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    RTCA RNA 3'-terminal phosphate cyclase [ Homo sapiens (human) ]

    Gene ID: 8634, updated on 5-Mar-2024

    Summary

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    Official Symbol
    RTCAprovided by HGNC
    Official Full Name
    RNA 3'-terminal phosphate cyclaseprovided by HGNC
    Primary source
    HGNC:HGNC:17981
    See related
    Ensembl:ENSG00000137996 MIM:611286; AllianceGenome:HGNC:17981
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RPC; RTC1; RTCD1
    Summary
    This gene encodes a member of the RNA 3'-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3'-phosphate of RNA substrates to a 2',3'-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]
    Expression
    Ubiquitous expression in duodenum (RPKM 10.7), kidney (RPKM 10.6) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    1p21.2
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (100266216..100292769)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (100114188..100140722)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (100731772..100758325)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene dihydrolipoamide branched chain transacylase E2 Neighboring gene brain protein I3 pseudogene 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:100708816-100709049 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100714559-100715118 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:100715119-100715678 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:100731463-100732012 Neighboring gene RTCA antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 14415 Neighboring gene microRNA 553 Neighboring gene OCT4 hESC enhancer GRCh37_chr1:100790862-100791444 Neighboring gene chromosome 5 open reading frame 15 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1380 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1119 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1120 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1381 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1382 Neighboring gene cell division cycle 14A Neighboring gene BCAS2 pseudogene 2

    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. Structure-activity relationships in human RNA 3'-phosphate cyclase. Tanaka N, et al. RNA, 2009 Oct. PMID 19690099, Free PMC Article
    2. RNA 3'-terminal phosphate cyclase from HeLa cells. Filipowicz W, et al. Methods Enzymol, 1990. PMID 2199762
    3. The cyclic phosphodiesterase CNP and RNA cyclase RtcA fine-tune noncanonical XBP1 splicing during ER stress. Unlu I, et al. J Biol Chem, 2018 Dec 14. PMID 30355738, Free PMC Article
    4. The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. Genschik P, et al. EMBO J, 1997 May 15. PMID 9184239, Free PMC Article
    5. Quantitative proteomics reveals that long non-coding RNA MALAT1 interacts with DBC1 to regulate p53 acetylation. Chen R, et al. Nucleic Acids Res, 2017 Sep 29. PMID 28973437, Free PMC Article

    See all (44) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CNP and RtcA fine-tune XBP1 output during ER stress
      Title: The cyclic phosphodiesterase CNP and RNA cyclase RtcA fine-tune noncanonical XBP1 splicing during ER stress.
    2. Rtc1 forms a stable binary complex with a 3'-phosphate terminated RNA, but not with an identical 3'-OH terminated RNA
      Title: Structure-activity relationships in human RNA 3'-phosphate cyclase.
    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA-3'-phosphate cyclase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA-3'-phosphate cyclase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of optical nerve axon regeneration IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA 3'-terminal phosphate cyclase
    Names
    RNA terminal phosphate cyclase domain 1
    RNA terminal phosphate cyclase domain-containing protein 1
    RTC domain-containing protein 1
    NP_001124313.1
    NP_003720.1

    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_001130841.2 → NP_001124313.1  RNA 3'-terminal phosphate cyclase isoform a

      See identical proteins and their annotated locations for NP_001124313.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
      Source sequence(s)
      AI587400, AL445928, AL663111, BC012604, CA437545, CF141820, DA361597, DB576272
      Consensus CDS
      CCDS44178.1
      UniProtKB/TrEMBL
      A8K8K1
      Related
      ENSP00000260563.4, ENST00000260563.4
      Conserved Domains (2) summary
      cd00874
      Location:8 → 353
      RNA_Cyclase_Class_II; RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in ...
      TIGR03399
      Location:6 → 350
      RNA_3prim_cycl; RNA 3'-phosphate cyclase

    2. NM_003729.4 → NP_003720.1  RNA 3'-terminal phosphate cyclase isoform b

      See identical proteins and their annotated locations for NP_003720.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform a.
      Source sequence(s)
      AI587400, AL663111, CA437545, CF141820, DA361597, DB576272, Y11651
      Consensus CDS
      CCDS768.1
      UniProtKB/Swiss-Prot
      O00442, Q5VVL5, Q5VVL6, Q96E99
      UniProtKB/TrEMBL
      A8K8K1
      Related
      ENSP00000359146.4, ENST00000370128.9
      Conserved Domains (2) summary
      cd00874
      Location:8 → 340
      RNA_Cyclase_Class_II; RNA 3' phosphate cyclase domain (class II). These proteins function as RNA cyclase to catalyze the ATP-dependent conversion of 3'-phosphate to a 2'.3'-cyclic phosphodiester at the end of RNA molecule. A conserved catalytic histidine residue is found in ...
      TIGR03399
      Location:6 → 337
      RNA_3prim_cycl; RNA 3'-phosphate cyclase

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      100266216..100292769
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      100114188..100140722
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O00442.1 GenPept UniProtKB/Swiss-Prot:O00442

    Gene LinkOut

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

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