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

Gene ID: 10171, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:17687
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
Summary
Predicted to enable endoribonuclease activity. Predicted to be involved in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nucleoplasm. Predicted to be active in nucleolus. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in liver (RPKM 21.6), fat (RPKM 15.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
9p24.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (4792944..4861066)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (4798060..4866205)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (4792944..4861066)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28149 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28150 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:4793195-4793694 Neighboring gene Sharpr-MPRA regulatory region 12609 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:4804057-4804558 Neighboring gene extracellular matrix protein 1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:4804559-4805058 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28152 Neighboring gene RPS5 pseudogene 6 Neighboring gene Sharpr-MPRA regulatory region 4294 Neighboring gene KLF4 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 10284 Neighboring gene uncharacterized LOC124902113 Neighboring gene microRNA 101-2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28154 Neighboring gene heterogeneous nuclear ribonucleoprotein A1 pseudogene 41 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:4984323-4985156 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28156 Neighboring gene Sharpr-MPRA regulatory region 14989 Neighboring gene Janus kinase 2 Neighboring gene insulin like 6 Neighboring gene casein kinase 1 gamma 2 pseudogene 1

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. A rare missense variant in RCL1 segregates with depression in extended families. Amin N, et al. Mol Psychiatry, 2018 May. PMID 28322274, Free PMC Article
  2. Purification of RNA 3'-terminal phosphate cyclase from HeLa cells. Covalent modification of the enzyme with different nucleotides. Vicente O, et al. Eur J Biochem, 1988 Sep 15. PMID 3416880
  3. 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
  4. Rcl1p, the yeast protein similar to the RNA 3'-phosphate cyclase, associates with U3 snoRNP and is required for 18S rRNA biogenesis. Billy E, et al. EMBO J, 2000 May 2. PMID 10790377, Free PMC Article
  5. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. Shameer K, et al. Hum Genet, 2014 Jan. PMID 24026423, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

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

EBI GWAS Catalog

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

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

Pathways from PubChem

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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 RNA endonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in biological_process ND
No biological Data available
more info
  
involved_in endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IEA
Inferred from Electronic Annotation
more info
  
involved_in endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IEA
Inferred from Electronic Annotation
more info
  
involved_in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ribosomal small subunit biogenesis IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of small-subunit processome IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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

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_001286699.2 → NP_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, AL518076, BC001025, BI859171, CA422524
    Consensus CDS
    CCDS75810.1
    UniProtKB/TrEMBL
    A0A087X1L9, Q5VZU3
    Conserved Domains (1) summary
    cl27058
    Location:1 → 213
    RTC; RNA 3'-terminal phosphate cyclase

  2. NM_001286700.2 → NP_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, AL560629, BC001025, BI859171, CA422524
    Consensus CDS
    CCDS75810.1
    UniProtKB/TrEMBL
    A0A087X1L9, Q5VZU3
    Related
    ENSP00000412000.2, ENST00000442869.5
    Conserved Domains (1) summary
    cl27058
    Location:1 → 213
    RTC; RNA 3'-terminal phosphate cyclase

  3. NM_001286701.2 → NP_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, AL158147, BI859171, CA422524, EF553527
    Consensus CDS
    CCDS69565.1
    UniProtKB/Swiss-Prot
    Q9Y2P8
    Related
    ENSP00000388096.2, ENST00000448872.6
    Conserved Domains (1) summary
    cl27058
    Location:7 → 185
    RTC; RNA 3'-terminal phosphate cyclase

  4. NM_005772.5 → NP_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
    D3DRI2, Q5VYW9, Q5VZU1, Q9H9D0, Q9NY00, Q9P044, Q9Y2P8
    Related
    ENSP00000371169.4, ENST00000381750.9
    Conserved Domains (1) summary
    TIGR03400
    Location:8 → 371
    18S_RNA_Rcl1p; 18S rRNA biogenesis protein RCL1

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    4792944..4861066
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    4798060..4866205
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2P8.3 GenPept UniProtKB/Swiss-Prot:Q9Y2P8

Gene LinkOut

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

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