Human Gene RTCB (uc003amm.2)
  Description: Homo sapiens RNA 2',3'-cyclic phosphate and 5'-OH ligase (RTCB), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr22:32,783,562-32,808,274 Size: 24,713 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr22:32,783,979-32,808,143 Size: 24,165 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:32,783,562-32,808,274)mRNA (may differ from genome)Protein (505 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHPRDMGIneXtProtOMIM
PubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RTCB_HUMAN
DESCRIPTION: RecName: Full=tRNA-splicing ligase RtcB homolog; EC=6.5.1.3;
FUNCTION: Catalytic subunit of the tRNA-splicing ligase complex that acts by directly joining spliced tRNA halves to mature-sized tRNAs by incorporating the precursor-derived splice junction phosphate into the mature tRNA as a canonical 3',5'- phosphodiester. May act as a RNA ligase with broad substrate specificity, and may function toward other RNAs.
CATALYTIC ACTIVITY: ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m).
SUBUNIT: Catalytic component of the tRNA-splicing ligase complex.
SUBCELLULAR LOCATION: Cytoplasm (By similarity).
SIMILARITY: Belongs to the RtcB family.
SEQUENCE CAUTION: Sequence=AAF29081.1; Type=Frameshift; Positions=295, 298; Sequence=AAF67477.1; Type=Frameshift; Positions=173, 180;

-  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

+  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: 52.87 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 1504.35 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 -48.10131-0.367 Picture PostScript Text
3' UTR -140.80417-0.338 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
IPR001233 - RtcB_family

Pfam Domains:
PF01139 - tRNA-splicing ligase RtcB

SCOP Domains:
103365 - Hypothetical protein PH1602

ModBase Predicted Comparative 3D Structure on Q9Y3I0
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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 orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsemblFlyBaseWormBase 
 Protein SequenceProtein SequenceProtein SequenceProtein Sequence 
 AlignmentAlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0003972 RNA ligase (ATP) activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008452 RNA ligase activity
GO:0016874 ligase activity
GO:0017166 vinculin binding
GO:0046872 metal ion binding

Biological Process:
GO:0001701 in utero embryonic development
GO:0001890 placenta development
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
GO:0006396 RNA processing
GO:0008033 tRNA processing

Cellular Component:
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005789 endoplasmic reticulum membrane
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle
GO:0072669 tRNA-splicing ligase complex


-  Descriptions from all associated GenBank mRNAs
  LF208842 - JP 2014500723-A/16345: Polycomb-Associated Non-Coding RNAs.
LF384682 - JP 2014500723-A/192185: Polycomb-Associated Non-Coding RNAs.
BC002970 - Homo sapiens chromosome 22 open reading frame 28, mRNA (cDNA clone MGC:1849 IMAGE:3533883), complete cds.
AL050255 - Novel gene similar to C. elegens hypothetical 55.2 KD protein F16A11.2, SW:P90838.
BC000151 - Homo sapiens chromosome 22 open reading frame 28, mRNA (cDNA clone MGC:5036 IMAGE:2984824), complete cds.
AL137272 - Homo sapiens mRNA; cDNA DKFZp434I1614 (from clone DKFZp434I1614).
BC016707 - Homo sapiens chromosome 22 open reading frame 28, mRNA (cDNA clone MGC:23730 IMAGE:4102148), complete cds.
AF161466 - Homo sapiens HSPC117 mRNA, complete cds.
JD066320 - Sequence 47344 from Patent EP1572962.
BC010308 - Homo sapiens chromosome 22 open reading frame 28, mRNA (cDNA clone MGC:5037 IMAGE:3451576), complete cds.
AF155658 - Homo sapiens putative 55 kDa protein mRNA, complete cds.
JD223525 - Sequence 204549 from Patent EP1572962.
LF323309 - JP 2014500723-A/130812: Polycomb-Associated Non-Coding RNAs.
JD110301 - Sequence 91325 from Patent EP1572962.
AK297826 - Homo sapiens cDNA FLJ58027 complete cds.
JD549533 - Sequence 530557 from Patent EP1572962.
JD279733 - Sequence 260757 from Patent EP1572962.
LF323310 - JP 2014500723-A/130813: Polycomb-Associated Non-Coding RNAs.
JD278850 - Sequence 259874 from Patent EP1572962.
JD229586 - Sequence 210610 from Patent EP1572962.
JD094182 - Sequence 75206 from Patent EP1572962.
JD059210 - Sequence 40234 from Patent EP1572962.
JD539432 - Sequence 520456 from Patent EP1572962.
JD419797 - Sequence 400821 from Patent EP1572962.
JD380195 - Sequence 361219 from Patent EP1572962.
CR456450 - Homo sapiens dJ149A16.6 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.dJ149A16.6).
AK297908 - Homo sapiens cDNA FLJ57752 complete cds.
JD245918 - Sequence 226942 from Patent EP1572962.
LF323311 - JP 2014500723-A/130814: Polycomb-Associated Non-Coding RNAs.
DQ890931 - Synthetic construct clone IMAGE:100003561; FLH167620.01X; RZPDo839D0390D chromosome 22 open reading frame 28 (C22orf28) gene, encodes complete protein.
CU013001 - Homo sapiens dJ149A16.6, mRNA (cDNA clone IMAGE:100000163), complete cds, with stop codon, in Gateway system.
AK312503 - Homo sapiens cDNA, FLJ92867.
KJ898904 - Synthetic construct Homo sapiens clone ccsbBroadEn_08298 C22orf28 gene, encodes complete protein.
KJ906173 - Synthetic construct Homo sapiens clone ccsbBroadEn_15843 C22orf28 gene, encodes complete protein.
KJ906174 - Synthetic construct Homo sapiens clone ccsbBroadEn_15844 C22orf28 gene, encodes complete protein.
AB527121 - Synthetic construct DNA, clone: pF1KE0338, Homo sapiens C22orf28 gene for chromosome 22 open reading frame 28, without stop codon, in Flexi system.
CU013289 - Homo sapiens dJ149A16.6, mRNA (cDNA clone IMAGE:100000067), complete cds, without stop codon, in Gateway system.
DQ894092 - Synthetic construct Homo sapiens clone IMAGE:100008552; FLH167616.01L; RZPDo839D0389D chromosome 22 open reading frame 28 (C22orf28) gene, encodes complete protein.
CR457175 - Homo sapiens full open reading frame cDNA clone RZPDo834B0912D for gene HSPC117, hypothetical protein HSPC117; complete cds, incl. stopcodon.
LF323313 - JP 2014500723-A/130816: Polycomb-Associated Non-Coding RNAs.
LF323314 - JP 2014500723-A/130817: Polycomb-Associated Non-Coding RNAs.
LF323315 - JP 2014500723-A/130818: Polycomb-Associated Non-Coding RNAs.
CU677691 - Synthetic construct Homo sapiens gateway clone IMAGE:100017378 5' read C22orf28 mRNA.
CU678324 - Synthetic construct Homo sapiens gateway clone IMAGE:100017377 5' read C22orf28 mRNA.
AK301945 - Homo sapiens cDNA FLJ57223 complete cds.
LF323316 - JP 2014500723-A/130819: Polycomb-Associated Non-Coding RNAs.
LF323319 - JP 2014500723-A/130822: Polycomb-Associated Non-Coding RNAs.
LF323321 - JP 2014500723-A/130824: Polycomb-Associated Non-Coding RNAs.
LF323323 - JP 2014500723-A/130826: Polycomb-Associated Non-Coding RNAs.
MA620259 - JP 2018138019-A/192185: Polycomb-Associated Non-Coding RNAs.
MA558886 - JP 2018138019-A/130812: Polycomb-Associated Non-Coding RNAs.
MA558887 - JP 2018138019-A/130813: Polycomb-Associated Non-Coding RNAs.
MA558888 - JP 2018138019-A/130814: Polycomb-Associated Non-Coding RNAs.
MA558890 - JP 2018138019-A/130816: Polycomb-Associated Non-Coding RNAs.
MA558891 - JP 2018138019-A/130817: Polycomb-Associated Non-Coding RNAs.
MA558892 - JP 2018138019-A/130818: Polycomb-Associated Non-Coding RNAs.
MA558893 - JP 2018138019-A/130819: Polycomb-Associated Non-Coding RNAs.
MA558896 - JP 2018138019-A/130822: Polycomb-Associated Non-Coding RNAs.
MA558898 - JP 2018138019-A/130824: Polycomb-Associated Non-Coding RNAs.
MA558900 - JP 2018138019-A/130826: Polycomb-Associated Non-Coding RNAs.
MA444419 - JP 2018138019-A/16345: Polycomb-Associated Non-Coding RNAs.

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

Protein Q9Y3I0 (Reactome details) participates in the following event(s):

R-HSA-5696816 tRNA ligase complex ligates tRNA exons
R-HSA-6784531 tRNA processing in the nucleus
R-HSA-72306 tRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: B2R6A8, C22orf28, HSPC117, NM_014306, NP_055121, Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3, Q9Y3I0, RTCB_HUMAN
UCSC ID: uc003amm.2
RefSeq Accession: NM_014306
Protein: Q9Y3I0 (aka RTCB_HUMAN)
CCDS: CCDS13905.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014306.4
exon count: 12CDS single in 3' UTR: no RNA size: 2081
ORF size: 1518CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3236.00frame shift in genome: no % Coverage: 99.28
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.