Aliases for RTCB Gene

Aliases for RTCB Gene

  • RNA 2',3'-Cyclic Phosphate And 5'-OH Ligase 2 3 5
  • 3'-Phosphate/5'-Hydroxy Nucleic Acid Ligase 3 4
  • Focal Adhesion-Associated Protein 2 3
  • TRNA-Splicing Ligase RtcB Homolog 2 3
  • RNA-Splicing Ligase RtcB Homolog 3 4
  • C22orf28 3 4
  • HSPC117 2 3
  • FAAP 2 3
  • Chromosome 22 Open Reading Frame 28 2
  • Ankyrin Repeat Domain 54 3
  • DJ149A16.6 3
  • EC 6.5.1.8 4
  • RTCB 5

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. Diseases associated with RTCB include Oropharyngeal Anthrax. Among its related pathways are tRNA processing and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA ligase (ATP) activity.

UniProtKB/Swiss-Prot Summary 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 , CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RTCB Gene

Genomics for RTCB Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RTCB Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTCB on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTCB

Genomic Locations for RTCB Gene

Latest Assembly
chr22:32,387,582-32,412,248
(GRCh38/hg38)
Size:
24,667 bases
Orientation:
Minus strand

Previous Assembly
chr22:32,783,569-32,808,234
(GRCh37/hg19 by Entrez Gene)
Size:
24,666 bases
Orientation:
Minus strand

chr22:32,783,569-32,808,242
(GRCh37/hg19 by Ensembl)
Size:
24,674 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:
    RNA-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.
    SequenceCaution:
    • Sequence=AAF29081.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=AAF67477.1; Type=Frameshift; Evidence={ECO:0000305};
    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.

neXtProt entry for RTCB Gene

Post-translational modifications for RTCB Gene

  • Ubiquitination at Lys67, Lys140, Lys206, Lys308, 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

InterPro:
Blocks:
  • Protein of unknown function UPF0027

Suggested Antigen Peptide Sequences for RTCB Gene

GenScript: Design optimal peptide antigens:
  • tRNA-splicing ligase RtcB homolog (RTCB_HUMAN)

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 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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(Ribonucleotide)(n)-3'-phosphate + 5'-hydroxy-(ribonucleotide)(m) + GTP = (ribonucleotide)(n+m) + GMP + diphosphate.; EC=6.5.1.8; Evidence={ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:24870230, ECO:0000305|PubMed:21311021};.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=(Ribonucleotide)(n)-2',3'-cyclophosphate + 5'-hydroxy-(ribonucleotide)(m) + GTP + H(2)O = (ribonucleotide)(n+m) + GMP + diphosphate (overall reaction).; EC=6.5.1.8; Evidence={ECO:0000255|HAMAP-Rule:MF_03144, ECO:0000269|PubMed:24870230, ECO:0000305|PubMed:21311021};.
UniProtKB/Swiss-Prot EnzymeRegulation:
Protein archease stimulates the activity of the tRNA ligase complex with high efficiency in the presence of GTP.

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:0000166 nucleotide binding IEA --
GO:0003723 RNA binding HDA 22658674
GO:0003972 RNA ligase (ATP) activity IBA,IMP 24870230
GO:0005515 protein binding IPI 24870230
GO:0005525 GTP binding IEA --
genes like me logo Genes that share ontologies with RTCB: view
genes like me logo Genes that share phenotypes with RTCB: view

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for 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}.

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
cytosol 5
cytoskeleton 2
endoplasmic reticulum 2
plasma membrane 1
extracellular 1
mitochondrion 1
lysosome 1
golgi apparatus 1
peroxisome 0

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 IBA,IDA 24608264
GO:0005654 nucleoplasm TAS --
GO:0005737 cytoplasm IEA,IDA 24608264
GO:0005829 cytosol IDA --
GO:0043231 intracellular membrane-bounded organelle IDA --
genes like me logo Genes that share ontologies with RTCB: view

Pathways & Interactions for RTCB Gene

PathCards logo

SuperPathways 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:0000971 tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate IBA 21873635
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
Sucrose Approved, Experimental, Investigational Pharma Target 0
Adenosine monophosphate Approved, Investigational Nutra 0
ATP Investigational Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
pyrophosphate
  • [(HO)2P(O)OP(O)(OH)2]
  • Acide diphosphorique
  • Diphosphorsaeure
  • H4P2O7
  • Pyrophosphoric acid
14000-31-8
genes like me logo Genes that share compounds with RTCB: view

Transcripts for RTCB Gene

mRNA/cDNA for RTCB Gene

1 REFSEQ mRNAs :
16 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTCB

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

Expression for RTCB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for RTCB Gene



Protein tissue co-expression partners for RTCB Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTCB

Evidence on tissue expression from TISSUES for RTCB Gene

  • Nervous system(5)
  • Liver(4.6)
  • Blood(4.5)
  • Adrenal gland(4.3)
  • Skin(3.8)
  • Lung(3.7)
  • Intestine(3.7)
  • Kidney(3.4)
  • Muscle(3.4)
  • Heart(2.2)
  • Eye(2.1)
  • Lymph node(2.1)
genes like me logo Genes that share expression patterns with RTCB: view

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 -- 30
  • 100 (a)
OneToMany
-- 30
  • 95 (a)
OneToMany
RTCB 29
  • 94.19 (n)
Chimpanzee
(Pan troglodytes)
Mammalia RTCB 30
  • 100 (a)
OneToOne
C22H22orf28 29
  • 99.6 (n)
Oppossum
(Monodelphis domestica)
Mammalia RTCB 30
  • 98 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RTCB 30
  • 98 (a)
OneToOne
Cow
(Bos Taurus)
Mammalia RTCB 29 30
  • 93.4 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rtcb 29 16 30
  • 91.82 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rtcb 29
  • 90.96 (n)
Chicken
(Gallus gallus)
Aves RTCB 30
  • 97 (a)
OneToOne
C22ORF28 29
  • 83.23 (n)
Lizard
(Anolis carolinensis)
Reptilia RTCB 30
  • 94 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rtcb 29
  • 79.8 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.6011 29
Zebrafish
(Danio rerio)
Actinopterygii rtcb 29 30
  • 77.16 (n)
OneToOne
wufe02f02 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG9987 29 30
  • 72.1 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008147 29
  • 68.85 (n)
Worm
(Caenorhabditis elegans)
Secernentea F16A11.2 29 30
  • 66.6 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 82 (a)
OneToOne
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.2249 29
Species where no ortholog for RTCB was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium 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)
Aminode:
Evolutionary constrained regions (ECRs) for RTCB: view image
Alliance of Genome Resources:
Additional Orthologs for RTCB

Paralogs for RTCB Gene

No data available for Paralogs for RTCB Gene

Variants for RTCB Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTCB Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
rs10222228 Benign: not provided 32,396,236(-) A/G
NM_014306.5(RTCB):c.828T>C (p.Ala276=)
SYNONYMOUS
rs41310258 Benign: not provided 32,395,164(-) C/G
NM_014306.5(RTCB):c.1041G>C (p.Val347=)
SYNONYMOUS
rs11545747 -- p.Val153Ala
rs17849275 -- p.Leu343Phe

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RTCB Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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)

Additional Variant Information for RTCB Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTCB
Leiden Open Variation Database (LOVD)
RTCB

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTCB Gene

Disorders for RTCB Gene

MalaCards: The human disease database

(1) MalaCards diseases for RTCB Gene - From: COP

Disorder Aliases PubMed IDs
oropharyngeal anthrax
- elite association - COSMIC cancer census association via MalaCards
Search RTCB in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RTCB

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

No data available for 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
  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
  3. Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors. (PMID: 24870230) Popow J … Martinez J (Nature 2014) 3 4
  4. 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
  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

Products for RTCB Gene

Sources for RTCB Gene