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Q9H6S0 (YTDC2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 93. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Probable ATP-dependent RNA helicase YTHDC2

EC=3.6.4.13
Gene names
Name:YTHDC2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1430 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

ATP + H2O = ADP + phosphate.

Domain

The YTH domain mediates RNA-binding By similarity.

Sequence similarities

Belongs to the DEAD box helicase family. DEAH subfamily.

Contains 2 ANK repeats.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Contains 1 R3H domain.

Contains 1 YTH domain.

Sequence caution

The sequence BAB15183.1 differs from that shown. Reason: Erroneous initiation.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Irak1Q99J342EBI-1057466,EBI-6117042From a different organism.
IRF4Q153062EBI-1057466,EBI-751345

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 14301430Probable ATP-dependent RNA helicase YTHDC2
PRO_0000249340

Regions

Domain38 – 10669R3H
Domain203 – 369167Helicase ATP-binding
Repeat506 – 53833ANK 1
Repeat539 – 57133ANK 2
Domain612 – 784173Helicase C-terminal
Domain1288 – 1418131YTH
Nucleotide binding216 – 2238ATP By similarity
Motif316 – 3194DEAH box
Compositional bias15 – 3117Gly-rich
Compositional bias1248 – 128134Ser-rich

Amino acid modifications

Modified residue231Phosphoserine Ref.7
Modified residue10891Phosphoserine Ref.6
Modified residue10921Phosphoserine Ref.4
Modified residue12631Phosphoserine By similarity
Modified residue12671Phosphoserine By similarity
Modified residue12811Phosphoserine Ref.4

Natural variations

Natural variant6521S → N.
Corresponds to variant rs10071816 [ dbSNP | Ensembl ].
VAR_058002
Natural variant14091L → Q. Ref.3
Corresponds to variant rs1132528 [ dbSNP | Ensembl ].
VAR_058003

Experimental info

Sequence conflict8601I → V in BAB15183. Ref.3
Sequence conflict9931L → S in BAB15183. Ref.3
Sequence conflict12301Q → R in BAB15183. Ref.3

Secondary structure

....................... 1430
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q9H6S0 [UniParc].

Last modified June 16, 2009. Version 2.
Checksum: A0C3B45771A3DE16

FASTA1,430160,248
        10         20         30         40         50         60 
MSRPSSVSPR QPAPGGGGGG GPSPCGPGGG GRAKGLKDIR IDEEVKIAVN IALERFRYGD 

        70         80         90        100        110        120 
QREMEFPSSL TSTERAFIHR LSQSLGLVSK SKGKGANRYL TVKKKDGSET AHAMMTCNLT 

       130        140        150        160        170        180 
HNTKHAVRSL IQRFPVTNKE RTELLPKTER GNVFAVEAEN REMSKTSGRL NNGIPQIPVK 

       190        200        210        220        230        240 
RGESEFDSFR QSLPVFEKQE EIVKIIKENK VVLIVGETGS GKTTQIPQFL LDDCFKNGIP 

       250        260        270        280        290        300 
CRIFCTQPRR LAAIAVAERV AAERRERIGQ TIGYQIRLES RVSPKTLLTF CTNGVLLRTL 

       310        320        330        340        350        360 
MAGDSTLSTV THVIVDEVHE RDRFSDFLLT KLRDLLQKHP TLKLILSSAA LDVNLFIRYF 

       370        380        390        400        410        420 
GSCPVIYIQG RPFEVKEMFL EDILRTTGYT NKEMLKYKKE KQQEEKQQTT LTEWYSAQEN 

       430        440        450        460        470        480 
SFKPESQRQR TVLNVTDEYD LLDDGGDAVF SQLTEKDVNC LEPWLIKEMD ACLSDIWLHK 

       490        500        510        520        530        540 
DIDAFAQVFH LILTENVSVD YRHSETSATA LMVAAGRGFA SQVEQLISMG ANVHSKASNG 

       550        560        570        580        590        600 
WMALDWAKHF GQTEIVDLLE SYSATLEFGN LDESSLVQTN GSDLSAEDRE LLKAYHHSFD 

       610        620        630        640        650        660 
DEKVDLDLIM HLLYNICHSC DAGAVLIFLP GYDEIVGLRD RILFDDKRFA DSTHRYQVFM 

       670        680        690        700        710        720 
LHSNMQTSDQ KKVLKNPPAG VRKIILSTNI AETSITVNDV VFVIDSGKVK EKSFDALNFV 

       730        740        750        760        770        780 
TMLKMVWISK ASAIQRKGRA GRCRPGICFR LFSRLRFQNM LEFQTPELLR MPLQELCLHT 

       790        800        810        820        830        840 
KLLAPVNCPI ADFLMKAPEP PPALIVRNAV QMLKTIDAMD TWEDLTELGY HLADLPVEPH 

       850        860        870        880        890        900 
LGKMVLCAVV LKCLDPILTI ACTLAYRDPF VLPTQASQKR AAMLCRKRFT AGAFSDHMAL 

       910        920        930        940        950        960 
LRAFQAWQKA RSDGWERAFC EKNFLSQATM EIIIGMRTQL LGQLRASGFV RARGGGDIRD 

       970        980        990       1000       1010       1020 
VNTNSENWAV VKAALVAGMY PNLVHVDREN LVLTGPKEKK VRFHPASVLS QPQYKKIPPA 

      1030       1040       1050       1060       1070       1080 
NGQAAAIKAL PTDWLIYDEM TRAHRIANIR CCSAVTPVTI LVFCGPARLA SNALQEPSSF 

      1090       1100       1110       1120       1130       1140 
RVDGIPNDSS DSEMEDKTTA NLAALKLDEW LHFTLEPEAA SLLLQLRQKW HSLFLRRMRA 

      1150       1160       1170       1180       1190       1200 
PSKPWSQVDE ATIRAIIAVL STEEQSAGLQ QPSGIGQRPR PMSSEELPLA SSWRSNNSRK 

      1210       1220       1230       1240       1250       1260 
SSADTEFSDE CTTAERVLMK SPSPALHPPQ KYKDRGILHP KRGTEDRSDQ SSLKSTDSSS 

      1270       1280       1290       1300       1310       1320 
YPSPCASPSP PSSGKGSKSP SPRPNMPVRY FIMKSSNLRN LEISQQKGIW STTPSNERKL 

      1330       1340       1350       1360       1370       1380 
NRAFWESSIV YLVFSVQGSG HFQGFSRMSS EIGREKSQDW GSAGLGGVFK VEWIRKESLP 

      1390       1400       1410       1420       1430 
FQFAHHLLNP WNDNKKVQIS RDGQELEPLV GEQLLQLWER LPLGEKNTTD 

« Hide

References

« Hide 'large scale' references
[1]"The DNA sequence and comparative analysis of human chromosome 5."
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S. expand/collapse author list , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[2]"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].
Tissue: Brain.
[3]"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] OF 730-1430, VARIANT GLN-1409.
[4]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1092 AND SER-1281, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[5]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[6]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1089, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[7]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-23, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[8]"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].
[9]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Solution structure of the YTH domain in YTH domain-containing protein 2."
RIKEN structural genomics initiative (RSGI)
Submitted (OCT-2007) to the PDB data bank
Cited for: STRUCTURE BY NMR OF 1288-1421.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AC093208 Genomic DNA. No translation available.
AC010389 Genomic DNA. No translation available.
BC137285 mRNA. Translation: AAI37286.1.
AK025593 mRNA. Translation: BAB15183.1. Different initiation.
CCDSCCDS4113.1.
RefSeqNP_073739.3. NM_022828.3.
UniGeneHs.231942.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2YU6NMR-A1288-1421[»]
ProteinModelPortalQ9H6S0.
SMRQ9H6S0. Positions 190-368, 492-1057, 1288-1421.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid122321. 11 interactions.
IntActQ9H6S0. 10 interactions.
MINTMINT-6944358.
STRING9606.ENSP00000161863.

PTM databases

PhosphoSiteQ9H6S0.

Polymorphism databases

DMDM239938805.

Proteomic databases

MaxQBQ9H6S0.
PaxDbQ9H6S0.
PeptideAtlasQ9H6S0.
PRIDEQ9H6S0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000161863; ENSP00000161863; ENSG00000047188.
GeneID64848.
KEGGhsa:64848.
UCSCuc003kqn.3. human.

Organism-specific databases

CTD64848.
GeneCardsGC05P112877.
HGNCHGNC:24721. YTHDC2.
HPAHPA037364.
neXtProtNX_Q9H6S0.
PharmGKBPA134912676.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1643.
HOGENOMHOG000155703.
HOVERGENHBG063891.
InParanoidQ9H6S0.
OMAPNMPVRY.
OrthoDBEOG7Z69BN.
PhylomeDBQ9H6S0.
TreeFamTF318311.

Gene expression databases

ArrayExpressQ9H6S0.
BgeeQ9H6S0.
CleanExHS_YTHDC2.
GenevestigatorQ9H6S0.

Family and domain databases

Gene3D1.25.40.20. 1 hit.
3.30.1370.50. 1 hit.
3.40.50.1820. 1 hit.
3.40.50.300. 2 hits.
InterProIPR029058. AB_hydrolase.
IPR002110. Ankyrin_rpt.
IPR020683. Ankyrin_rpt-contain_dom.
IPR011545. DNA/RNA_helicase_DEAD/DEAH_N.
IPR011709. DUF1605.
IPR007502. Helicase-assoc_dom.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR001374. R3H_ss-bd.
IPR007275. YTH_domain.
[Graphical view]
PfamPF12796. Ank_2. 1 hit.
PF00270. DEAD. 1 hit.
PF04408. HA2. 1 hit.
PF00271. Helicase_C. 1 hit.
PF07717. OB_NTP_bind. 1 hit.
PF01424. R3H. 1 hit.
PF04146. YTH. 1 hit.
[Graphical view]
SMARTSM00248. ANK. 2 hits.
SM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF48403. SSF48403. 1 hit.
SSF52540. SSF52540. 2 hits.
SSF82708. SSF82708. 1 hit.
PROSITEPS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51061. R3H. 1 hit.
PS50882. YTH. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ9H6S0.
GenomeRNAi64848.
NextBio66962.
PROQ9H6S0.

Entry information

Entry nameYTDC2_HUMAN
AccessionPrimary (citable) accession number: Q9H6S0
Secondary accession number(s): B2RP66
Entry history
Integrated into UniProtKB/Swiss-Prot: September 5, 2006
Last sequence update: June 16, 2009
Last modified: July 9, 2014
This is version 93 of the entry and version 2 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

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

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 5

Human chromosome 5: entries, gene names and cross-references to MIM