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OBI1 ORC ubiquitin ligase 1 [ Homo sapiens (human) ]

Gene ID: 79596, updated on 5-Mar-2024

Summary

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Official Symbol
OBI1provided by HGNC
Official Full Name
ORC ubiquitin ligase 1provided by HGNC
Primary source
HGNC:HGNC:20308
See related
Ensembl:ENSG00000152193 MIM:615906; AllianceGenome:HGNC:20308
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
RNF219; C13orf7
Summary
Enables chromatin binding activity and ubiquitin-protein transferase activity. Involved in protein autoubiquitination; protein monoubiquitination; and regulation of DNA replication. Located in chromatin. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 8.1), brain (RPKM 4.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
13q31.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (78614289..78659155, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (77840023..77884889, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (79188424..79233290, complement)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene OBI1 antisense RNA 1 Neighboring gene elongin C pseudogene 23 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:79169924-79170652 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5424 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:79180755-79181616 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr13:79181617-79182476 Neighboring gene uncharacterized LOC780529 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr13:79231698-79232658 Neighboring gene POU class 4 homeobox 1 Neighboring gene uncharacterized LOC105370272 Neighboring gene ribosomal protein L21 pseudogene 111 Neighboring gene long intergenic non-protein coding RNA 331

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
  • 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. A potential association of RNF219-AS1 with ADHD: Evidence from categorical analysis of clinical phenotypes and from quantitative exploration of executive function and white matter microstructure endophenotypes. Fu GH, et al. CNS Neurosci Ther, 2021 May. PMID 33644999, Free PMC Article
  2. Ring finger protein 219 regulates inflammatory responses by stabilizing sirtuin 1. Hwang JS, et al. Br J Pharmacol, 2020 Oct. PMID 32220064, Free PMC Article
  3. RNF219/α-Catenin/LGALS3 Axis Promotes Hepatocellular Carcinoma Bone Metastasis and Associated Skeletal Complications. Zhang S, et al. Adv Sci (Weinh), 2021 Feb. PMID 33643786, Free PMC Article
  4. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation. Poetz F, et al. Nat Commun, 2021 Dec 9. PMID 34887419, Free PMC Article
  5. STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1. Durzynska I, et al. Structure, 2017 Feb 7. PMID 28089446, Free PMC Article

See all (72) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. RNF219 Promotes Nasopharyngeal Carcinoma Progression by Activating the NF-kappaB Pathway.
    Title: RNF219 Promotes Nasopharyngeal Carcinoma Progression by Activating the NF-κB Pathway.
  2. A potential association of RNF219-AS1 with ADHD: Evidence from categorical analysis of clinical phenotypes and from quantitative exploration of executive function and white matter microstructure endophenotypes.
    Title: A potential association of RNF219-AS1 with ADHD: Evidence from categorical analysis of clinical phenotypes and from quantitative exploration of executive function and white matter microstructure endophenotypes.
  3. RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
    Title: RNF219 attenuates global mRNA decay through inhibition of CCR4-NOT complex-mediated deadenylation.
  4. RNF219 silencing result in defective replication origin firing, as shown by reduced CDC45/MCM2-7/GINS complex formation, without affecting pre-replicative complex establishment. RNF219 catalyses the multi-mono-ubiquitylation of a subset of chromatin-bound ORC3 and ORC5 during S-phase.
    Title: The ORC ubiquitin ligase OBI1 promotes DNA replication origin firing.
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
Genome-wide association of lipid-lowering response to statins in combined study populations.
EBI GWAS Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ13449, FLJ25774, DKFZp686A01276, DKFZp686N15250, DKFZp686O03173

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin-protein transferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in protein autoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein monoubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of DNA replication IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ORC ubiquitin ligase 1
Names
ring finger protein 219
NP_078822.3
XP_011533527.1
XP_024305178.1
XP_054230934.1
XP_054230935.1

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_024546.4 → NP_078822.3  ORC ubiquitin ligase 1

    See identical proteins and their annotated locations for NP_078822.3

    Status: VALIDATED

    Source sequence(s)
    AK023511, BC028586, BI550796, BM674566
    Consensus CDS
    CCDS31997.1
    UniProtKB/Swiss-Prot
    B2RN99, Q5W0B1, Q8TBY2, Q9H0T2, Q9H8M0
    Related
    ENSP00000282003.6, ENST00000282003.7
    Conserved Domains (3) summary
    COG1196
    Location:74 → 269
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    COG5432
    Location:18 → 165
    RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
    cd16562
    Location:15 → 56
    RING-HC_RNF219; RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    78614289..78659155 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011535225.2 → XP_011533527.1  ORC ubiquitin ligase 1 isoform X1

    See identical proteins and their annotated locations for XP_011533527.1

    Conserved Domains (2) summary
    PRK12704
    Location:83 → 189
    PRK12704; phosphodiesterase; Provisional
    TIGR04211
    Location:29 → 132
    SH3_and_anchor; SH3 domain protein

  2. XM_024449410.2 → XP_024305178.1  ORC ubiquitin ligase 1 isoform X1

    Conserved Domains (2) summary
    PRK12704
    Location:83 → 189
    PRK12704; phosphodiesterase; Provisional
    TIGR04211
    Location:29 → 132
    SH3_and_anchor; SH3 domain protein

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    77840023..77884889 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374959.1 → XP_054230934.1  ORC ubiquitin ligase 1 isoform X1

  2. XM_054374960.1 → XP_054230935.1  ORC ubiquitin ligase 1 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5W0B1.1 GenPept UniProtKB/Swiss-Prot:Q5W0B1

Gene LinkOut

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

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