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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
  • TRNA-Splicing Ligase RtcB Homolog 2 3
  • C22orf28 3 4
  • Chromosome 22 Open Reading Frame 28 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. An important paralog of this gene is PRDM4.

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.

Additional gene information for RTCB Gene

No data available for Entrez Gene Summary , CIViC 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

Enhancers for RTCB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH22H031658 1.4 ENCODE dbSUPER 34.5 +751.2 751241 5 HDGF PKNOX1 MLX ARID4B SIN3A FEZF1 DMAP1 ZNF2 YY1 ZNF143 TUG1 RTCB MORC2 PRR14L DEPDC5 RNF185 RPS17P16 EIF4ENIF1 ENSG00000240591 PISD
GH22H031623 2.1 VISTA Ensembl ENCODE dbSUPER 11.1 +784.6 784604 8 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 ZNF766 SP3 MXD4 TUG1 PRR14L DEPDC5 SLC5A4 LOC100422292 MORC2 SFI1 DUSP18 RTCB PIK3IP1-AS1
GH22H031752 1.1 ENCODE 12.1 +658.4 658424 3 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF207 TUG1 PRR14L DEPDC5 RTCB MORC2 RNU6-201P RNF185 PIK3IP1
GH22H031969 1 ENCODE 10.3 +441.7 441709 1 PKNOX1 ATF1 SIN3A GLI4 ZNF2 GLIS2 ZNF207 ZNF143 ZNF548 ATF7 IGLCOR22-2 LINC02558 RN7SL305P ENSG00000227813 AP1B1P2 ENSG00000230120 ENSG00000214125 RFPL3S EIF4ENIF1 RTCB
GH22H032410 1.2 FANTOM5 ENCODE 5.3 +0.7 740 2 ATF1 ARID4B SIN3A FEZF1 DMAP1 YY1 GLIS2 ZNF143 ZNF207 FOS LOC100422292 FBXO7 RFPL3S ENSG00000241954 IGLVIVOR22-2 LOC339666 BPIFC RTCB RFPL2 RFPL3
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RTCB on UCSC Golden Path with GeneCards custom track

Promoters for RTCB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000145450 287 1600 ATF1 ARID4B SIN3A FEZF1 DMAP1 YY1 GLIS2 ZNF143 ZNF207 FOS

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

Post-translational modifications for RTCB Gene

  • Ubiquitination at isoforms=67, Lys140, isoforms=206, isoforms=308, and Lys496
  • 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

Gene Families for RTCB Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

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

Function for RTCB Gene

Molecular function for RTCB Gene

UniProtKB/Swiss-Prot CatalyticActivity:
ATP + (ribonucleotide)(n)-3-hydroxyl + 5-phospho-(ribonucleotide)(m) = (ribonucleotide)(n+m) + AMP + diphosphate.
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

Phenotypes From GWAS Catalog for RTCB Gene

Gene Ontology (GO) - Molecular Function for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0003972 RNA ligase (ATP) activity IMP 24870230
GO:0005515 protein binding IPI 25814554
GO:0005524 ATP binding IEA --
GO:0008452 RNA ligase activity IEA --
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

CRISPR Products

miRNA for RTCB Gene

miRTarBase miRNAs that target RTCB

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTCB
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTCB gene
Compartment Confidence
nucleus 5
endoplasmic reticulum 5
cytosol 5
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
  • Vesicles (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RTCB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA,IDA 24608264
GO:0005635 nuclear envelope IDA 25087875
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 24608264
GO:0005789 endoplasmic reticulum membrane IDA 25087875
genes like me logo Genes that share ontologies with RTCB: view

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:0006388 tRNA splicing, via endonucleolytic cleavage and ligation TAS --
GO:0006396 RNA processing IEA --
GO:0008033 tRNA processing IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Adenosine monophosphate Approved Nutra 0
Sucrose Experimental Pharma Target 0
ATP Nutra Agonist 0

(1) Additional Compounds for RTCB Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • (4-)Diphosphoric acid ion
  • (P2O74-)Diphosphate
  • Diphosphate
  • Diphosphoric acid
  • PPi
14000-31-8
genes like me logo Genes that share compounds with RTCB: view

Transcripts for RTCB Gene

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for RTCB
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for RTCB Gene



Protein tissue co-expression partners for RTCB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RTCB Gene:

RTCB

Evidence on tissue expression from TISSUES for RTCB Gene

  • Nervous system(4.9)
  • Liver(4.5)
  • Blood(4.4)
  • Adrenal gland(4.3)
  • Intestine(3.4)
  • Lung(3.4)
  • Skin(3.4)
  • Kidney(2.9)
  • Muscle(2.9)
genes like me logo Genes that share expression patterns with RTCB: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer 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
dog
(Canis familiaris)
Mammalia -- 34
  • 100 (a)
OneToMany
-- 34
  • 95 (a)
OneToMany
RTCB 33
  • 94.19 (n)
chimpanzee
(Pan troglodytes)
Mammalia RTCB 34
  • 100 (a)
OneToOne
C22H22orf28 33
  • 99.6 (n)
oppossum
(Monodelphis domestica)
Mammalia RTCB 34
  • 98 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RTCB 34
  • 98 (a)
OneToOne
cow
(Bos Taurus)
Mammalia RTCB 33 34
  • 93.4 (n)
mouse
(Mus musculus)
Mammalia Rtcb 33 16 34
  • 91.82 (n)
rat
(Rattus norvegicus)
Mammalia Rtcb 33
  • 90.96 (n)
chicken
(Gallus gallus)
Aves RTCB 34
  • 97 (a)
OneToOne
C22ORF28 33
  • 83.23 (n)
lizard
(Anolis carolinensis)
Reptilia RTCB 34
  • 94 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rtcb 33
  • 79.8 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6011 33
zebrafish
(Danio rerio)
Actinopterygii rtcb 33 34
  • 77.16 (n)
wufe02f02 33
fruit fly
(Drosophila melanogaster)
Insecta CG9987 33 34
  • 72.1 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008147 33
  • 68.85 (n)
worm
(Caenorhabditis elegans)
Secernentea F16A11.2 33 34
  • 66.6 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 82 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2249 33
Species where no ortholog for RTCB was found in the sources mined by GeneCards:
  • 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

Paralogs for RTCB Gene

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

Variants for RTCB Gene

Sequence variations from dbSNP and Humsavar for RTCB Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type
rs1000096523 -- 32,413,266(+) TTAAT(A/G)TCATT upstream-variant-2KB
rs1000393652 -- 32,411,814(+) TTTCG(-/TATT)TATTT intron-variant
rs1000395900 -- 32,405,839(+) TAACA(C/G)CAAAG intron-variant
rs1000548359 -- 32,391,020(+) TAATC(G/T)TGAAC intron-variant
rs1000588958 -- 32,409,222(+) ATGAA(C/T)CAAAA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for RTCB Gene

Variant ID Type Subtype PubMed ID
esv2422247 CNV duplication 17116639
esv2676701 CNV deletion 23128226
esv2724148 CNV deletion 23290073
esv3558074 CNV deletion 23714750
nsv1055701 CNV gain 25217958
nsv1066118 CNV gain 25217958
nsv459874 CNV gain 19166990
nsv588895 CNV gain 21841781

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

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTCB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot 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 (New York, N.Y.) 2011) 2 3 4 60
  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 QH … Chen Z (Genome research 2000) 2 3 4 60
  3. hCLE/C14orf166 associates with DDX1-HSPC117-FAM98B in a novel transcription-dependent shuttling RNA-transporting complex. (PMID: 24608264) Pérez-González A … Nieto A (PloS one 2014) 3 4 60
  4. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. (PMID: 24870230) Popow J … Martinez J (Nature 2014) 3 4 60
  5. Archaeal 3'-phosphate RNA splicing ligase characterization identifies the missing component in tRNA maturation. (PMID: 21209330) Englert M … Söll D (Proceedings of the National Academy of Sciences of the United States of America 2011) 2 3 60

Products for RTCB Gene

Sources for RTCB Gene

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