Q9H6S0 (YTDC2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Probable ATP-dependent RNA helicase YTHDC2
EC=3.6.4.13

Gene names

Name:

YTHDC2

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	1430 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Catalytic activity	ATP + H2O = ADP + phosphate.
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.

Ontologies

Keywords
Coding sequence diversity	Polymorphism
Domain	ANK repeat Repeat
Ligand	ATP-binding Nucleotide-binding
Molecular function	Helicase Hydrolase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATP-dependent helicase activity Inferred from electronic annotation. Source: InterPro nucleic acid binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Irak1	Q99J34	2	EBI-1057466,EBI-6117042	From a different organism.
IRF4	Q15306	2	EBI-1057466,EBI-751345

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1430

1430

Probable ATP-dependent RNA helicase YTHDC2

PRO_0000249340

Regions

Domain

38 – 106

69

R3H

Domain

203 – 369

167

Helicase ATP-binding

Repeat

506 – 538

33

ANK 1

Repeat

539 – 571

33

ANK 2

Domain

612 – 784

173

Helicase C-terminal

Domain

1288 – 1418

131

YTH

Nucleotide binding

216 – 223

8

ATP By similarity

Motif

316 – 319

4

DEAH box

Compositional bias

15 – 31

17

Gly-rich

Compositional bias

1248 – 1281

34

Ser-rich

Amino acid modifications

Modified residue

23

1

Phosphoserine Ref.6

Modified residue

1089

1

Phosphoserine Ref.5

Modified residue

1092

1

Phosphoserine Ref.4

Modified residue

1281

1

Phosphoserine Ref.4

Natural variations

Natural variant

652

1

S → N.
Corresponds to variant rs10071816 [ dbSNP | Ensembl ].

VAR_058002

Natural variant

1409

1

L → Q. Ref.3
Corresponds to variant rs1132528 [ dbSNP | Ensembl ].

VAR_058003

Experimental info

Sequence conflict

860

1

I → V in BAB15183. Ref.3

Sequence conflict

993

1

L → S in BAB15183. Ref.3

Sequence conflict

1230

1

Q → R in BAB15183. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

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.

.

.

.

.

1430

Helix Strand Turn

Details...

Beta strand

1289 – 1298

10

Helix

1299 – 1306

8

Beta strand

1309 – 1311

3

Helix

1317 – 1326

10

Beta strand

1330 – 1342

13

Beta strand

1344 – 1348

5

Beta strand

1352 – 1354

3

Beta strand

1368 – 1375

8

Helix

1381 – 1384

4

Beta strand

1404 – 1406

3

Helix

1410 – 1415

6

Helix

1416 – 1419

4

Sequences

	Sequence		Length	Mass (Da)
	Q9H6S0 [UniParc]. Last modified June 16, 2009. Version 2. Checksum: A0C3B45771A3DE16	FASTA	1,430	160,248
	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

References

	« Hide 'large scale' referencesShow '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. , 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. , 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, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[5]	"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, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[6]	"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, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"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].
[8]	"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].
[9]	"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.

IPI

IPI00010200.

RefSeq

NP_073739.3. NM_022828.3.

UniGene

Hs.231942.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2YU6	NMR	-	A	1288-1421	[»]

ProteinModelPortal

Q9H6S0.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q9H6S0. 7 interactions.

STRING

9606.ENSP00000161863.

PTM databases

PhosphoSite

Q9H6S0.

Polymorphism databases

DMDM

239938805.

Proteomic databases

PaxDb

Q9H6S0.

PeptideAtlas

Q9H6S0.

PRIDE

Q9H6S0.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000161863; ENSP00000161863; ENSG00000047188.

GeneID

64848.

KEGG

hsa:64848.

UCSC

uc003kqn.3. human.

Organism-specific databases

CTD

64848.

GeneCards

GC05P112877.

HGNC

HGNC:24721. YTHDC2.

HPA

HPA037364.

neXtProt

NX_Q9H6S0.

PharmGKB

PA134912676.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1643.

HOGENOM

HOG000155703.

HOVERGEN

HBG063891.

InParanoid

Q9H6S0.

OMA

RAFWESS.

OrthoDB

EOG4JWVCN.

PhylomeDB

Q9H6S0.

Gene expression databases

ArrayExpress

Q9H6S0.

Bgee

Q9H6S0.

CleanEx

HS_YTHDC2.

Genevestigator

Q9H6S0.

GermOnline

ENSG00000047188. Homo sapiens.

Family and domain databases

Gene3D

1.25.40.20. 1 hit.

InterPro

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.
IPR001374. R3H_ss-bd.
IPR007275. YTH_domain.
[Graphical view]

Pfam

PF12796. 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]

SMART

SM00248. ANK. 2 hits.
SM00487. DEXDc. 1 hit.
SM00847. HA2. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]

SUPFAM

SSF48403. ANK. 1 hit.

PROSITE

PS50297. ANK_REP_REGION. 1 hit.
PS50088. ANK_REPEAT. 1 hit.
PS00690. DEAH_ATP_HELICASE. False negative.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
PS51061. R3H. 1 hit.
PS50882. YTH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q9H6S0.

GenomeRNAi

64848.

NextBio

66962.

Entry information

Entry name

YTDC2_HUMAN

Accession

Primary (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:	May 1, 2013
This is version 82 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.