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Aliases for RTCB Gene

Aliases for RTCB Gene

  • RNA 2',3'-Cyclic Phosphate And 5'-OH Ligase 2
  • C22orf28 3 4 6
  • RNA 2,3-Cyclic Phosphate And 5-OH Ligase 2 3
  • Focal Adhesion-Associated Protein 2 3
  • HSPC117 3 6
  • Chromosome 22 Open Reading Frame 28 2
  • TRNA-Splicing Ligase RtcB Homolog 3
  • Ankyrin Repeat Domain 54 3
  • DJ149A16.6 3
  • EC 6.5.1.3 4
  • FAAP 3

External Ids for RTCB Gene

Previous Symbols for RTCB Gene

  • C22orf28

Summaries for RTCB Gene

GeneCards Summary for RTCB Gene

RTCB (RNA 2',3'-Cyclic Phosphate And 5'-OH Ligase) is a Protein Coding gene. GO annotations related to this gene include vinculin binding and RNA ligase (ATP) activity.

UniProtKB/Swiss-Prot for RTCB Gene

  • 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 an RNA ligase with broad substrate specificity, and may function toward other RNAs.

No data available for Entrez Gene Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RTCB Gene

Genomics for RTCB Gene

Genomic Location for RTCB Gene

Start:
32,387,575 bp from pter
End:
32,412,287 bp from pter
Size:
24,713 bases
Orientation:
Minus strand

Genomic View for RTCB Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for RTCB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTCB Gene

No data available for Regulatory Elements for RTCB Gene

Proteins for RTCB Gene

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

    Protein Symbol:
    Q9Y3I0-RTCB_HUMAN
    Recommended name:
    tRNA-splicing ligase RtcB homolog
    Protein Accession:
    Q9Y3I0
    Secondary Accessions:
    • B2R6A8
    • Q6IAI0
    • Q9BWL4
    • Q9NTH1
    • Q9P037
    • Q9P0J3

    Protein attributes for RTCB Gene

    Size:
    505 amino acids
    Molecular mass:
    55210 Da
    Cofactor:
    Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Note=Binds 2 manganese ions per subunit.;
    Quaternary structure:
    • Catalytic component of the tRNA-splicing ligase complex.
    Miscellaneous:
    • Ligation probably proceeds through 3 nucleotidyl transfer steps, with 2,3-cyclic phosphate termini being hydrolyzed to 3-P termini in a step that precedes 3-P activation with GMP. In the first nucleotidyl transfer step, RTCB reacts with GTP to form a covalent RTCB-histidine-GMP intermediate with release of PPi; in the second step, the GMP moiety is transferred to the RNA 3-P; in the third step, the 5-OH from the opposite RNA strand attacks the activated 3-P to form a 3,5-phosphodiester bond and release GMP (PubMed:24870230).
    SequenceCaution:
    • Sequence=AAF29081.1; Type=Frameshift; Positions=295, 298; Evidence={ECO:0000305}; Sequence=AAF67477.1; Type=Frameshift; Positions=173, 180; Evidence={ECO:0000305};

neXtProt entry for RTCB Gene

Proteomics data for RTCB Gene at MOPED

Post-translational modifications for RTCB Gene

  • Modification sites at PhosphoSitePlus
  • Ubiquitination at Lys67, Lys140, Lys206, Lys308, and Lys496

Other Protein References for RTCB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTCB Gene

Domains for RTCB Gene

Protein Domains for RTCB Gene

UniProtKB/Swiss-Prot:

RTCB_HUMAN
Family:
  • Belongs to the RtcB family.:
    • Q9Y3I0
genes like me logo Genes that share domains with RTCB: view

No data available for Gene Families for RTCB Gene

Function for RTCB Gene

Molecular function for RTCB Gene

UniProtKB/Swiss-Prot CatalyticActivity: ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m).
UniProtKB/Swiss-Prot 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 an RNA ligase with broad substrate specificity, and may function toward other RNAs.

Enzyme Numbers (IUBMB) for RTCB Gene

Gene Ontology (GO) - Molecular Function for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003972 RNA ligase (ATP) activity IMP 24870230
GO:0005524 ATP binding IEA --
GO:0008452 RNA ligase activity --
GO:0017166 vinculin binding IPI 15163412
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with RTCB: view

miRNA for RTCB Gene

miRTarBase miRNAs that target RTCB

No data available for Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for RTCB Gene

Localization for RTCB Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTCB Gene

Nucleus. Cytoplasm. Note=Enters into the nucleus in case of active transcription while it accumulates in cytosol when transcription level is low. {ECO:0000269 PubMed:24608264}.

Gene Ontology (GO) - Cellular Components for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 24608264
GO:0005635 nuclear envelope IDA 25087875
GO:0005737 cytoplasm IDA 24608264
GO:0005789 endoplasmic reticulum membrane IDA 25087875
GO:0072669 tRNA-splicing ligase complex IDA 21311021
genes like me logo Genes that share ontologies with RTCB: view

Pathways for RTCB Gene

SuperPathways for RTCB Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0001890 placenta development IEA --
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation IDA 21311021
GO:0006396 RNA processing --
genes like me logo Genes that share ontologies with RTCB: view

No data available for Pathways by source for RTCB Gene

Transcripts for RTCB Gene

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

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4a · 4b ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13
SP1: - -
SP2: - - - -
SP3: -
SP4: -
SP5: - - -
SP6:

Relevant External Links for RTCB Gene

GeneLoc Exon Structure for
RTCB
ECgene alternative splicing isoforms for
RTCB

Expression for RTCB Gene

mRNA expression in normal human tissues for RTCB Gene

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for RTCB Gene

genes like me logo Genes that share expressions with RTCB: view

Orthologs for RTCB Gene

This gene was present in the common ancestor of animals.

Orthologs for RTCB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia C22H22orf28 36
  • 99.6 (n)
  • 100 (a)
RTCB 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RTCB 36
  • 93.4 (n)
  • 99.6 (a)
RTCB 37
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 37
  • 100 (a)
OneToMany
-- 37
  • 95 (a)
OneToMany
RTCB 36
  • 94.19 (n)
  • 99.8 (a)
mouse
(Mus musculus)
Mammalia D10Wsu52e 16
Rtcb 36
  • 91.82 (n)
  • 99.41 (a)
Rtcb 37
  • 99 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RTCB 37
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RTCB 37
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rtcb 36
  • 90.96 (n)
  • 99.21 (a)
chicken
(Gallus gallus)
Aves C22ORF28 36
  • 83.23 (n)
  • 97.43 (a)
RTCB 37
  • 97 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RTCB 37
  • 94 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.6011 36
tropical clawed frog
(Silurana tropicalis)
Amphibia rtcb 36
  • 79.8 (n)
  • 94.65 (a)
zebrafish
(Danio rerio)
Actinopterygii rtcb 36
  • 77.16 (n)
  • 94.06 (a)
rtcb 37
  • 94 (a)
OneToOne
wufe02f02 36
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008147 36
  • 68.85 (n)
  • 80.52 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG9987 36
  • 72.1 (n)
  • 85.49 (a)
CG9987 37
  • 85 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea F16A11.2 36
  • 66.6 (n)
  • 73.07 (a)
F16A11.2 37
  • 73 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2249 36
sea squirt
(Ciona savignyi)
Ascidiacea -- 37
  • 82 (a)
OneToOne
Species with no ortholog for RTCB:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • 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)

Evolution for RTCB Gene

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

Paralogs for RTCB Gene

No data available for Paralogs for RTCB Gene

Variants for RTCB Gene

Sequence variations from dbSNP and Humsavar for RTCB Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type MAF
rs11635 -- 32,388,064(+) GTATT(C/T)ACCAC reference, synonymous-codon
rs12530 -- 32,387,917(+) TCTGA(C/T)GTCAG utr-variant-3-prime
rs13110 -- 32,392,261(+) TTGGG(A/T)GAGGC reference, synonymous-codon
rs15935 -- 32,387,908(+) CGCCT(A/T)GAGTC utr-variant-3-prime
rs713790 -- 32,399,064(+) TGTAT(A/G)TATGT intron-variant

Relevant External Links for RTCB Gene

HapMap Linkage Disequilibrium report
RTCB

No data available for Structural Variations from Database of Genomic Variants (DGV) for RTCB Gene

Disorders for RTCB Gene

No disorders were found for RTCB Gene.

No data available for UniProtKB/Swiss-Prot for RTCB Gene

Publications for RTCB Gene

  1. HSPC117 is the essential subunit of a human tRNA splicing ligase complex. (PMID: 21311021) Popow J. … Martinez J. (Science 2011) 2 3 4
  2. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang Q.-H. … Chen Z. (Genome Res. 2000) 2 3 4
  3. The DNA sequence of human chromosome 22. (PMID: 10591208) Dunham I. … Wright H. (Nature 1999) 3 4
  4. Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning. (PMID: 10931946) Hu R.-M. … Chen J.-L. (Proc. Natl. Acad. Sci. U.S.A. 2000) 3 4
  5. Reevaluating human gene annotation: a second-generation analysis of chromosome 22. (PMID: 12529303) Collins J.E. … Dunham I. (Genome Res. 2003) 3 4

Products for RTCB Gene

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat
  • QIAGEN qRT-PCR Assays for microRNAs that regulate RTCB
    • QuantiTect SYBR Green Assays in human,mouse,rat
    • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
    • QuantiFast Probe-based Assays in human,mouse,rat
    • Predesigned siRNA for gene silencing in human,mouse,rat for RTCB
    • Block miRNA regulation of RTCB using miScript Target Protectors

    Sources for RTCB Gene

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