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Q9Y3I0 (RTCB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 108. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
tRNA-splicing ligase RtcB homolog

EC=6.5.1.3
Gene names
Name:RTCB
Synonyms:C22orf28
ORF Names:HSPC117
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length505 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.15

Catalytic activity

ATP + (ribonucleotide)(n) + (ribonucleotide)(m) = AMP + diphosphate + (ribonucleotide)(n+m). Ref.15

Subunit structure

Catalytic component of the tRNA-splicing ligase complex. Ref.12 Ref.15

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_03144.

Sequence similarities

Belongs to the RtcB family.

Sequence caution

The sequence AAF29081.1 differs from that shown. Reason: Frameshift at positions 295 and 298.

The sequence AAF67477.1 differs from that shown. Reason: Frameshift at positions 173 and 180.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 505505tRNA-splicing ligase RtcB homolog HAMAP-Rule MF_03144
PRO_0000255241

Sites

Metal binding1221Zinc Potential
Metal binding2271Zinc Potential
Metal binding2591Zinc Potential

Natural variations

Natural variant1531V → A.
Corresponds to variant rs11545747 [ dbSNP | Ensembl ].
VAR_052485
Natural variant3431L → F. Ref.9
Corresponds to variant rs17849275 [ dbSNP | Ensembl ].
VAR_028853

Experimental info

Mutagenesis1221C → A: Abolishes tRNA ligase activity. Ref.15
Sequence conflict2961A → P in AAF29081. Ref.2
Sequence conflict3031G → V in AAF29081. Ref.2
Sequence conflict3031G → V in AAF67477. Ref.3
Sequence conflict4271C → R in CAG33456. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Q9Y3I0 [UniParc].

Last modified November 1, 1999. Version 1.
Checksum: C7C0CC2C95BDD27B

FASTA50555,210
        10         20         30         40         50         60 
MSRSYNDELQ FLEKINKNCW RIKKGFVPNM QVEGVFYVND ALEKLMFEEL RNACRGGGVG 

        70         80         90        100        110        120 
GFLPAMKQIG NVAALPGIVH RSIGLPDVHS GYGFAIGNMA AFDMNDPEAV VSPGGVGFDI 

       130        140        150        160        170        180 
NCGVRLLRTN LDESDVQPVK EQLAQAMFDH IPVGVGSKGV IPMNAKDLEE ALEMGVDWSL 

       190        200        210        220        230        240 
REGYAWAEDK EHCEEYGRML QADPNKVSAR AKKRGLPQLG TLGAGNHYAE IQVVDEIFNE 

       250        260        270        280        290        300 
YAAKKMGIDH KGQVCVMIHS GSRGLGHQVA TDALVAMEKA MKRDKIIVND RQLACARIAS 

       310        320        330        340        350        360 
PEGQDYLKGM AAAGNYAWVN RSSMTFLTRQ AFAKVFNTTP DDLDLHVIYD VSHNIAKVEQ 

       370        380        390        400        410        420 
HVVDGKERTL LVHRKGSTRA FPPHHPLIAV DYQLTGQPVL IGGTMGTCSY VLTGTEQGMT 

       430        440        450        460        470        480 
ETFGTTCHGA GRALSRAKSR RNLDFQDVLD KLADMGIAIR VASPKLVMEE APESYKNVTD 

       490        500 
VVNTCHDAGI SKKAIKLRPI AVIKG 

« Hide

References

« Hide 'large scale' references
[1]"Reevaluating human gene annotation: a second-generation analysis of chromosome 22."
Collins J.E., Goward M.E., Cole C.G., Smink L.J., Huckle E.J., Knowles S., Bye J.M., Beare D.M., Dunham I.
Genome Res. 13:27-36(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[2]"Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells."
Zhang Q.-H., Ye M., Wu X.-Y., Ren S.-X., Zhao M., Zhao C.-J., Fu G., Shen Y., Fan H.-Y., Lu G., Zhong M., Xu X.-R., Han Z.-G., Zhang J.-W., Tao J., Huang Q.-H., Zhou J., Hu G.-X. expand/collapse author list , Gu J., Chen S.-J., Chen Z.
Genome Res. 10:1546-1560(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Umbilical cord blood.
[3]"Gene expression profiling in the human hypothalamus-pituitary-adrenal axis and full-length cDNA cloning."
Hu R.-M., Han Z.-G., Song H.-D., Peng Y.-D., Huang Q.-H., Ren S.-X., Gu Y.-J., Huang C.-H., Li Y.-B., Jiang C.-L., Fu G., Zhang Q.-H., Gu B.-W., Dai M., Mao Y.-F., Gao G.-F., Rong R., Ye M. expand/collapse author list , Zhou J., Xu S.-H., Gu J., Shi J.-X., Jin W.-R., Zhang C.-K., Wu T.-M., Huang G.-Y., Chen Z., Chen M.-D., Chen J.-L.
Proc. Natl. Acad. Sci. U.S.A. 97:9543-9548(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Adrenal gland.
[4]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[5]"A genome annotation-driven approach to cloning the human ORFeome."
Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I.
Genome Biol. 5:R84.1-R84.11(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: Thalamus.
[7]"The DNA sequence of human chromosome 22."
Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. expand/collapse author list , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H.
Nature 402:489-495(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[9]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT PHE-343.
Tissue: Choriocarcinoma and Lung carcinoma.
[10]Bienvenut W.V., Boldt K., von Kriegsheim A.F., Kolch W.
Submitted (JUL-2007) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 4-14; 45-51; 56-81; 141-158; 199-206; 264-279; 298-308; 442-460 AND 466-476, IDENTIFICATION BY MASS SPECTROMETRY.
Tissue: Hepatoma.
[11]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 309-505.
Tissue: Testis.
[12]"Kinesin transports RNA: isolation and characterization of an RNA-transporting granule."
Kanai Y., Dohmae N., Hirokawa N.
Neuron 43:513-525(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A RNA TRANSPORT COMPLEX.
[13]"Proteomic analysis of SUMO4 substrates in HEK293 cells under serum starvation-induced stress."
Guo D., Han J., Adam B.-L., Colburn N.H., Wang M.-H., Dong Z., Eizirik D.L., She J.-X., Wang C.-Y.
Biochem. Biophys. Res. Commun. 337:1308-1318(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY.
[14]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"HSPC117 is the essential subunit of a human tRNA splicing ligase complex."
Popow J., Englert M., Weitzer S., Schleiffer A., Mierzwa B., Mechtler K., Trowitzsch S., Will C.L., Luhrmann R., Soll D., Martinez J.
Science 331:760-764(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, CATALYTIC ACTIVITY, IDENTIFICATION IN THE TRNA SPLICING LIGASE COMPLEX, MUTAGENESIS OF CYS-122.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AL050255 mRNA. Translation: CAB43357.1.
AF161466 mRNA. Translation: AAF29081.1. Frameshift.
AF155658 mRNA. Translation: AAF67477.1. Frameshift.
CR457175 mRNA. Translation: CAG33456.1.
CR456450 mRNA. Translation: CAG30336.1.
AK312503 mRNA. Translation: BAG35405.1.
AL021937 Genomic DNA. Translation: CAB38260.1.
CH471095 Genomic DNA. Translation: EAW60021.1.
BC000151 mRNA. Translation: AAH00151.1.
BC002970 mRNA. Translation: AAH02970.1.
BC010308 mRNA. Translation: AAH10308.1.
BC016707 mRNA. Translation: AAH16707.1.
AL137272 mRNA. Translation: CAB70670.1.
PIRT46344.
RefSeqNP_055121.1. NM_014306.4.
UniGeneHs.474643.

3D structure databases

ProteinModelPortalQ9Y3I0.
SMRQ9Y3I0. Positions 12-505.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119569. 40 interactions.
IntActQ9Y3I0. 14 interactions.
MINTMINT-4654730.
STRING9606.ENSP00000216038.

PTM databases

PhosphoSiteQ9Y3I0.

Polymorphism databases

DMDM74753486.

2D gel databases

UCD-2DPAGEQ9Y3I0.

Proteomic databases

PaxDbQ9Y3I0.
PeptideAtlasQ9Y3I0.
PRIDEQ9Y3I0.

Protocols and materials databases

DNASU51493.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000216038; ENSP00000216038; ENSG00000100220.
GeneID51493.
KEGGhsa:51493.
UCSCuc003amm.2. human.

Organism-specific databases

CTD51493.
GeneCardsGC22M032784.
HGNCHGNC:26935. RTCB.
HPAHPA001103.
MIM613901. gene.
neXtProtNX_Q9Y3I0.
PharmGKBPA145149387.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1690.
HOVERGENHBG081383.
InParanoidQ9Y3I0.
KOK14415.
OMAGRMLNAD.
OrthoDBEOG7DRJ2Q.
PhylomeDBQ9Y3I0.
TreeFamTF314404.

Gene expression databases

ArrayExpressQ9Y3I0.
BgeeQ9Y3I0.
CleanExHS_C22orf28.
GenevestigatorQ9Y3I0.

Family and domain databases

HAMAPMF_03144. RtcB_euk.
InterProIPR001233. RtcB.
IPR027513. RtcB_euk.
[Graphical view]
PANTHERPTHR11118. PTHR11118. 1 hit.
PfamPF01139. RtcB. 1 hit.
[Graphical view]
SUPFAMSSF103365. SSF103365. 1 hit.
PROSITEPS01288. UPF0027. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSC22orf28. human.
GenomeRNAi51493.
NextBio55157.
SOURCESearch...

Entry information

Entry nameRTCB_HUMAN
AccessionPrimary (citable) accession number: Q9Y3I0
Secondary accession number(s): B2R6A8 expand/collapse secondary AC list , Q6IAI0, Q9BWL4, Q9NTH1, Q9P037, Q9P0J3
Entry history
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: November 1, 1999
Last modified: April 16, 2014
This is version 108 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

Uncharacterized protein families (UPF)

List of uncharacterized protein family (UPF) entries

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 22

Human chromosome 22: entries, gene names and cross-references to MIM