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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

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