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Aliases for RTCB Gene

Aliases for RTCB Gene

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

External Ids for RTCB Gene

Previous HGNC Symbols for RTCB Gene

  • C22orf28

Previous GeneCards Identifiers for RTCB Gene

  • GC22M032784

Summaries for RTCB Gene

GeneCards Summary for RTCB Gene

RTCB (RNA 2',3'-Cyclic Phosphate And 5'-OH Ligase) is a Protein Coding gene. Among its related pathways are Gene Expression and tRNA processing. GO annotations related to this gene include poly(A) RNA 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

Regulatory Elements for RTCB Gene

Promoters for RTCB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around RTCB on UCSC Golden Path with GeneCards custom track

Genomic Location for RTCB Gene

Chromosome:
22
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

Genes around RTCB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTCB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTCB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence 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;
    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

  • Ubiquitination at Lys 67, Lys 140, Lys 206, Lys 308, and Lys 496
  • Modification sites at PhosphoSitePlus

Other Protein References for RTCB Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RTCB Gene

Domains & Families for RTCB Gene

Protein Domains for RTCB Gene

Suggested Antigen Peptide Sequences for RTCB Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y3I0

UniProtKB/Swiss-Prot:

RTCB_HUMAN :
  • Belongs to the RtcB family.
Family:
  • Belongs to the RtcB family.
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:0017166 vinculin binding IPI 15163412
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with RTCB: view

Phenotypes for RTCB Gene

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

Animal Model Products

miRNA for RTCB Gene

miRTarBase miRNAs that target RTCB

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets 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:0005635 nuclear envelope IDA 25087875
GO:0005737 cytoplasm IEA,IDA 24608264
genes like me logo Genes that share ontologies with RTCB: view

No data available for Subcellular locations from COMPARTMENTS for RTCB Gene

Pathways & Interactions for RTCB Gene

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

Pathways by source for RTCB Gene

Gene Ontology (GO) - Biological Process for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001701 in utero embryonic development IEA --
GO:0008033 tRNA processing TAS --
genes like me logo Genes that share ontologies with RTCB: view

No data available for SIGNOR curated interactions for RTCB Gene

Drugs & Compounds for RTCB Gene

(4) Drugs for RTCB Gene - From: HMDB and DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved Nutra 0
Adenosine triphosphate Approved Nutra 0
Sucrose Experimental Pharma Target 0
Diphosphate Experimental Pharma 0
genes like me logo Genes that share compounds with RTCB: view

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RTCB Gene

This gene is overexpressed in Lymph node (10.1) and Peripheral blood mononuclear cells (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for RTCB Gene



genes like me logo Genes that share expression patterns with RTCB: view

Protein tissue co-expression partners for RTCB Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RTCB Gene

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 RTCB 36
  • 100 (a)
OneToOne
C22H22orf28 35
  • 99.6 (n)
  • 100 (a)
cow
(Bos Taurus)
Mammalia RTCB 35
  • 93.4 (n)
  • 99.6 (a)
RTCB 36
  • 100 (a)
OneToOne
dog
(Canis familiaris)
Mammalia -- 36
  • 100 (a)
OneToMany
-- 36
  • 95 (a)
OneToMany
RTCB 35
  • 94.19 (n)
  • 99.8 (a)
mouse
(Mus musculus)
Mammalia Rtcb 16
Rtcb 36
  • 99 (a)
OneToOne
Rtcb 35
  • 91.82 (n)
  • 99.41 (a)
oppossum
(Monodelphis domestica)
Mammalia RTCB 36
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RTCB 36
  • 98 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Rtcb 35
  • 90.96 (n)
  • 99.21 (a)
chicken
(Gallus gallus)
Aves C22ORF28 35
  • 83.23 (n)
  • 97.43 (a)
RTCB 36
  • 97 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RTCB 36
  • 94 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.6011 35
tropical clawed frog
(Silurana tropicalis)
Amphibia rtcb 35
  • 79.8 (n)
  • 94.65 (a)
zebrafish
(Danio rerio)
Actinopterygii rtcb 36
  • 94 (a)
OneToOne
rtcb 35
  • 77.16 (n)
  • 94.06 (a)
wufe02f02 35
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008147 35
  • 68.85 (n)
  • 80.52 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG9987 36
  • 85 (a)
OneToOne
CG9987 35
  • 72.1 (n)
  • 85.49 (a)
worm
(Caenorhabditis elegans)
Secernentea F16A11.2 35
  • 66.6 (n)
  • 73.07 (a)
F16A11.2 36
  • 73 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2249 35
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 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
rs17849275 - 32,395,176(+) AGGTC(A/C/T)AAGTC reference, synonymous-codon, missense
rs11545747 - 32,401,786(-) TCCTG(C/T)TGGGG reference, missense
rs15935 -- 32,387,908(+) CGCCT(A/T)GAGTC utr-variant-3-prime
rs3070412 -- 32,409,823(+) CTTTT(G/T)TTTTT intron-variant
rs2049946 -- 32,402,772(+) acagg(G/T)tcttg intron-variant

Variation tolerance for RTCB Gene

Residual Variation Intolerance Score: 8.54% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.06; 80.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RTCB Gene

HapMap Linkage Disequilibrium report
RTCB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for RTCB Gene

Disorders for RTCB Gene

Relevant External Links for RTCB

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RTCB

No disorders were found for RTCB Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas 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 67
  2. Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. (PMID: 21209330) Englert M. … SAPll D. (Proc. Natl. Acad. Sci. U.S.A. 2011) 2 3
  3. 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. Interaction of amyotrophic lateral sclerosis/frontotemporal lobar degeneration-associated fused-in-sarcoma with proteins involved in metabolic and protein degradation pathways. (PMID: 25192599) Wang T. … Xu J. (Neurobiol. Aging 2015) 3
  5. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. (PMID: 25737280) Murn J. … Shi Y. (Genes Dev. 2015) 3

Products for RTCB Gene

Sources for RTCB Gene

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