Human Gene RTCA (ENST00000260563.4_1) from GENCODE V47lift37
  Description: RNA 3'-terminal phosphate cyclase, transcript variant 1 (from RefSeq NM_001130841.2)
Gencode Transcript: ENST00000260563.4_1
Gencode Gene: ENSG00000137996.13_6
Transcript (Including UTRs)
   Position: hg19 chr1:100,731,805-100,757,327 Size: 25,523 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr1:100,731,932-100,757,060 Size: 25,129 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:100,731,805-100,757,327)mRNA (may differ from genome)Protein (379 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RTCA_HUMAN
DESCRIPTION: RecName: Full=RNA 3'-terminal phosphate cyclase; Short=RNA cyclase; Short=RNA-3'-phosphate cyclase; EC=6.5.1.4; AltName: Full=RNA terminal phosphate cyclase domain-containing protein 1; Short=RTC domain-containing protein 1;
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-N3'P to produce RNA- N3'PP5'A; (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.
CATALYTIC ACTIVITY: ATP + RNA 3'-terminal-phosphate = AMP + diphosphate + RNA terminal-2',3'-cyclic-phosphate.
SUBUNIT: Monomer.
SUBCELLULAR LOCATION: Nucleus, nucleoplasm.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the RNA 3'-terminal cyclase family. Type 1 subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.05 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 455.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.70127-0.383 Picture PostScript Text
3' UTR -46.00267-0.172 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013791 - RNA3'-term_phos_cycl_insert
IPR023797 - RNA3'_phos_cyclase_dom
IPR000228 - RNA3'_term_phos_cyc
IPR017770 - RNA3'_term_phos_cyc_type_1
IPR020719 - RNA3'_term_phos_cycl-like_CS
IPR013796 - RNA3'_term_phos_cycl_insert
IPR013792 - RNA3'P_cycl/enolpyr_Trfase_a/b

Pfam Domains:
PF01137 - RNA 3'-terminal phosphate cyclase
PF05189 - RNA 3'-terminal phosphate cyclase (RTC), insert domain

SCOP Domains:
52913 - RNA 3'-terminal phosphate cyclase, RPTC, insert domain
55205 - EPT/RTPC-like

ModBase Predicted Comparative 3D Structure on O00442
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003824 catalytic activity
GO:0003963 RNA-3'-phosphate cyclase activity
GO:0005524 ATP binding
GO:0016874 ligase activity

Biological Process:
GO:0006396 RNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  JF432517 - Synthetic construct Homo sapiens clone IMAGE:100073739 RNA terminal phosphate cyclase domain 1 (RTCD1) gene, encodes complete protein.
KJ897883 - Synthetic construct Homo sapiens clone ccsbBroadEn_07277 RTCD1 gene, encodes complete protein.
AK299793 - Homo sapiens cDNA FLJ54857 complete cds, highly similar to RNA 3'-terminal phosphate cyclase (EC 6.5.1.4).
LF383830 - JP 2014500723-A/191333: Polycomb-Associated Non-Coding RNAs.
AK309394 - Homo sapiens cDNA, FLJ99435.
Y11651 - H.sapiens mRNA for phosphate cyclase.
AK292366 - Homo sapiens cDNA FLJ76936 complete cds, highly similar to Homo sapiens RNA terminal phosphate cyclase domain 1 (RTCD1), mRNA.
AK307445 - Homo sapiens cDNA, FLJ97393.
BC012604 - Homo sapiens RNA terminal phosphate cyclase domain 1, mRNA (cDNA clone MGC:13604 IMAGE:4281547), complete cds.
LF353144 - JP 2014500723-A/160647: Polycomb-Associated Non-Coding RNAs.
JD020621 - Sequence 1645 from Patent EP1572962.
LF353138 - JP 2014500723-A/160641: Polycomb-Associated Non-Coding RNAs.
LF353135 - JP 2014500723-A/160638: Polycomb-Associated Non-Coding RNAs.
JD428881 - Sequence 409905 from Patent EP1572962.
JD468040 - Sequence 449064 from Patent EP1572962.
MA619407 - JP 2018138019-A/191333: Polycomb-Associated Non-Coding RNAs.
MA588721 - JP 2018138019-A/160647: Polycomb-Associated Non-Coding RNAs.
MA588715 - JP 2018138019-A/160641: Polycomb-Associated Non-Coding RNAs.
MA588712 - JP 2018138019-A/160638: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000260563.1, ENST00000260563.2, ENST00000260563.3, NM_001130841, O00442, Q5VVL5, Q5VVL6, Q96E99, RPC, RPC1, RTC1, RTCA_HUMAN, RTCD1, uc317gku.1
UCSC ID: ENST00000260563.4_1
RefSeq Accession: NM_001130841.2
Protein: O00442 (aka RTCA_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.