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RCL1 RNA terminal phosphate cyclase like 1 [ Homo sapiens (human) ]

Gene ID: 10171, updated on 13-Mar-2020

Summary

Official Symbol
RCL1provided by HGNC
Official Full Name
RNA terminal phosphate cyclase like 1provided by HGNC
Primary source
HGNC:HGNC:17687
See related
Ensembl:ENSG00000120158 MIM:611405
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
RNAC; RPCL1
Expression
Ubiquitous expression in liver (RPKM 21.6), fat (RPKM 15.5) and 25 other tissues See more
Orthologs

Genomic context

See RCL1 in Genome Data Viewer
Location:
9p24.1
Exon count:
11
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 9 NC_000009.12 (4792834..4861077)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (4792834..4861066)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene extracellular matrix protein 1 pseudogene 1 Neighboring gene ribosomal protein S5 pseudogene 6 Neighboring gene Kruppel like factor 4 pseudogene 1 Neighboring gene microRNA 101-2 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 41 Neighboring gene Sharpr-MPRA regulatory region 14989 Neighboring gene Janus kinase 2 Neighboring gene insulin like 6

Genomic regions, transcripts, and products

Expression

  • 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

Phenotypes

NHGRI GWAS Catalog

Description
A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects.
NHGRI GWA Catalog
Genome-wide association study of hematological and biochemical traits in a Japanese population.
NHGRI GWA Catalog
GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
NHGRI GWA Catalog
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
NHGRI GWA Catalog
New gene functions in megakaryopoiesis and platelet formation.
NHGRI GWA Catalog
Seventy-five genetic loci influencing the human red blood cell.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
endoribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
RNA 3'-terminal phosphate cyclase-like protein
Names
RNA cyclase homolog

NCBI Reference Sequences (RefSeq)

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_001286699.1NP_001273628.1  RNA 3'-terminal phosphate cyclase-like protein isoform b

    See identical proteins and their annotated locations for NP_001273628.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks two alternate exons in the 5' region and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AF067172, AI688431, AL158147, AL353151, AL518076, BC001025, BI859171, CA422524, DB448951
    Consensus CDS
    CCDS75810.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    UniProtKB/TrEMBL
    Q5VZU3
    Conserved Domains (1) summary
    cl27058
    Location:1213
    RTC; RNA 3'-terminal phosphate cyclase
  2. NM_001286700.1NP_001273629.1  RNA 3'-terminal phosphate cyclase-like protein isoform b

    See identical proteins and their annotated locations for NP_001273629.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the 5' region and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (b) is shorter at the N-terminus, compared to isoform a. Both variants 2 and 3 encode isoform b.
    Source sequence(s)
    AF067172, AI688431, AL353151, AL560629, BC001025, BI859171, CA422524, DB448951
    Consensus CDS
    CCDS75810.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    UniProtKB/TrEMBL
    Q5VZU3
    Related
    ENSP00000412000.2, ENST00000442869.5
    Conserved Domains (1) summary
    cl27058
    Location:1213
    RTC; RNA 3'-terminal phosphate cyclase
  3. NM_001286701.1NP_001273630.1  RNA 3'-terminal phosphate cyclase-like protein isoform c

    See identical proteins and their annotated locations for NP_001273630.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks five exons in the 5' region but includes an alternate 5' terminal exon, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.
    Source sequence(s)
    AF067172, AI688431, BI859171, CA422524, EF553527
    Consensus CDS
    CCDS69565.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000388096.2, ENST00000448872.6
    Conserved Domains (1) summary
    cl27058
    Location:7185
    RTC; RNA 3'-terminal phosphate cyclase
  4. NM_005772.5NP_005763.3  RNA 3'-terminal phosphate cyclase-like protein isoform a

    See identical proteins and their annotated locations for NP_005763.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AF067172, AI688431, BC001025, BI859171, CA422524
    Consensus CDS
    CCDS6456.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000371169.4, ENST00000381750.9
    Conserved Domains (1) summary
    TIGR03400
    Location:8371
    18S_RNA_Rcl1p; 18S rRNA biogenesis protein RCL1

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p13 Primary Assembly

    Range
    4792834..4861077
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006716715.3XP_006716778.1  RNA 3'-terminal phosphate cyclase-like protein isoform X1

    Conserved Domains (1) summary
    cl00288
    Location:1235
    EPT_RTPC-like; This domain family includes the Enolpyruvate transferase (EPT) family and the RNA 3' phosphate cyclase family (RTPC). These 2 families differ in that EPT is formed by 3 repeats of an alpha-beta structural domain while RTPC has 3 similar repeats with a ...
  2. XM_017014176.1XP_016869665.1  RNA 3'-terminal phosphate cyclase-like protein isoform X2

    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000371147.1, ENST00000381728.5
    Conserved Domains (1) summary
    cl27058
    Location:7185
    RTC; RNA 3'-terminal phosphate cyclase
  3. XM_011517673.3XP_011515975.1  RNA 3'-terminal phosphate cyclase-like protein isoform X2

    See identical proteins and their annotated locations for XP_011515975.1

    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000371149.1, ENST00000381730.5
    Conserved Domains (1) summary
    cl27058
    Location:7185
    RTC; RNA 3'-terminal phosphate cyclase
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