 1.6) and 12 other tissues See more
Orthologs
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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 Variation Viewer (GRCh37.p13)

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

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