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
Data last updated at UCSC: 2013-06-14
Sequence and Links to Tools and Databases
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
Comparative Toxicogenomics Database (CTD)
The following chemicals interact with this gene
Common Gene Haplotype Alleles
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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
Microarray Expression Data
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mRNA Secondary Structure of 3' and 5' UTRs
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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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.
Gene Ontology (GO) Annotations with Structured Vocabulary
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
Other Names for This Gene
Alternate Gene Symbols: B2R6A8, C22orf28, HSPC117, NM_014306, NP_055121, Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3, Q9Y3I0, RTCB_HUMANUCSC ID: uc003amm.2RefSeq 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:
12 CDS single in 3' UTR:
no
RNA size:
2081
ORF size:
1518 CDS single in intron:
no
Alignment % ID:
100.00
txCdsPredict score:
3236.00 frame 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
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Methods, Credits, and Use Restrictions
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for details on how this gene model was made and data restrictions if any.