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RTCB RNA 2',3'-cyclic phosphate and 5'-OH ligase [ Homo sapiens (human) ]

Gene ID: 51493, updated on 7-Apr-2024

Summary

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Official Symbol
RTCBprovided by HGNC
Official Full Name
RNA 2',3'-cyclic phosphate and 5'-OH ligaseprovided by HGNC
Primary source
HGNC:HGNC:26935
See related
Ensembl:ENSG00000100220 MIM:613901; AllianceGenome:HGNC:26935
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
FAAP; HSPC117; C22orf28; DJ149A16.6
Summary
Enables RNA ligase (ATP) activity and vinculin binding activity. Involved in tRNA splicing, via endonucleolytic cleavage and ligation. Located in cytosol and nucleoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in duodenum (RPKM 45.6), small intestine (RPKM 40.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
22q12.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (32387582..32412247, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (32851498..32876163, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (32783569..32808234, complement)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene immunoglobulin lambda constant/OR22-2 (pseudogene) Neighboring gene uncharacterized LOC339666 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:32790650-32790847 Neighboring gene RGL4 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18876 Neighboring gene BPI fold containing family C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18877 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:32870558-32871058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:32871059-32871559 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63238 Neighboring gene F-box protein 7 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_63240

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. Homology model of the human tRNA splicing ligase RtcB. Nandy A, et al. Proteins, 2017 Nov. PMID 28707320
  2. HSPC117 is regulated by epigenetic modification and is involved in the migration of JEG-3 cells. Ma H, et al. Int J Mol Sci, 2014 Jun 17. PMID 24941254, Free PMC Article
  3. [Pregnancies after conization of the cervix uteri]. Garcia-Huidobro M. Rev Chil Obstet Ginecol, 1971. PMID 5163412
  4. Molecular architecture of the human tRNA ligase complex. Kroupova A, et al. Elife, 2021 Dec 2. PMID 34854379, Free PMC Article
  5. Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. Englert M, et al. Proc Natl Acad Sci U S A, 2011 Jan 25. PMID 21209330, Free PMC Article

See all (167) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
    Title: Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
  2. The RNA-Splicing Ligase RTCB Promotes Influenza A Virus Replication by Suppressing Innate Immunity via Interaction with RNA Helicase DDX1.
    Title: The RNA-Splicing Ligase RTCB Promotes Influenza A Virus Replication by Suppressing Innate Immunity via Interaction with RNA Helicase DDX1.
  3. Molecular architecture of the human tRNA ligase complex.
    Title: Molecular architecture of the human tRNA ligase complex.
  4. This paper presents a homology model of human RtcB (hRtcB). The structure was analyzed in terms of stereochemical quality, folding reliability, secondary structure, druggability of the active site binding pocket and its metal-binding microenvironment.
    Title: Homology model of the human tRNA splicing ligase RtcB.
  5. RTCB, the catalytic subunit of the tRNA ligase complex, and its co-factor archease mediate XBP1 mRNA splicing both in vitro and in vivo.
    Title: The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells.
  6. hCLE/C14orf166 associates with DDX1, HSPC117, and FAM98B in a novel transcription-dependent shuttling RNA-transporting complex.
    Title: hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex.
  7. Over-expression of HSPC117 mRNA reduced MMP 2 and MMP 14 mRNA expression, while TIMP 2 mRNA expression was up-regulated.
    Title: HSPC117 is regulated by epigenetic modification and is involved in the migration of JEG-3 cells.
  8. study identified HSPC117, a member of the UPF0027 (RtcB) family, as the essential subunit of a tRNA ligase complex; RNA interference-mediated depletion of HSPC117 inhibited maturation of intron-containing pre-tRNA both in vitro and in living cells
    Title: HSPC117 is the essential subunit of a human tRNA splicing ligase complex.
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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Rev rev HIV-1 Rev interacting protein, chromosome 22 open reading frame 28 (C22orf28), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
enables RNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA ligase (ATP) activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA ligase (ATP) activity IMP
Inferred from Mutant Phenotype
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 vinculin binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in in utero embryonic development IEA
Inferred from Electronic Annotation
more info
  
involved_in placenta development IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA splicing, via endonucleolytic cleavage and ligation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in tRNA splicing, via endonucleolytic cleavage and ligation NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm NAS
Non-traceable Author Statement
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
  
located_in nuclear envelope IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of tRNA-splicing ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of tRNA-splicing ligase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of tRNA-splicing ligase complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
RNA-splicing ligase RtcB homolog
Names
3'-phosphate/5'-hydroxy nucleic acid ligase
ankyrin repeat domain 54
focal adhesion-associated protein
tRNA-splicing ligase RtcB homolog
NP_055121.1

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_014306.5 → NP_055121.1  RNA-splicing ligase RtcB homolog

    See identical proteins and their annotated locations for NP_055121.1

    Status: VALIDATED

    Source sequence(s)
    AL050255, DC396330
    Consensus CDS
    CCDS13905.1
    UniProtKB/Swiss-Prot
    B2R6A8, Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3, Q9Y3I0
    UniProtKB/TrEMBL
    B4DNA0
    Related
    ENSP00000216038.5, ENST00000216038.6
    Conserved Domains (1) summary
    pfam01139
    Location:68 → 505
    RtcB; tRNA-splicing ligase RtcB

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_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    32387582..32412247 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    32851498..32876163 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y3I0.1 GenPept UniProtKB/Swiss-Prot:Q9Y3I0

Gene LinkOut

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

Chemical Information
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