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Protein

YTH domain-containing protein 1

Gene

Ythdc1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs (By similarity). M6A is a modification present at internal sites of mRNAs and some non-coding RNAs and plays a role in the efficiency of mRNA splicing, processing and stability (By similarity). Acts as a key regulator of exon-inclusion or exon-skipping during alternative splicing via interaction with mRNA splicing factors SRSF3 and SRSF10 (By similarity). Specifically binds m6A-containing mRNAs and promotes recruitment of SRSF3 to its mRNA-binding elements adjacent to m6A sites, leading to exon-inclusion during alternative splicing (By similarity). In contrast, interaction with SRSF3 prevents interaction with SRSF10, a splicing factor that promotes exon skipping: this prevents SRSF10 from binding to its mRNA-binding sites close to m6A-containing regions, leading to inhibit exon skipping during alternative splicing (By similarity). May also regulate alternative splice site selection (By similarity). Also involved in nuclear export of m6A-containing mRNAs via interaction with SRSF3: interaction with SRSF3 facilitates m6A-containing mRNA-binding to both SRSF3 and NXF1, promoting mRNA nuclear export (By similarity). Also recognizes and binds m6A on other RNA molecules (By similarity). Involved in random X inactivation mediated by Xist RNA: recognizes and binds m6A-containing Xist and promotes transcription repression activity of Xist (By similarity). Involved in S-adenosyl-L-methionine homeostasis by regulating expression of MAT2A transcripts, probably by binding m6A-containing MAT2A mRNAs (PubMed:29262316).By similarity1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei378N6-methyladenosineBy similarity1
Binding sitei429N6-methyladenosineBy similarity1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRNA-binding
Biological processmRNA processing, mRNA splicing

Names & Taxonomyi

Protein namesi
Recommended name:
YTH domain-containing protein 1Curated
Gene namesi
Name:Ythdc1Imported
Synonyms:Kiaa19661 Publication
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:2443713 Ythdc1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00004255451 – 736YTH domain-containing protein 1Add BLAST736

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei35PhosphoserineBy similarity1
Cross-linki96Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei118PhosphoserineBy similarity1
Modified residuei120PhosphoserineBy similarity1
Modified residuei146PhosphoserineBy similarity1
Modified residuei148PhosphothreonineBy similarity1
Modified residuei309PhosphoserineCombined sources1
Modified residuei316PhosphoserineBy similarity1
Modified residuei318PhosphoserineBy similarity1
Modified residuei319PhosphoserineBy similarity1
Modified residuei321PhosphoserineBy similarity1
Modified residuei425PhosphoserineCombined sources1
Modified residuei436PhosphoserineBy similarity1
Modified residuei546PhosphoserineBy similarity1

Post-translational modificationi

Tyrosine phosphorylated.By similarity

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiE9Q5K9
PaxDbiE9Q5K9
PeptideAtlasiE9Q5K9
PRIDEiE9Q5K9

PTM databases

iPTMnetiE9Q5K9
PhosphoSitePlusiE9Q5K9

Expressioni

Gene expression databases

BgeeiENSMUSG00000035851
ExpressionAtlasiE9Q5K9 baseline and differential
GenevisibleiE9Q5K9 MM

Interactioni

Subunit structurei

Interacts with KHDRBS1/SAM68 (By similarity). Interacts with SRSF1 (By similarity). Interacts with SRSF2 (By similarity). Interacts with TRA2B (By similarity). Interacts with SRSF3 (By similarity). Interacts with SRSF10 (By similarity). Interacts with KHDRBS3 (By similarity). Interacts with EMD (By similarity). Interacts with RBMX (By similarity). Interacts with ZCCHC8 (By similarity).By similarity

Protein-protein interaction databases

IntActiE9Q5K9, 3 interactors
MINTiE9Q5K9
STRINGi10090.ENSMUSP00000039133

Structurei

3D structure databases

ProteinModelPortaliE9Q5K9
SMRiE9Q5K9
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini356 – 493YTHPROSITE-ProRule annotationAdd BLAST138

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni362 – 364N6-methyladenosine bindingBy similarity3

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi172 – 261Glu-richAdd BLAST90
Compositional biasi610 – 652Pro-richAdd BLAST43
Compositional biasi656 – 736Arg-richAdd BLAST81

Domaini

The YTH domain mediates RNA-binding.By similarity

Phylogenomic databases

eggNOGiKOG1902 Eukaryota
ENOG4111F6P LUCA
GeneTreeiENSGT00870000136533
HOGENOMiHOG000088650
KOiK20100
OMAiESTDTKR
OrthoDBiEOG091G0CXN

Family and domain databases

InterProiView protein in InterPro
IPR007275 YTH_domain
PfamiView protein in Pfam
PF04146 YTH, 1 hit
PROSITEiView protein in PROSITE
PS50882 YTH, 1 hit

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: E9Q5K9-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MAADSREEKD GELNVLDDIL TEVPEQDDEL YNPESEQDKN EKKGSKRKSE
60 70 80 90 100
RMESTDTKRQ KPSIHSRQLI SKPLSSSVSN NKRIVSTKGK SVTEYKNEEY
110 120 130 140 150
QRSERNKRLD ADRKIRLSSS SSREPYKSQP EKTCLRKRDS ERRAKSPTPD
160 170 180 190 200
GSERIGLEVD RRASRSSQSS KEEVNSEDYG SDHETGSSGS SEQGNNTENE
210 220 230 240 250
EEGGEEDVEE DEEVDEDAED DEEVDEDAEE EEEEDEEEEE DEDEDEEEEE
260 270 280 290 300
YEQDERDQKE EGNDYDTRSE ASDSGSESVS FTDGSVRSGS GTDGSDEKKK
310 320 330 340 350
ERKRARGISP IVFDRSGSSA SESYAGSEKK HEKLSSSVRA VRKDQTSKLK
360 370 380 390 400
YVLQDARFFL IKSNNHENVS LAKAKGVWST LPVNEKKLNL AFRSARSVIL
410 420 430 440 450
IFSVRESGKF QGFARLSSES HHGGSPIHWV LPAGMSAKML GGVFKIDWIC
460 470 480 490 500
RRELPFTKSA HLTNPWNEHK PVKIGRDGQE IELECGTQLC LLFPPDESID
510 520 530 540 550
LYQLIHKMRH KRRMHSQPRS RGRPSRREPV RDVGRRRPED YDIHNSRKKP
560 570 580 590 600
RIDYPPEFHQ RPGYVKDPRY QEVDSFTNLI PNRRFSGVRR DVFLNGSYND
610 620 630 640 650
YVREFHNMGP PPPWQGMPPY PGIEQPPHHP YYQHHAPPPQ AHPPYSGHHP
660 670 680 690 700
VPHEARYRDK RVHDYDMRVD DFLRRTQAVV SGRRSRPRER DRERERDRPR
710 720 730
DNRRDRERDR GRDRERERER ICDRDRDRGE RGRYRR
Length:736
Mass (Da):85,649
Last modified:February 19, 2014 - v2
Checksum:iDBB90CA82B28A9E0
GO
Isoform 2 (identifier: E9Q5K9-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     575-582: Missing.

Note: No experimental confirmation available.
Show »
Length:728
Mass (Da):84,762
Checksum:i62E7EE67EDAA2E45
GO
Isoform 3 (identifier: E9Q5K9-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     326-343: Missing.
     575-582: Missing.

Show »
Length:710
Mass (Da):82,754
Checksum:i27849237AFDA9BFD
GO

Sequence cautioni

The sequence AAH48817 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti680V → A in BAD32590 (PubMed:15368895).Curated1
Sequence conflicti733R → C in AAH48817 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_053719326 – 343Missing in isoform 3. CuratedAdd BLAST18
Alternative sequenceiVSP_053720575 – 582Missing in isoform 2 and isoform 3. 2 Publications8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AC102016 Genomic DNA No translation available.
AK173312 Transcribed RNA Translation: BAD32590.1
BC022697 mRNA Translation: AAH22697.1
BC048817 mRNA Translation: AAH48817.1 Different initiation.
CCDSiCCDS39127.1 [E9Q5K9-1]
CCDS84898.1 [E9Q5K9-2]
CCDS84899.1 [E9Q5K9-3]
RefSeqiNP_001334304.1, NM_001347375.1 [E9Q5K9-2]
NP_001334305.1, NM_001347376.1 [E9Q5K9-3]
NP_808348.2, NM_177680.3 [E9Q5K9-1]
UniGeneiMm.196325

Genome annotation databases

EnsembliENSMUST00000038384; ENSMUSP00000039133; ENSMUSG00000035851 [E9Q5K9-1]
ENSMUST00000119339; ENSMUSP00000113000; ENSMUSG00000035851 [E9Q5K9-3]
ENSMUST00000120498; ENSMUSP00000113951; ENSMUSG00000035851 [E9Q5K9-2]
GeneIDi231386
KEGGimmu:231386
UCSCiuc008xxw.1 mouse [E9Q5K9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiYTDC1_MOUSE
AccessioniPrimary (citable) accession number: E9Q5K9
Secondary accession number(s): E9PW44
, E9Q7Z8, Q69Z54, Q80V25, Q8R5E6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: February 19, 2014
Last modified: June 20, 2018
This is version 47 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

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