Human Gene RCL1 (uc003zis.2)
  Description: Homo sapiens RNA terminal phosphate cyclase-like 1 (RCL1), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr9:4,792,834-4,861,064 Size: 68,231 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr9:4,793,092-4,860,275 Size: 67,184 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr9:4,792,834-4,861,064)mRNA (may differ from genome)Protein (373 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RCL1_HUMAN
DESCRIPTION: RecName: Full=RNA 3'-terminal phosphate cyclase-like protein;
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).
SUBCELLULAR LOCATION: Nucleus, nucleolus (By similarity).
SIMILARITY: Belongs to the RNA 3'-terminal cyclase family. Type 2 subfamily.
SEQUENCE CAUTION: Sequence=AAD32456.1; Type=Frameshift; Positions=13, 58;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): RCL1
CDC HuGE Published Literature: RCL1
Positive Disease Associations: Colitis, Ulcerative , Crohn Disease , Erythrocyte Indices , Exercise Test , Heart Failure , Hemoglobin A, Glycosylated , mean corpuscular hemoglobin , mean corpuscular volume
Related Studies:
  1. Colitis, Ulcerative
    Dermot P B McGovern et al. Nature genetics 2010, Genome-wide association identifies multiple ulcerative colitis susceptibility loci., Nature genetics. [PubMed 20228799]
  2. Colitis, Ulcerative
    Carl A Anderson et al. Nature genetics 2011, Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47., Nature genetics. [PubMed 21297633]
  3. Crohn Disease
    Jeffrey C Barrett et al. Nature genetics 2008, Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease., Nature genetics. [PubMed 18587394]
           more ... click here to view the complete list

-  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: 14.07 RPKM in Liver
Total median expression: 199.12 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -127.30258-0.493 Picture PostScript Text
3' UTR -231.60789-0.294 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
IPR023797 - RNA3'_phos_cyclase_dom
IPR000228 - RNA3'_term_phos_cyc
IPR016443 - RNA3'_term_phos_cyc_type_2
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:
55205 - EPT/RTPC-like

ModBase Predicted Comparative 3D Structure on Q9Y2P8
FrontTopSide
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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsemblFlyBaseWormBaseSGD
 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004521 endoribonuclease activity
GO:0003963 RNA-3'-phosphate cyclase activity

Biological Process:
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)
GO:0000479 endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0008150 biological_process
GO:0042254 ribosome biogenesis

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AK022904 - Homo sapiens cDNA FLJ12842 fis, clone NT2RP2003286, weakly similar to PROBABLE RNA 3'-TERMINAL PHOSPHATE CYCLASE (EC 6.5.1.4).
BC001025 - Homo sapiens RNA terminal phosphate cyclase-like 1, mRNA (cDNA clone MGC:1390 IMAGE:3343468), complete cds.
AK225872 - Homo sapiens mRNA for RNA 3'-terminal phosphate cyclase-like protein variant, clone: FCC124C05.
JF432531 - Synthetic construct Homo sapiens clone IMAGE:100073753 RNA terminal phosphate cyclase-like 1 (RCL1) gene, encodes complete protein.
KJ892945 - Synthetic construct Homo sapiens clone ccsbBroadEn_02339 RCL1 gene, encodes complete protein.
EU831474 - Synthetic construct Homo sapiens clone HAIB:100066503; DKFZo008G0417 RNA terminal phosphate cyclase-like 1 protein (RCL1) gene, encodes complete protein.
EU831561 - Synthetic construct Homo sapiens clone HAIB:100066590; DKFZo004G0418 RNA terminal phosphate cyclase-like 1 protein (RCL1) gene, encodes complete protein.
AJ276894 - Homo sapiens mRNA for RNA 3'-terminal phosphate cyclase-like protein (rcl1 gene).
AF067172 - Homo sapiens RNA cyclase homolog mRNA, complete cds.
AF161456 - Homo sapiens HSPC338 mRNA, partial cds.
EF553527 - Homo sapiens clone DKFZp781H0277 RCL1 (RCL1) mRNA, complete cds.
JD303771 - Sequence 284795 from Patent EP1572962.
JD203595 - Sequence 184619 from Patent EP1572962.
JD458607 - Sequence 439631 from Patent EP1572962.
JD142630 - Sequence 123654 from Patent EP1572962.
JD055448 - Sequence 36472 from Patent EP1572962.
JD126659 - Sequence 107683 from Patent EP1572962.
JD124036 - Sequence 105060 from Patent EP1572962.
AK021739 - Homo sapiens cDNA FLJ11677 fis, clone HEMBA1004778.
JD149769 - Sequence 130793 from Patent EP1572962.
JD293054 - Sequence 274078 from Patent EP1572962.
JD320340 - Sequence 301364 from Patent EP1572962.
JD065258 - Sequence 46282 from Patent EP1572962.
JD429222 - Sequence 410246 from Patent EP1572962.
JD537568 - Sequence 518592 from Patent EP1572962.
JD423422 - Sequence 404446 from Patent EP1572962.
JD200930 - Sequence 181954 from Patent EP1572962.
JD200929 - Sequence 181953 from Patent EP1572962.
JD360565 - Sequence 341589 from Patent EP1572962.
JD346965 - Sequence 327989 from Patent EP1572962.
JD206997 - Sequence 188021 from Patent EP1572962.
JD163107 - Sequence 144131 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y2P8 (Reactome details) participates in the following event(s):

R-HSA-6790906 EMG1 of the SSU processome methylates pseudouridine-1248 of 18S rRNA yielding N(1)-methylpseudouridine-1248
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-6790901 rRNA modification in the nucleus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: D3DRI2, HSPC338, NM_005772, NP_005763, Q5VYW9, Q9H9D0, Q9NY00, Q9P044, Q9Y2P8, RCL1_HUMAN, RNAC, RPC2, RPCL1, RTC2
UCSC ID: uc003zis.2
RefSeq Accession: NM_005772
Protein: Q9Y2P8 (aka RCL1_HUMAN)
CCDS: CCDS6456.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005772.3
exon count: 9CDS single in 3' UTR: no RNA size: 2169
ORF size: 1122CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2444.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.