Q96MU7 (YTDC1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
YTH domain-containing protein 1

Alternative name(s):
Putative splicing factor YT521

Gene names

Name:	YTHDC1
Synonyms:	KIAA1966, YT521

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	727 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	May be part of a signal transduction pathway that influences splice site selection By similarity.
Subunit structure	Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, TRA2B/SFRS10, SC35 and SF2 By similarity. Interacts with RBMX. Ref.5 Ref.16
Subcellular location	Nucleus By similarity. Note: Localizes to a novel subnuclear structure, the YT bodies By similarity.
Sequence similarities	Contains 1 YTH domain.
Sequence caution	The sequence AAY41024.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence BAB71181.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	mRNA processing mRNA splicing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing Polymorphism
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Molecular function	protein binding Inferred from physical interaction Ref.16. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q96MU7-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q96MU7-2)

The sequence of this isoform differs from the canonical sequence as follows:
     325-342: Missing.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 727

727

YTH domain-containing protein 1

PRO_0000223076

Regions

Domain

355 – 492

138

YTH

Compositional bias

172 – 260

89

Glu-rich

Compositional bias

508 – 581

74

Arg-rich

Compositional bias

601 – 643

43

Pro-rich

Compositional bias

647 – 727

81

Arg-rich

Amino acid modifications

Modified residue

118

1

Phosphoserine Ref.12

Modified residue

146

1

Phosphoserine Ref.6 Ref.7 Ref.8

Modified residue

148

1

Phosphothreonine Ref.6 Ref.7

Modified residue

275

1

Phosphoserine Ref.6

Modified residue

308

1

Phosphoserine Ref.6 Ref.8 Ref.9 Ref.10 Ref.12 Ref.13 Ref.14 Ref.15

Modified residue

315

1

Phosphoserine Ref.8 Ref.14

Modified residue

317

1

Phosphoserine Ref.8 Ref.14

Modified residue

318

1

Phosphoserine Ref.8 Ref.14

Modified residue

320

1

Phosphoserine Ref.6 Ref.8 Ref.14

Modified residue

322

1

Phosphoserine Ref.8

Modified residue

323

1

Phosphotyrosine Ref.8

Modified residue

326

1

Phosphoserine Ref.6 Ref.8

Modified residue

424

1

Phosphoserine Ref.14 Ref.15

Modified residue

515

1

Phosphoserine Ref.8

Modified residue

545

1

Phosphoserine Ref.11

Modified residue

577

1

Phosphoserine Ref.12

Natural variations

Alternative sequence

325 – 342

18

Missing in isoform 2.

VSP_006818

Natural variant

183

1

H → R.
Corresponds to variant rs3813832 [ dbSNP | Ensembl ].

VAR_053746

Experimental info

Sequence conflict

619

1

H → Q in BAB71181. Ref.1

Secondary structure

1

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727

Helix Strand Turn

Details...

Helix

346 – 351

6

Turn

352 – 354

3

Beta strand

356 – 363

8

Helix

365 – 374

10

Helix

381 – 393

13

Beta strand

397 – 403

7

Turn

404 – 406

3

Beta strand

407 – 420

14

Helix

436 – 439

4

Beta strand

441 – 449

9

Helix

455 – 458

4

Turn

464 – 466

3

Beta strand

467 – 469

3

Beta strand

478 – 480

3

Helix

482 – 491

10

Beta strand

496 – 498

3

Helix

501 – 508

8

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified May 24, 2004. Version 3. Checksum: 536032FD44582EAF	FASTA	727	84,700
	10 20 30 40 50 60 MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSD RMESTDTKRQ 70 80 90 100 110 120 KPSVHSRQLV SKPLSSSVSN NKRIVSTKGK SATEYKNEEY QRSERNKRLD ADRKIRLSSS 130 140 150 160 170 180 ASREPYKNQP EKTCVRKRDP ERRAKSPTPD GSERIGLEVD RRASRSSQSS KEEVNSEEYG 190 200 210 220 230 240 SDHETGSSGS SDEQGNNTEN EEEGVEEDVE EDEEVEEDAE EDEEVDEDGE EEEEEEEEEE 250 260 270 280 290 300 EEEEEEEEEY EQDERDQKEE GNDYDTRSEA SDSGSESVSF TDGSVRSGSG TDGSDEKKKE 310 320 330 340 350 360 RKRARGISPI VFDRSGSSAS ESYAGSEKKH EKLSSSVRAV RKDQTSKLKY VLQDARFFLI 370 380 390 400 410 420 KSNNHENVSL AKAKGVWSTL PVNEKKLNLA FRSARSVILI FSVRESGKFQ GFARLSSESH 430 440 450 460 470 480 HGGSPIHWVL PAGMSAKMLG GVFKIDWICR RELPFTKSAH LTNPWNEHKP VKIGRDGQEI 490 500 510 520 530 540 ELECGTQLCL LFPPDESIDL YQVIHKMRHK RRMHSQPRSR GRPSRREPVR DVGRRRPEDY 550 560 570 580 590 600 DIHNSRKKPR IDYPPEFHQR PGYLKDPRYQ EVDRRFSGVR RDVFLNGSYN DYVREFHNMG 610 620 630 640 650 660 PPPPWQGMPP YPGMEQPPHH PYYQHHAPPP QAHPPYSGHH PVPHEARYRD KRVHDYDMRV 670 680 690 700 710 720 DDFLRRTQAV VSGRRSRPRE RDRERERDRP RDNRRDRERD RGRDRERERE RLCDRDRDRG ERGRYRR
	Isoform 2 [UniParc]. Checksum: C02121B27DDEFF0E	FASTA	709	82,692
	10 20 30 40 50 60 MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSD RMESTDTKRQ 70 80 90 100 110 120 KPSVHSRQLV SKPLSSSVSN NKRIVSTKGK SATEYKNEEY QRSERNKRLD ADRKIRLSSS 130 140 150 160 170 180 ASREPYKNQP EKTCVRKRDP ERRAKSPTPD GSERIGLEVD RRASRSSQSS KEEVNSEEYG 190 200 210 220 230 240 SDHETGSSGS SDEQGNNTEN EEEGVEEDVE EDEEVEEDAE EDEEVDEDGE EEEEEEEEEE 250 260 270 280 290 300 EEEEEEEEEY EQDERDQKEE GNDYDTRSEA SDSGSESVSF TDGSVRSGSG TDGSDEKKKE 310 320 330 340 350 360 RKRARGISPI VFDRSGSSAS ESYADQTSKL KYVLQDARFF LIKSNNHENV SLAKAKGVWS 370 380 390 400 410 420 TLPVNEKKLN LAFRSARSVI LIFSVRESGK FQGFARLSSE SHHGGSPIHW VLPAGMSAKM 430 440 450 460 470 480 LGGVFKIDWI CRRELPFTKS AHLTNPWNEH KPVKIGRDGQ EIELECGTQL CLLFPPDESI 490 500 510 520 530 540 DLYQVIHKMR HKRRMHSQPR SRGRPSRREP VRDVGRRRPE DYDIHNSRKK PRIDYPPEFH 550 560 570 580 590 600 QRPGYLKDPR YQEVDRRFSG VRRDVFLNGS YNDYVREFHN MGPPPPWQGM PPYPGMEQPP 610 620 630 640 650 660 HHPYYQHHAP PPQAHPPYSG HHPVPHEARY RDKRVHDYDM RVDDFLRRTQ AVVSGRRSRP 670 680 690 700 RERDRERERD RPRDNRRDRE RDRGRDRERE RERLCDRDRD RGERGRYRR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[2]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed: 15815621] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Skin.
[4]	"Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins." Nagase T., Kikuno R., Ohara O. DNA Res. 8:319-327(2001) [PubMed: 11853319] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 248-727 (ISOFORM 1). Tissue: Brain.
[5]	"Emerin interacts in vitro with the splicing-associated factor, YT521-B." Wilkinson F.L., Holaska J.M., Zhang Z., Sharma A., Manilal S., Holt I., Stamm S., Wilson K.L., Morris G.E. Eur. J. Biochem. 270:2459-2466(2003) [PubMed: 12755701] [Abstract] Cited for: INTERACTION WITH EMD.
[6]	"Large-scale characterization of HeLa cell nuclear phosphoproteins." Beausoleil S.A., Jedrychowski M., Schwartz D., Elias J.E., Villen J., Li J., Cohn M.A., Cantley L.C., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 101:12130-12135(2004) [PubMed: 15302935] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146; THR-148; SER-275; SER-308; SER-320 AND SER-326, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"Global phosphoproteome of HT-29 human colon adenocarcinoma cells." Kim J.-E., Tannenbaum S.R., White F.M. J. Proteome Res. 4:1339-1346(2005) [PubMed: 16083285] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146 AND THR-148, MASS SPECTROMETRY. Tissue: Colon adenocarcinoma.
[8]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed: 17081983] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-146; SER-308; SER-315; SER-317; SER-318; SER-320; SER-322; TYR-323; SER-326 AND SER-515, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[9]	"A probability-based approach for high-throughput protein phosphorylation analysis and site localization." Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P. Nat. Biotechnol. 24:1285-1292(2006) [PubMed: 16964243] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[10]	"Phosphoproteome analysis of the human mitotic spindle." Nousiainen M., Sillje H.H.W., Sauer G., Nigg E.A., Koerner R. Proc. Natl. Acad. Sci. U.S.A. 103:5391-5396(2006) [PubMed: 16565220] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308, MASS SPECTROMETRY. Tissue: Cervix adenocarcinoma.
[11]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed: 17924679] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-545, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[12]	"Evaluation of the low-specificity protease elastase for large-scale phosphoproteome analysis." Wang B., Malik R., Nigg E.A., Korner R. Anal. Chem. 80:9526-9533(2008) [PubMed: 19007248] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-118; SER-308 AND SER-577, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[13]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed: 18691976] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[14]	"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: 18669648] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308; SER-315; SER-317; SER-318; SER-320 AND SER-424, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[15]	"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: 19413330] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-308 AND SER-424, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[16]	"Heterogeneous nuclear ribonucleoprotein G regulates splice site selection by binding to CC(A/C)-rich regions in pre-mRNA." Heinrich B., Zhang Z., Raitskin O., Hiller M., Benderska N., Hartmann A.M., Bracco L., Elliott D., Ben-Ari S., Soreq H., Sperling J., Sperling R., Stamm S. J. Biol. Chem. 284:14303-14315(2009) [PubMed: 19282290] [Abstract] Cited for: INTERACTION WITH RBMX.
[17]	"Solution structure of the YTH domain in YTH domain-containing protein 1 (putative splicing factor yt521)." RIKEN structural genomics initiative (RSGI) Submitted (OCT-2007) to the PDB data bank Cited for: STRUCTURE BY NMR OF 334-509.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AK056430 mRNA. Translation: BAB71181.1. Different initiation.
AC074378 Genomic DNA. Translation: AAY41024.1. Sequence problems.
BC041119 mRNA. Translation: AAH41119.1.
BC053863 mRNA. Translation: AAH53863.1.
AB075846 mRNA. Translation: BAB85552.1.

IPI

IPI00144293.
IPI00376222.

RefSeq

NP_001026902.1. NM_001031732.2.
NP_588611.2. NM_133370.2.

UniGene

Hs.175955.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2YUD	NMR	-	A	337-509	[»]

ProteinModelPortal

Q96MU7.

SMR

Q96MU7. Positions 334-509.

ModBase

Search...

Protein-protein interaction databases

IntAct

Q96MU7. 18 interactions.

STRING

Q96MU7.

PTM databases

PhosphoSite

Q96MU7.

Polymorphism databases

DMDM

47606762.

Proteomic databases

PRIDE

Q96MU7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000344157; ENSP00000339245; ENSG00000083896.

GeneID

91746.

KEGG

hsa:91746.

UCSC

uc003hdx.1. human.
uc003hdy.1. human.

Organism-specific databases

CTD

91746.

GeneCards

GC04M069176.

HGNC

HGNC:30626. YTHDC1.

HPA

HPA036462.
HPA036463.

neXtProt

NX_Q96MU7.

PharmGKB

PA143485673.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG15717.

GeneTree

ENSGT00570000079050.

HOGENOM

HBG715473.

HOVERGEN

HBG055528.

InParanoid

Q96MU7.

OMA

RKSDRME.

OrthoDB

EOG4ZW5BC.

PhylomeDB

Q96MU7.

Gene expression databases

ArrayExpress

Q96MU7.

Bgee

Q96MU7.

CleanEx

HS_YTHDC1.

Genevestigator

Q96MU7.

GermOnline

ENSG00000083896. Homo sapiens.

Family and domain databases

InterPro

IPR007275. YTH_domain.
[Graphical view]

Pfam

PF04146. YTH. 1 hit.
[Graphical view]

PROSITE

PS50882. YTH. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

77419.

Entry information

Entry name

YTDC1_HUMAN

Accession

Primary (citable) accession number: Q96MU7
Secondary accession number(s): Q4W5Q3, Q7Z622, Q8TF35

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 12, 2003
Last sequence update:	May 24, 2004
Last modified:	January 25, 2012
This is version 96 of the entry and version 3 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.