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

Gene ID: 10171, updated on 8-Jul-2018
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; Vega:OTTHUMG00000019474
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
See RCL1 in Genome Data Viewer
Location:
9p24.1
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 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 Janus kinase 2 Neighboring gene insulin like 6 Neighboring gene casein kinase 1 gamma 2 pseudogene 1

  • 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 Jun 15 11:32:44 2016

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
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
  • Ribosome biogenesis in eukaryotes, organism-specific biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, organism-specific biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • Ribosome biogenesis in eukaryotes, conserved biosystem (from KEGG)
    Ribosome biogenesis in eukaryotes, conserved biosystemRibosomes are the cellular factories responsible for making proteins. In eukaryotes, ribosome biogenesis involves the production and correct assembly of four rRNAs and about 80 ribosomal proteins. It...
  • rRNA modification in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA modification in the nucleus and cytosol, organism-specific biosystemHuman ribosomal RNAs (rRNAs) contain about 200 residues that are enzymatically modified after transcription in the nucleolus (Maden and Khan 1977, Maden 1988, Maden and Hughes 1997, reviewed in Herna...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA-3'-phosphate cyclase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
 
Preferred Names
RNA 3'-terminal phosphate cyclase-like protein
Names
RNA cyclase homolog

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, OTTHUMP00000021019, ENST00000442869.5, OTTHUMT00000051589
    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_005772.4NP_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, AL353151, BC001025, BI859171, CA422524, DB448951
    Consensus CDS
    CCDS6456.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000371169.4, OTTHUMP00000021017, ENST00000381750.8, OTTHUMT00000051587
    Conserved Domains (1) summary
    TIGR03400
    Location:8371
    18S_RNA_Rcl1p; 18S rRNA biogenesis protein RCL1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 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, OTTHUMP00000021021, ENST00000381728.5, OTTHUMT00000051592
    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, OTTHUMP00000021018, ENST00000381730.5
    Conserved Domains (1) summary
    cl27058
    Location:7185
    RTC; RNA 3'-terminal phosphate cyclase
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