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Aliases for RTCA Gene

Aliases for RTCA Gene

  • RNA 3'-Terminal Phosphate Cyclase 2
  • RNA 3-Terminal Phosphate Cyclase 2 3 5
  • RNA Terminal Phosphate Cyclase Domain-Containing Protein 1 3 4
  • RNA Terminal Phosphate Cyclase Domain 1 2 3
  • RTC Domain-Containing Protein 1 3 4
  • RTCD1 3 4
  • RTC1 3 4
  • RPC 3 4
  • RTC Domain Containing 1 2
  • RNA-3-Phosphate Cyclase 4
  • RNA Cyclase 4
  • EC 6.5.1.4 4
  • RPC1 4

External Ids for RTCA Gene

Previous HGNC Symbols for RTCA Gene

  • RTCD1

Previous GeneCards Identifiers for RTCA Gene

  • GC01P100732

Summaries for RTCA Gene

Entrez Gene Summary for RTCA Gene

  • This gene encodes a member of the RNA 3'-phosphate cyclase family. The encoded protein plays a role in RNA metabolism by catalyzing the ATP-dependent conversion of the 3'-phosphate of RNA substrates to a 2',3'-cyclic phosphodiester. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

GeneCards Summary for RTCA Gene

RTCA (RNA 3'-Terminal Phosphate Cyclase) is a Protein Coding gene. GO annotations related to this gene include poly(A) RNA binding and RNA-3-phosphate cyclase activity. An important paralog of this gene is RCL1.

UniProtKB/Swiss-Prot for RTCA Gene

  • Catalyzes the conversion of 3-phosphate to a 2,3-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3P to produce RNA-N3PP5A; (C) and attack of the adjacent 2-hydroxyl on the 3-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTCA Gene

Genomics for RTCA Gene

Regulatory Elements for RTCA Gene

Enhancers for RTCA 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
GH01G100265 1.1 ENCODE 24.4 +0.2 184 2.6 HDGF FOXA2 ARNT AGO1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 RTCA RTCA-AS1 GC01P100282
GH01G100248 1.1 ENCODE 24 -16.5 -16515 2.0 HDGF PKNOX1 MLX ARNT WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 RTCA FRRS1 DBT ENSG00000230287
GH01G100046 1.6 FANTOM5 Ensembl ENCODE 12.3 -217.7 -217709 4.5 PKNOX1 FOXA2 WRNIP1 ZNF133 ARID4B YY1 TCF12 ELK1 ZNF202 SP5 LRRC39 RTCA SASS6 FRRS1 MFSD14A ENSG00000241073
GH01G100036 1.4 ENCODE dbSUPER 11.6 -227.4 -227432 4.1 FOXA2 MLX CREB3L1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 MFSD14A LRRC39 SLC30A7 SASS6 BRI3P1 RTCA AGL ENSG00000241073
GH01G100130 1.2 ENCODE 12.4 -134.1 -134090 4.1 CREB3L1 DMAP1 YY1 ZNF143 SP3 NFYC ZNF610 GLIS1 NBN NR2C1 RTCA SASS6 SLC35A3 ENSG00000226952
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTCA on UCSC Golden Path with GeneCards custom track

Promoters for RTCA Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000010621 242 2001 HDGF FOXA2 ARNT AGO1 WRNIP1 ARID4B SIN3A DMAP1 ZNF2 YY1

Genomic Location for RTCA Gene

Chromosome:
1
Start:
100,266,158 bp from pter
End:
100,292,769 bp from pter
Size:
26,612 bases
Orientation:
Plus strand

Genomic View for RTCA Gene

Genes around RTCA on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RTCA Gene

Proteins for RTCA Gene

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

    Protein Symbol:
    O00442-RTCA_HUMAN
    Recommended name:
    RNA 3-terminal phosphate cyclase
    Protein Accession:
    O00442
    Secondary Accessions:
    • Q5VVL5
    • Q5VVL6
    • Q96E99

    Protein attributes for RTCA Gene

    Size:
    366 amino acids
    Molecular mass:
    39337 Da
    Quaternary structure:
    • Monomer.

    Alternative splice isoforms for RTCA Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RTCA Gene

Post-translational modifications for RTCA Gene

  • Ubiquitination at Lys163
  • Modification sites at PhosphoSitePlus

Other Protein References for RTCA Gene

No data available for DME Specific Peptides for RTCA Gene

Domains & Families for RTCA Gene

Suggested Antigen Peptide Sequences for RTCA Gene

Graphical View of Domain Structure for InterPro Entry

O00442

UniProtKB/Swiss-Prot:

RTCA_HUMAN :
  • Belongs to the RNA 3-terminal cyclase family. Type 1 subfamily.
Family:
  • Belongs to the RNA 3-terminal cyclase family. Type 1 subfamily.
genes like me logo Genes that share domains with RTCA: view

No data available for Gene Families for RTCA Gene

Function for RTCA Gene

Molecular function for RTCA Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + (RNA)-3-(3-phospho-ribonucleoside) = AMP + diphosphate + (RNA)-3-(2,3-cyclophospho)-ribonucleoside.
UniProtKB/Swiss-Prot Function:
Catalyzes the conversion of 3-phosphate to a 2,3-cyclic phosphodiester at the end of RNA. The mechanism of action of the enzyme occurs in 3 steps: (A) adenylation of the enzyme by ATP; (B) transfer of adenylate to an RNA-N3P to produce RNA-N3PP5A; (C) and attack of the adjacent 2-hydroxyl on the 3-phosphorus in the diester linkage to produce the cyclic end product. The biological role of this enzyme is unknown but it is likely to function in some aspects of cellular RNA processing.

Enzyme Numbers (IUBMB) for RTCA Gene

Gene Ontology (GO) - Molecular Function for RTCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0003824 catalytic activity IEA --
GO:0003963 RNA-3-phosphate cyclase activity IEA --
GO:0005524 ATP binding IEA --
GO:0016874 ligase activity IEA --
genes like me logo Genes that share ontologies with RTCA: view
genes like me logo Genes that share phenotypes with RTCA: view

Animal Models for RTCA Gene

MGI Knock Outs for RTCA:
  • Rtca tm1a(EUCOMM)Hmgu

Animal Model Products

Inhibitory RNA Products

Clone Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for RTCA Gene

Localization for RTCA Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTCA Gene

Nucleus, nucleoplasm.

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 RTCA gene
Compartment Confidence
nucleus 5
mitochondrion 2
extracellular 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for RTCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,IEA --
genes like me logo Genes that share ontologies with RTCA: view

Pathways & Interactions for RTCA Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTCA Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with RTCA: view

No data available for Pathways by source and SIGNOR curated interactions for RTCA Gene

Drugs & Compounds for RTCA Gene

(3) Drugs for RTCA Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0

(2) Additional Compounds for RTCA Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N-Acetyl-9-O-acetylneuraminic acid
  • 9-O-Acetyl-N-acetylneuraminate
  • 9-O-Acetyl-N-acetylneuraminic acid
  • N,9-O-Diacetylneuraminate
  • N,9-O-Diacetylneuraminic acid
  • N-Acetyl-9-O-acetylneuraminate
55717-54-9
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with RTCA: view

Transcripts for RTCA Gene

Unigene Clusters for RTCA Gene

RNA 3-terminal phosphate cyclase:
Representative Sequences:

Inhibitory RNA Products

Clone Products

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

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12
SP1: - - -
SP2: - - - -
SP3: - - -
SP4: - -
SP5: -

Relevant External Links for RTCA Gene

GeneLoc Exon Structure for
RTCA
ECgene alternative splicing isoforms for
RTCA

Expression for RTCA Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RTCA Gene

This gene is overexpressed in Peripheral blood mononuclear cells (11.9).

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



Protein tissue co-expression partners for RTCA Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTCA Gene:

RTCA

SOURCE GeneReport for Unigene cluster for RTCA Gene:

Hs.484222

mRNA Expression by UniProt/SwissProt for RTCA Gene:

O00442-RTCA_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for RTCA Gene

  • Nervous system(4.3)
  • Blood(4.1)
  • Gall bladder(2)
genes like me logo Genes that share expression patterns with RTCA: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RTCA Gene

Orthologs for RTCA Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for RTCA Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RTCD1 34
  • 99.38 (n)
RTCA 35
  • 99 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RTCA 34 35
  • 92.81 (n)
dog
(Canis familiaris)
Mammalia RTCA 34 35
  • 92.62 (n)
oppossum
(Monodelphis domestica)
Mammalia RTCA 35
  • 90 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rtcd1 34
  • 86.52 (n)
mouse
(Mus musculus)
Mammalia Rtca 34 16 35
  • 85.79 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RTCA 35
  • 85 (a)
OneToOne
chicken
(Gallus gallus)
Aves RTCA 34 35
  • 78.9 (n)
lizard
(Anolis carolinensis)
Reptilia RTCA 35
  • 82 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rtca 34
  • 68.61 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.7944 34
zebrafish
(Danio rerio)
Actinopterygii rtca 34 35
  • 67.77 (n)
sbcb158 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.10661 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004820 34
  • 52.27 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG4061 34 35
  • 46.5 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RCL1 35
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 53 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5419 34
Species where no ortholog for RTCA was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • 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)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for RTCA Gene

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

Paralogs for RTCA Gene

Paralogs for RTCA Gene

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

Variants for RTCA Gene

Sequence variations from dbSNP and Humsavar for RTCA Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000150682 -- 100,280,849(+) ATACA(A/G)AAATT intron-variant, upstream-variant-2KB
rs1000162035 -- 100,281,423(+) ATGAT(A/G)TTGGA intron-variant, downstream-variant-500B
rs1000171084 -- 100,270,214(+) TTTTA(G/T)TTTTA intron-variant
rs1000487267 -- 100,282,517(+) AGCAC(G/T)TAATT intron-variant
rs1000541523 -- 100,268,926(+) GCTCA(C/T)GCCTG intron-variant

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

Variant ID Type Subtype PubMed ID
esv3586936 CNV loss 21293372
nsv522987 CNV gain 19592680
nsv524345 CNV loss 19592680

Variation tolerance for RTCA Gene

Residual Variation Intolerance Score: 60.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.37; 42.06% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTCA Gene

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

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

Disorders for RTCA Gene

Relevant External Links for RTCA

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTCA

No disorders were found for RTCA Gene.

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

Publications for RTCA Gene

  1. The human RNA 3'-terminal phosphate cyclase is a member of a new family of proteins conserved in Eucarya, Bacteria and Archaea. (PMID: 9184239) Genschik P. … Filipowicz W. (EMBO J. 1997) 2 3 4 64
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  3. RNA 3'-terminal phosphate cyclase from HeLa cells. (PMID: 2199762) Filipowicz W. … Vincente O. (Methods Enzymol. 1990) 3 4 64
  4. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 64
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3 64

Products for RTCA Gene

Sources for RTCA Gene

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