Free for academic non-profit institutions. Other users need a Commercial license

Aliases for RCL1 Gene

Aliases for RCL1 Gene

  • RNA Terminal Phosphate Cyclase Like 1 2 3 5
  • RPCL1 3 4
  • RNAC 3 4
  • RNA 3-Terminal Phosphate Cyclase-Like Protein 3
  • RNA Terminal Phosphate Cyclase-Like 1 2
  • RNA Cyclase Homolog 3
  • RPC2 4
  • RTC2 4

External Ids for RCL1 Gene

Summaries for RCL1 Gene

GeneCards Summary for RCL1 Gene

RCL1 (RNA Terminal Phosphate Cyclase Like 1) is a Protein Coding gene. Among its related pathways are Ribosome biogenesis in eukaryotes and rRNA processing in the nucleus and cytosol. GO annotations related to this gene include RNA binding and RNA-3-phosphate cyclase activity. An important paralog of this gene is RTCA.

UniProtKB/Swiss-Prot for RCL1 Gene

  • Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA (By similarity).

Gene Wiki entry for RCL1 Gene

Additional gene information for RCL1 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RCL1 Gene

Genomics for RCL1 Gene

Regulatory Elements for RCL1 Gene

Enhancers for RCL1 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH09H004828 1.5 Ensembl ENCODE dbSUPER 33 +39.1 39075 6 PKNOX1 FOXA2 ATF1 ARNT SIN3A TCF12 GATA2 FOS ATF7 RUNX3 RCL1 JAK2 GC09P004850 KLF4P1
GH09H004815 1 Ensembl ENCODE 36.3 +22.7 22723 0 TBL1XR1 EBF1 RELA POLR2A EED ZSCAN29 RUNX3 IKZF2 CREM ZBED1 RCL1 ENSG00000228165 MIR101-2 JAK2 KLF4P1 GC09P004850
GH09H004821 0.7 ENCODE 30.4 +29.4 29424 0 FOXA2 HLF MAX REST RAD21 FOXA1 YY1 NFIL3 JUND ATF3 RCL1 ENSG00000228165 MIR101-2 JAK2 KLF4P1 GC09P004850
GH09H004791 1.1 ENCODE 17.3 +0.5 485 3 PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 FOS SP3 RCL1 JAK2 MIR101-2 ENSG00000228165 KLF4P1
GH09H004835 0.6 FANTOM5 dbSUPER 19.3 +42.5 42529 0 RCL1 CDC37L1 GC09P004850 KLF4P1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RCL1 on UCSC Golden Path with GeneCards custom track

Promoters for RCL1 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000232779 266 2201 PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 ZNF143 ZNF207 FOS SP3

Genomic Location for RCL1 Gene

Chromosome:
9
Start:
4,792,834 bp from pter
End:
4,885,917 bp from pter
Size:
93,084 bases
Orientation:
Plus strand

Genomic View for RCL1 Gene

Genes around RCL1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RCL1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RCL1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RCL1 Gene

Proteins for RCL1 Gene

  • Protein details for RCL1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y2P8-RCL1_HUMAN
    Recommended name:
    RNA 3-terminal phosphate cyclase-like protein
    Protein Accession:
    Q9Y2P8
    Secondary Accessions:
    • D3DRI2
    • Q5VYW9
    • Q5VZU1
    • Q9H9D0
    • Q9NY00
    • Q9P044

    Protein attributes for RCL1 Gene

    Size:
    373 amino acids
    Molecular mass:
    40843 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAD32456.1; Type=Frameshift; Positions=13, 58; Evidence={ECO:0000305};

    Alternative splice isoforms for RCL1 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RCL1 Gene

Post-translational modifications for RCL1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RCL1 Gene

Domains & Families for RCL1 Gene

Gene Families for RCL1 Gene

Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for RCL1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y2P8

UniProtKB/Swiss-Prot:

RCL1_HUMAN :
  • Belongs to the RNA 3-terminal cyclase family. Type 2 subfamily.
Family:
  • Belongs to the RNA 3-terminal cyclase family. Type 2 subfamily.
genes like me logo Genes that share domains with RCL1: view

Function for RCL1 Gene

Molecular function for RCL1 Gene

UniProtKB/Swiss-Prot Function:
Does not have cyclase activity. Plays a role in 40S-ribosomal-subunit biogenesis in the early pre-rRNA processing steps at sites A0, A1 and A2 that are required for proper maturation of the 18S RNA (By similarity).

Phenotypes From GWAS Catalog for RCL1 Gene

Gene Ontology (GO) - Molecular Function for RCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0003963 NOT RNA-3-phosphate cyclase activity IBA --
GO:0004521 endoribonuclease activity IBA --
genes like me logo Genes that share ontologies with RCL1: view
genes like me logo Genes that share phenotypes with RCL1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for RCL1

CRISPR Products

miRNA for RCL1 Gene

miRTarBase miRNAs that target RCL1

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RCL1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RCL1 Gene

Localization for RCL1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RCL1 Gene

Nucleus, nucleolus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RCL1 gene
Compartment Confidence
nucleus 5
mitochondrion 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IBA --
genes like me logo Genes that share ontologies with RCL1: view

Pathways & Interactions for RCL1 Gene

genes like me logo Genes that share pathways with RCL1: view

Gene Ontology (GO) - Biological Process for RCL1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000447 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 --
GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA --
GO:0000480 endonucleolytic cleavage in 5-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IEA --
GO:0006364 rRNA processing TAS --
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with RCL1: view

No data available for SIGNOR curated interactions for RCL1 Gene

Drugs & Compounds for RCL1 Gene

No Compound Related Data Available

Transcripts for RCL1 Gene

Unigene Clusters for RCL1 Gene

RNA terminal phosphate cyclase-like 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RCL1
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for RCL1 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11a · 11b
SP1: - - - - - - -
SP2: - - - - - - - - -
SP3: - - -
SP4: - - - - - - - - - - - - - -
SP5: - - - - - - - - - - -
SP6: - -
SP7: -
SP8: -
SP9: - -

Relevant External Links for RCL1 Gene

GeneLoc Exon Structure for
RCL1
ECgene alternative splicing isoforms for
RCL1

Expression for RCL1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RCL1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RCL1 Gene

This gene is overexpressed in Liver (x5.2) and Pancreas (x4.7).

Protein differential expression in normal tissues from HIPED for RCL1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (18.2), Lung (10.2), and CD8 Tcells (6.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for RCL1 Gene



Protein tissue co-expression partners for RCL1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RCL1 Gene:

RCL1

SOURCE GeneReport for Unigene cluster for RCL1 Gene:

Hs.194121

Evidence on tissue expression from TISSUES for RCL1 Gene

  • Blood(4.3)
  • Eye(4.1)
genes like me logo Genes that share expression patterns with RCL1: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RCL1 Gene

Orthologs for RCL1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for RCL1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RCL1 33 34
  • 99.02 (n)
dog
(Canis familiaris)
Mammalia RCL1 33 34
  • 91.42 (n)
cow
(Bos Taurus)
Mammalia RCL1 33 34
  • 91.33 (n)
oppossum
(Monodelphis domestica)
Mammalia RCL1 34
  • 89 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rcl1 33
  • 88.78 (n)
mouse
(Mus musculus)
Mammalia Rcl1 33 16 34
  • 88.56 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RCL1 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves RCL1 33 34
  • 77.51 (n)
lizard
(Anolis carolinensis)
Reptilia RCL1 34
  • 85 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rcl1 33
  • 68.55 (n)
African clawed frog
(Xenopus laevis)
Amphibia MGC53171 33
zebrafish
(Danio rerio)
Actinopterygii rcl1 33 34
  • 68.12 (n)
Dr.6949 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9982 33
fruit fly
(Drosophila melanogaster)
Insecta Rtc1 33 34
  • 56.85 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010498 33
  • 55.83 (n)
worm
(Caenorhabditis elegans)
Secernentea ZK1127.5 33 34
  • 53.08 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C05984g 33
  • 47.54 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RCL1 33 34 36
  • 47.14 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL015W 33
  • 46.89 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G22100 33
  • 50.7 (n)
rice
(Oryza sativa)
Liliopsida Os03g0833700 33
  • 51.79 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC12G12.06c 33
  • 49.81 (n)
Species where no ortholog for RCL1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RCL1 Gene

ENSEMBL:
Gene Tree for RCL1 (if available)
TreeFam:
Gene Tree for RCL1 (if available)

Paralogs for RCL1 Gene

Paralogs for RCL1 Gene

Pseudogenes.org Pseudogenes for RCL1 Gene

genes like me logo Genes that share paralogs with RCL1: view

Variants for RCL1 Gene

Sequence variations from dbSNP and Humsavar for RCL1 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs1000002375 -- 4,823,221(+) GAAGA(A/G)TAGGT intron-variant
rs1000045818 -- 4,856,653(+) AAGAT(C/G/T)GTTTG intron-variant
rs1000086453 -- 4,805,387(+) CTAAA(-/AAG)AAGAA intron-variant
rs1000101938 -- 4,849,946(+) AGGAT(A/G)TGAGC intron-variant, upstream-variant-2KB
rs1000124662 -- 4,860,976(+) GTGAT(A/G)TAAGT utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for RCL1 Gene

Variant ID Type Subtype PubMed ID
esv2738158 CNV deletion 23290073
nsv6459 CNV insertion 18451855
nsv824824 CNV loss 20364138

Variation tolerance for RCL1 Gene

Residual Variation Intolerance Score: 61.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.05; 50.40% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RCL1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RCL1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RCL1 Gene

Disorders for RCL1 Gene

Relevant External Links for RCL1

Genetic Association Database (GAD)
RCL1
Human Genome Epidemiology (HuGE) Navigator
RCL1
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RCL1

No disorders were found for RCL1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for RCL1 Gene

Publications for RCL1 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 45 60
  2. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PMID: 19862010) Ganesh SK … Lin JP (Nature genetics 2009) 3 45 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. DNA sequence and analysis of human chromosome 9. (PMID: 15164053) Humphray SJ … Dunham I (Nature 2004) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for RCL1 Gene

Sources for RCL1 Gene

Content
Loading form....