U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 51493, updated on 3-Nov-2024

    Summary

    Go to the top of the page Help
    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 (GTP) 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, Nov 2024]
    Expression
    Ubiquitous expression in duodenum (RPKM 45.6), small intestine (RPKM 40.2) and 25 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See RTCB in Genome Data Viewer
    Location:
    22q12.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (32387582..32412247, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (32851498..32876163, complement)
    RS_2024_09 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

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. [Pregnancies after conization of the cervix uteri]. Garcia-Huidobro M. Rev Chil Obstet Ginecol, 1971. PMID 5163412
    2. Homology model of the human tRNA splicing ligase RtcB. Nandy A, et al. Proteins, 2017 Nov. PMID 28707320
    3. 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
    4. Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease. Gerber JL, et al. Nat Commun, 2024 Mar 16. PMID 38493148, Free PMC Article
    5. SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9. Schmidt N, et al. Cell, 2023 Oct 26. PMID 37794589, Free PMC Article

    See all (202) 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

    Go to the top of the page Help

    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

    Go to the top of the page Help

    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

    Go to the top of the page Help

    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

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    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 (GTP) activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA ligase (GTP) 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 splicing, via endonucleolytic cleavage and ligation 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

    Go to the top of the page Help
    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)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_2024_08

    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
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous