RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase)

Gene

• Entrez ID: 51493
• Gene name: RNA 2',3'-cyclic phosphate and 5'-OH ligase
• Gene symbol: RTCB
• Synonyms (NCBI Gene): C22orf28, DJ149A16.6, FAAP, HSPC117
• Chromosome: 22
• Chromosome location: 22q12.3

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT029675	hsa-miR-26b-5p	Microarray	19088304
MIRT049368	hsa-miR-92a-3p	CLASH	23622248
MIRT042566	hsa-miR-423-3p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0001701	Process	In utero embryonic development	IEA
GO:0001890	Process	Placenta development	IEA
GO:0003723	Function	RNA binding	HDA	22658674, 22681889
GO:0005515	Function	Protein binding	IPI	24608264, 24870230, 25814554, 30833792, 35271311
GO:0005525	Function	GTP binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	24608264
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	21311021
GO:0005635	Component	Nuclear envelope	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	24608264
GO:0005737	Component	Cytoplasm	IEA
GO:0005737	Component	Cytoplasm	NAS	21311021
GO:0005789	Component	Endoplasmic reticulum membrane	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IBA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IDA	21311021, 24870230
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	IEA
GO:0006388	Process	TRNA splicing, via endonucleolytic cleavage and ligation	NAS	24870230
GO:0006396	Process	RNA processing	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0016874	Function	Ligase activity	IEA
GO:0016886	Function	Ligase activity, forming phosphoric ester bonds	IEA
GO:0017166	Function	Vinculin binding	IPI	15163412
GO:0046872	Function	Metal ion binding	IEA
GO:0072669	Component	TRNA-splicing ligase complex	IBA
GO:0072669	Component	TRNA-splicing ligase complex	IDA	21311021, 24870230
GO:0072669	Component	TRNA-splicing ligase complex	IEA
GO:0072669	Component	TRNA-splicing ligase complex	NAS	24870230
GO:0170057	Function	RNA ligase (GTP) activity	IBA
GO:0170057	Function	RNA ligase (GTP) activity	IDA	21311021
GO:0170057	Function	RNA ligase (GTP) activity	IEA
GO:0170057	Function	RNA ligase (GTP) activity	IMP	24870230

Other IDs

• MIM: 613901
• HGNC: 26935
• e!Ensembl: ENSG00000100220

Protein

• UniProt ID: Q9Y3I0
• Protein name: RNA-splicing ligase RtcB homolog (EC 6.5.1.8) (3'-phosphate/5'-hydroxy nucleic acid ligase)
• Protein 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'-phosphodiest
• PDB: 7P3B, 8BTT, 8ODO, 8ODP, 8ORJ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01139	RtcB	68 → 505	tRNA-splicing ligase RtcB	Family

• Sequence:

  MSRSYNDELQFLEKINKNCWRIKKGFVPNMQVEGVFYVNDALEKLMFEELRNACRGGGVG
  GFLPAMKQIGNVAALPGIVHRSIGLPDVHSGYGFAIGNMAAFDMNDPEAVVSPGGVGFDI
  NCGVRLLRTNLDESDVQPVKEQLAQAMFDHIPVGVGSKGVIPMNAKDLEEALEMGVDWSL
  REGYAWAEDKEHCEEYGRMLQADPNKVSARAKKRGLPQLGTLGAGNHYAEIQVVDEIFNE
  YAAKKMGIDHKGQVCVMIHSGSRGLGHQVATDALVAMEKAMKRDKIIVNDRQLACARIAS
  PEGQDYLKGMAAAGNYAWVNRSSMTFLTRQAFAKVFNTTPDDLDLHVIYDVSHNIAKVEQ
  HVVDGKERTLLVHRKGSTRAFPPHHPLIAVDYQLTGQPVLIGGTMGTCSYVLTGTEQGMT
  ETFGTTCHGAGRALSRAKSRRNLDFQDVLDKLADMGIAIRVASPKLVMEEAPESYKNVTD
  VVNTCHDAGISKKAIKLRPIAVIKG

• Sequence length: 505

Pathways

Reactome:

tRNA processing in the nucleus

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Sarcoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCOLIOSIS	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Breast Carcinoma	Breast Carcinoma	BEFREE	29187905		★☆☆☆☆ Found in Text Mining only
Head and Neck Neoplasms	Head and neck neoplasm	Pubtator	32610494	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	29187905		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	29187905		★☆☆☆☆ Found in Text Mining only