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Protein

YTH domain-containing protein 1

Gene

Ythdc1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Regulator of alternative splicing that specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs. 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. Acts as a key regulator of exon-inclusion or exon-skipping during alternative splicing via interaction with mRNA splicing factors SRSF3 and SRSF10. 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. 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. May also regulate alternative splice site selection.By similarity

Sites

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

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Biological processi

mRNA processing, mRNA splicing

Keywords - Ligandi

RNA-binding

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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:2443713. Ythdc1.

Subcellular locationi

  • Nucleus By similarity
  • Nucleus speckle By similarity

  • Note: Localizes to a novel subnuclear structure, the YT bodies.By similarity

GO - Cellular componenti

Complete GO annotation...

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).By similarity

Protein-protein interaction databases

IntActiE9Q5K9. 3 interactors.
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

Sequence similaritiesi

Contains 1 YTH domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1902. Eukaryota.
ENOG4111F6P. LUCA.
GeneTreeiENSGT00390000017549.
HOGENOMiHOG000088650.
KOiK20100.
OMAiESTDTKR.
OrthoDBiEOG091G0CXN.

Family and domain databases

InterProiIPR007275. YTH_domain.
[Graphical view]
PfamiPF04146. YTH. 1 hit.
[Graphical view]
PROSITEiPS50882. YTH. 1 hit.
[Graphical view]

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]
RefSeqiNP_808348.2. NM_177680.3. [E9Q5K9-1]
XP_017176331.1. XM_017320842.1. [E9Q5K9-2]
XP_017176333.1. XM_017320844.1. [E9Q5K9-3]
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

Cross-referencesi

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]
RefSeqiNP_808348.2. NM_177680.3. [E9Q5K9-1]
XP_017176331.1. XM_017320842.1. [E9Q5K9-2]
XP_017176333.1. XM_017320844.1. [E9Q5K9-3]
UniGeneiMm.196325.

3D structure databases

ProteinModelPortaliE9Q5K9.
SMRiE9Q5K9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiE9Q5K9. 3 interactors.
STRINGi10090.ENSMUSP00000039133.

PTM databases

iPTMnetiE9Q5K9.
PhosphoSitePlusiE9Q5K9.

Proteomic databases

MaxQBiE9Q5K9.
PaxDbiE9Q5K9.
PeptideAtlasiE9Q5K9.
PRIDEiE9Q5K9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi91746.
MGIiMGI:2443713. Ythdc1.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1902. Eukaryota.
ENOG4111F6P. LUCA.
GeneTreeiENSGT00390000017549.
HOGENOMiHOG000088650.
KOiK20100.
OMAiESTDTKR.
OrthoDBiEOG091G0CXN.

Miscellaneous databases

PROiE9Q5K9.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000035851.
ExpressionAtlasiE9Q5K9. baseline and differential.
GenevisibleiE9Q5K9. MM.

Family and domain databases

InterProiIPR007275. YTH_domain.
[Graphical view]
PfamiPF04146. YTH. 1 hit.
[Graphical view]
PROSITEiPS50882. YTH. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiYTDC1_MOUSE
AccessioniPrimary (citable) accession number: E9Q5K9
Secondary accession number(s): E9PW44
, E9Q7Z8, Q69Z54, Q80V25, Q8R5E6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 19, 2014
Last sequence update: February 19, 2014
Last modified: November 2, 2016
This is version 41 of the entry and version 2 of the sequence. [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
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.