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

    Gene ID: 10171, updated on 10-Dec-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 RNA endonuclease activity. Involved in ribosomal small subunit biogenesis. Part of small-subunit processome. [provided by Alliance of Genome Resources, Dec 2024]
    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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    See RCL1 in Genome Data Viewer
    Location:
    9p24.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (4792944..4861066)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (4798060..4866205)
    RS_2024_09 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. 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
    2. 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
    3. Stability and function of RCL1 are dependent on the interaction with BMS1. Wang Y, et al. J Mol Cell Biol, 2024 Jan 5. PMID 37451810, 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. 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

    See all (89) 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)

    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 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_2024_08

    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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