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Protein

YTH domain-containing protein 1

Gene

Ythdc1

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Specifically recognizes and binds N6-methyladenosine (m6A)-containing RNAs, and acts as a regulator of alternative splicing (PubMed:25389274). 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 (PubMed:25389274). 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 (PubMed:10564280, PubMed:9473574).By similarity3 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei380N6-methyladenosineBy similarity1
Binding sitei431N6-methyladenosineBy similarity1

GO - Molecular functioni

  • N6-methyladenosine-containing RNA binding Source: UniProtKB
  • poly(A) RNA binding Source: Ensembl
  • RNA binding Source: UniProtKB

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 1
Alternative name(s):
RA301-binding protein
Splicing factor YT5211 Publication
Gene namesi
Name:Ythdc1
Synonyms:Yt5211 Publication
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 14

Organism-specific databases

RGDi621706. Ythdc1.

Subcellular locationi

  • Nucleus 1 Publication
  • Nucleus speckle By similarity

  • Note: Localizes to a novel subnuclear structure, the YT bodies.1 Publication

GO - Cellular componenti

  • nuclear body Source: RGD
  • nuclear speck Source: UniProtKB
  • nucleoplasm Source: RGD
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002230771 – 738YTH domain-containing protein 1Add BLAST738

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei35PhosphoserineCombined sources1
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 residuei311PhosphoserineCombined sources1
Modified residuei318PhosphoserineBy similarity1
Modified residuei320PhosphoserineBy similarity1
Modified residuei321PhosphoserineBy similarity1
Modified residuei323PhosphoserineBy similarity1
Modified residuei427PhosphoserineBy similarity1
Modified residuei438PhosphoserineBy similarity1
Modified residuei548PhosphoserineBy similarity1

Post-translational modificationi

Tyrosine phosphorylated.1 Publication

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ9QY02.
PRIDEiQ9QY02.

PTM databases

iPTMnetiQ9QY02.
PhosphoSitePlusiQ9QY02.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Gene expression databases

BgeeiENSRNOG00000001996.
GenevisibleiQ9QY02. RN.

Interactioni

Subunit structurei

Interacts with KHDRBS1/SAM68 (PubMed:10564280). Interacts with SRSF1 (PubMed:10564280). Interacts with SRSF2 (PubMed:10564280). Interacts with SRSF3. Interacts with TRA2B (PubMed:10564280). Interacts with SRSF10 (By similarity). Interacts with KHDRBS3 (PubMed:11118435). Interacts with EMD (By similarity). Interacts with RBMX (PubMed:10564280).By similarity3 Publications

Protein-protein interaction databases

BioGridi251046. 1 interactor.
STRINGi10116.ENSRNOP00000002736.

Structurei

Secondary structure

1738
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi349 – 351Combined sources3
Helixi352 – 355Combined sources4
Beta strandi359 – 363Combined sources5
Helixi368 – 377Combined sources10
Helixi384 – 396Combined sources13
Beta strandi400 – 405Combined sources6
Turni407 – 409Combined sources3
Beta strandi411 – 418Combined sources8
Helixi439 – 441Combined sources3
Beta strandi446 – 452Combined sources7
Helixi458 – 460Combined sources3
Turni467 – 470Combined sources4
Beta strandi481 – 483Combined sources3
Helixi485 – 494Combined sources10
Helixi499 – 501Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MTVNMR-A347-502[»]
SMRiQ9QY02.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini358 – 495YTHPROSITE-ProRule annotationAdd BLAST138

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni364 – 366N6-methyladenosine bindingBy similarity3

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi172 – 263Glu-richAdd BLAST92
Compositional biasi612 – 654Pro-richAdd BLAST43
Compositional biasi658 – 738Arg-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.
HOVERGENiHBG055528.
InParanoidiQ9QY02.
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 (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9QY02-1) [UniParc]FASTAAdd to basket
Also known as: YT521-B1 Publication

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
RMESIDTKRQ KPSIHSRQLI SKPLSSSVSN NKRIVSTKGK SVTEYKNEEY
110 120 130 140 150
QRSERNKRLD ADRKIRLSSS SSREPYKSQP EKPCLRKRDS ERRAKSPTPD
160 170 180 190 200
GSERIGLEVD RRASRSSQSS KEEGNSEEYG SDHETGSSAS SEQGNNTENE
210 220 230 240 250
EEGGEEDVEE DEEVDEDGDD DEEVDEDAEE EEDEEEDEEE EDEEEEEEEE
260 270 280 290 300
EEYEQDERDQ KEEGNDYDTR SEASDSGSES VSFTDGSVRS GSGTDGSDEK
310 320 330 340 350
KKERKRARGI SPIVFDRSGS SASESYAGSE KKHEKLSSSV RAVRKDQTSK
360 370 380 390 400
LKYVLQDARF FLIKSNNHEN VSLAKAKGVW STLPVNEKKL NLAFRSARSV
410 420 430 440 450
ILIFSVRESG KFQGFARLSS ESHHGGSPIH WVLPAGMSAK MLGGVFKIDW
460 470 480 490 500
ICRRELPFTK SAHLTNPWNE HKPVKIGRDG QEIELECGTQ LCLLFPPDES
510 520 530 540 550
IDLYQLIHKM RHKRRMHSQP RSRGRPSRRE PVRDVGRRRP EDYDIHNSRK
560 570 580 590 600
KPRIDYPPEF HQRPGYLKDP RYQEVDSFTN LIPNRRFSGV RRDVFLNGSY
610 620 630 640 650
NDYVREFHNM GPPPPWQGMP PYPGIEQPPH HPYYQHHAPP PQAHPPYSGH
660 670 680 690 700
HPVPHEARYR DKRVHDYDMR VDDFLRRTQA VVSGRRSRPR ERDRERERDR
710 720 730
PRDNRRDRER DRGRDRERER ERICDRDRDR GERGRYRR
Length:738
Mass (Da):85,902
Last modified:February 19, 2014 - v2
Checksum:i9FC68314E029FA98
GO
Isoform 2 (identifier: Q9QY02-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     328-345: Missing.
     577-584: Missing.

Show »
Length:712
Mass (Da):83,006
Checksum:iF1F56DDD71AE580F
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti353Y → S in BAA23885 (PubMed:9473574).Curated1
Sequence conflicti353Y → S in AAD55973 (PubMed:10564280).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_006819328 – 345Missing in isoform 2. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_006820577 – 584Missing in isoform 2. 1 Publication8

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78303 mRNA. Translation: BAA23885.1.
AF144731 mRNA. Translation: AAD55973.1.
AABR06078005 Genomic DNA. No translation available.
CH473981 Genomic DNA. Translation: EDL89830.1.
RefSeqiNP_596914.1. NM_133423.1.
XP_006250870.1. XM_006250808.3. [Q9QY02-2]
UniGeneiRn.48752.

Genome annotation databases

EnsembliENSRNOT00000002736; ENSRNOP00000002736; ENSRNOG00000001996. [Q9QY02-1]
GeneIDi170956.
KEGGirno:170956.
UCSCiRGD:621706. rat. [Q9QY02-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D78303 mRNA. Translation: BAA23885.1.
AF144731 mRNA. Translation: AAD55973.1.
AABR06078005 Genomic DNA. No translation available.
CH473981 Genomic DNA. Translation: EDL89830.1.
RefSeqiNP_596914.1. NM_133423.1.
XP_006250870.1. XM_006250808.3. [Q9QY02-2]
UniGeneiRn.48752.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2MTVNMR-A347-502[»]
SMRiQ9QY02.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi251046. 1 interactor.
STRINGi10116.ENSRNOP00000002736.

PTM databases

iPTMnetiQ9QY02.
PhosphoSitePlusiQ9QY02.

Proteomic databases

PaxDbiQ9QY02.
PRIDEiQ9QY02.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000002736; ENSRNOP00000002736; ENSRNOG00000001996. [Q9QY02-1]
GeneIDi170956.
KEGGirno:170956.
UCSCiRGD:621706. rat. [Q9QY02-1]

Organism-specific databases

CTDi91746.
RGDi621706. Ythdc1.

Phylogenomic databases

eggNOGiKOG1902. Eukaryota.
ENOG4111F6P. LUCA.
GeneTreeiENSGT00390000017549.
HOGENOMiHOG000088650.
HOVERGENiHBG055528.
InParanoidiQ9QY02.
KOiK20100.
OMAiESTDTKR.
OrthoDBiEOG091G0CXN.

Miscellaneous databases

PROiQ9QY02.

Gene expression databases

BgeeiENSRNOG00000001996.
GenevisibleiQ9QY02. RN.

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_RAT
AccessioniPrimary (citable) accession number: Q9QY02
Secondary accession number(s): G3V690, O54729
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 12, 2003
Last sequence update: February 19, 2014
Last modified: November 2, 2016
This is version 109 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  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.