Aliases &
Descriptions
for YTHDC1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase)
About This Section
|
| Aliases & Descriptions |
|---|
| YTH domain containing 11 2 | | Putative splicing factor YT5212 3 | | KIAA19661 2 3 | | YTH domain-containing protein 12 | | YT5211 2 3 | | splicing factor YT521-B2 | | YT521-B1 2 | | |
Export aliases for YTHDC1 gene to outside databasesPrevious GC identifers: GC04M069008 GC04M068858 GC04M069176 |
Summaries
for YTHDC1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7Function: May be part of a signal transduction pathway that influences splice site selection (By similarity)
Gene Wiki entry for YTHDC1 |
Genomic Views
for YTHDC1 gene
(According to
GeneLoc and/or
HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to
UCSC (hg19) and
Ensembl (release 60),
Regulatory elements and Epigenetics data according to
Qiagen and/or
SABiosciences)
About This Section
|
Regulatory elements:
 SABiosciences Regulatory transcription factor binding sites in the YTHDC1 gene promoter:
E2F-4 E2F-3a E2F-2 E2F-1 E2F E2F-5 FOXO1a FOXF2 ITF-2 Tal-1beta
Other transcription factors
Search SABiosciences Chromatin IP Primers for YTHDC1
Epigenetics:
|  | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays for YTHDC1  |
Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track
Entrez Gene cytogenetic band: 4q13.2 Ensembl cytogenetic band: 4q13.2 HGNC cytogenetic band: 4q13.3YTHDC1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
GeneLoc gene densities for chromosome 4 GeneLoc Exon Structure GeneLoc location for GC04M065089: view genomic region
(about GC identifiers)
Start:
|
65,089,319 bp from pter |
End:
|
65,129,187 bp from pter |
Size:
|
39,869 bases |
Orientation:
|
minus strand |
2 alternative locations:
| Chr4-,ALT_REF_LOCI_8 69,234,939-69,274,658 | Chr4- 69,176,105-69,215,807 |
RefSeq DNA sequence:- NC_000004.11 NT_022778.16 NT_167250.1
|
Proteins
for YTHDC1 gene
(According to
1UniProtKB,
neXtProt,
and/or Ensembl,
Phosphorylation sites according to 2Phosphosite,
RefSeq according to NCBI,
PDB rendering according to OCA and/or Proteopedia,
Recombinant Proteins
from
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Enzo Life Sciences,
OriGene,
Novus Biologicals,
Sino Biological, and/or
ProSpec,
Biochemical Assays by
Millipore,
Sigma-Aldrich,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Dec 2010 and
Entrez Gene,
Antibodies by
Millipore,
Sigma-Aldrich,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals, and/or
Epitomics)
About This Section
|
UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7 (See
protein sequence)Recommended Name: YTH domain-containing protein 1 Size: 727 amino acids; 84700 Da
Subunit: Interacts with EMD, KHDRBS1/SAM68, KHDRBS3, TRA2B/SFRS10, SC35 and SF2 (By similarity)
Subcellular location: Nucleus (By similarity). Note=Localizes to a novel subnuclear structure, the YT bodies (Bysimilarity)
Sequence caution: Sequence=AAY41024.1; Type=Erroneous gene model prediction; Sequence=BAB71181.1; Type=Erroneousinitiation;
PDB structures from  and Proteopedia  :2YUD (3D)
Secondary accessions: Q4W5Q3 Q7Z622 Q8TF35Alternative splicing: 2 isoforms: Q96MU7-1 Q96MU7-2 Explore the universe of human proteins at neXtProt for YTHDC1: NX_Q96MU7
Post-translational modifications:
View phosphorylation sites using PhosphoSite2
REFSEQ proteins (2 alternative transcripts):
NP_001026902.1 NP_588611.2
ENSEMBL proteins: ENSP00000339245 ENSP00000347888
Human Recombinant Proteins
3 Gene Ontology (GO) cellular component terms (GO ID links to tree view): About this table
YTHDC1 for ontologies About GeneDecksing
Antibodies for YTHDC1:
Assays for YTHDC1: |
Protein
Domains/
Families
for YTHDC1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
YTHDC1 for domains About GeneDecksing
1 InterPro domain/family:Graphical View of Domain Structure for InterPro Entry Q96MU7ProtoNet protein and cluster: Q96MU7 1 Blocks protein family: IPB007275 YT521-B-like protein
UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7Similarity: Contains 1 YTH domain |
Gene Function
for YTHDC1 gene
(According to UniProtKB,
IUBMB,and/or
Genatlas, Animal models from MGI Dec 24 2010,
shRNA from
OriGene,
Sigma-Aldrich,
RNAi from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Clones from Millipore,
Sigma-Aldrich,
OriGene,
GenScript,
Sino Biological,
Cell Lines from GenScript,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene.)
About This Section
|
UniProtKB/Swiss-Prot: YTDC1_HUMAN, Q96MU7Function: May be part of a signal transduction pathway that influences splice site selection (By similarity)
1 Gene Ontology (GO) molecular function term (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005515 | protein binding |
IEA | -- |
About this table
YTHDC1 for ontologies About GeneDecksing
|
Pathways & Interactions
for YTHDC1 gene
(Pathways according to
Millipore,
Cell Signaling Technology,
Sigma-Aldrich,
KEGG
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
PCR Arrays from
SABiosciences,
Proteins Network according to
SABiosciences,
Sigma-Aldrich,
Interactions according to 1UniProtKB,
2MINT, and/or
3STRING,
with links to IntAct and
Ensembl,
Ontologies according to Gene Ontology Consortium 01 Dec 2010 via
Entrez Gene).
About This Section
|
SABiosciences Custom Pathway-Focused PCR Arrays for YTHDC1
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YTHDC1
2 Gene Ontology (GO) biological process terms (GO ID links to tree view): | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0000398 | nuclear mRNA splicing, via spliceosome |
IEA | -- | | GO:0008380 | RNA splicing |
IEA | -- |
About this table
YTHDC1 for ontologies About GeneDecksing
|
Drugs & Compounds
for YTHDC1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
Sigma-Aldrich, Tocris Bioscience, and/or
Novoseek and Drugs according to
Enzo Life Sciences and/or
PharmGKB)
About This Section
|
 Browse Tocris compounds for YTHDC1
|
Transcripts
for YTHDC1 gene(GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 228 Homo sapiens; Dec 8 2010) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or
AceView,
transcript ids from Ensembl
with links to UCSC,
non coding RNAs according to
RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc,
alternative splicing isoforms according to ASD and/or
ECgene,
RNAi Products from
Millipore,
siRNAs from
Sigma-Aldrich,
OriGene,
Qiagen,
Super-pooled esiRNAs from Sigma-Aldrich,
shRNA from
Sigma-Aldrich,
OriGene,
microRNA from Sigma-Aldrich,
Qiagen,
SABiosciences,
Tagged/untagged cDNA clones from
OriGene,
Sigma-Aldrich,
GenScript,
Primers from
OriGene and/or
SABiosciences)
About This Section
|
REFSEQ mRNAs for YTHDC1 gene (2 alternative transcripts): NM_001031732.2 NM_133370.2 Additional cDNA sequence: AB075846.1 AK056430.1 AK090836.1 AK098515.1 AL049340.1 AL157447.1 AL832559.1 BC041119.1 BC053863.1 19 DOTS entries: DT.319276 DT.95226740 DT.208534 DT.100030794 DT.310194 DT.319271 DT.40206935 DT.95095287 DT.121236845 DT.92434776 DT.97826357 DT.310195 DT.92410275 DT.92419278 DT.92434777 DT.100680976 DT.99939310 DT.91754711 DT.95226769 24/271 AceView cDNA sequences (see all 271): AL598932 AI867928 BM677688 BQ231724 BU508352 CA422945 AI383836 BU622854 AV705969 AI989475 AB075846 CA448429 CA441489 BU616437 CB152758 AV650131 CA436862 AK098515 CB151726 BQ029994 BC041119 AA808827 BQ717244 BU735768
 highest scoring ESTs for YTHDC1:AI990739 AI082831 AI350438 AI380475 AI478440 AI798629 AI989475 AI990284 AK056430 AL120288 Unigene Cluster for YTHDC1: YTH domain containing 1 Hs.175955 [show with all ESTs]Unigene Representative Sequence: NM_001031732
GeneLoc Exon Structure
5/13 Alternative Splicing Database (ASD) splice patterns (SP) for YTHDC1 (see all 13)
| ExUns: | 1a | · | 1b | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5a | · | 5b | ^ | 6 | ^ | 7a | · | 7b | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13a | · | 13b | · | 13c | ^ | 14a | · | 14b | ^ | 15 | ^ | 16 | ^ | 17 | ^ | 18 | ^ | 19 | ^ | 20a | · |
|---|
|
| SP1: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | - | | |
| SP2: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | - | | |
| SP3: | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - | | - | | | | | | - | | |
| SP4: | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | | | | | | | | - | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
| ExUns: | 20b | · | 20c | ^ | 21 | ^ | 22a | · | 22b | · | 22c | ^ | 23a | · | 23b |
|---|
|
| SP1: | - | | | | | | - | | | | | | | | | | |
| SP2: | | | | | | | | | | | | | | | | | |
| SP3: | | | | | | | - | | | | | | | | | | |
| SP4: | | | | | | | | | | | | | | | | | |
| SP5: | | | | | | | | | | | | | | | | |
About this scheme
ECgene alternative splicing isoforms for YTHDC1
6 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000510746 ENST00000505251 ENST00000344157(uc003hdx.2 uc003hdy.2)
ENST00000507529 ENST00000355665 ENST00000506175
|
Expression
for YTHDC1 gene
(Experimental results according to
1GeneNote
and GNF BioGPS,
probe sets-to-genes annotations according to
2GeneAnnot ,
3GeneTide ,
Sets of similar genes according to GeneDecks,
Electronic Northern calculations according to data from
UniGene (Build 228 Homo sapiens),
SAGE tags according to
CGAP,
plus additional links to
SOURCE, and/or
GNF
BioGPS, and/or
EXPOLDB, and/or
UniProtKB,
Primers from
OriGene and/or
SABiosciences
)
About This Section
| YTHDC1 expression in normal and diseased human tissues
1 / 2 / 3 13 probe-sets matching YTHDC1 gene
Affymetrix
probe-set |
Array |
GeneAnnot data |
GeneNote data |
GeneTide data |
| # genes |
Sensitivity |
Specificity |
Correlation |
Length |
Gb_Accession |
Consensus |
Uniqueness |
Score |
Rank |
| 75055_i_at2, 3
|
U95-E |
1 |
1.00 |
1.00 |
0.26 |
0.11 |
AI990284 |
0.80 |
1.00 |
0.91 |
1 |
| 39897_at2, 3
|
U95-A |
1 |
1.00 |
1.00 |
0.71 |
1.74 |
N36997 |
0.80 |
1.00 |
0.91 |
1 |
| 91604_at2, 3
|
U95-D |
1 |
0.88 |
1.00 |
0.49 |
1.28 |
AI521494 |
0.60 |
1.00 |
0.82 |
1 |
| 87919_at2, 3
|
U95-E |
1 |
0.88 |
1.00 |
0.23 |
0.46 |
AI990739 |
1.00 |
1.00 |
1.00 |
1 |
| 83578_at2, 3
|
U95-D |
1 |
0.81 |
1.00 |
0.34 |
1.01 |
AI400684 |
0.60 |
1.00 |
0.82 |
1 |
| 46050_r_at2, 3
|
U95-B |
1 |
0.81 |
1.00 |
0.50 |
0.49 |
AL120288 |
0.80 |
1.00 |
0.91 |
1 |
| 75057_r_at2, 3
|
U95-E |
1 |
0.81 |
1.00 |
0.25 |
0.57 |
AI990284 |
0.80 |
1.00 |
0.91 |
1 |
| 212455_at2, 3
|
U133-A |
1 |
1.00 |
1.00 |
-- |
-- |
N36997 |
0.80 |
1.00 |
0.91 |
1 |
| 228556_at2, 3
|
U133-B |
1 |
0.91 |
1.00 |
-- |
-- |
AI990739 |
1.00 |
1.00 |
1.00 |
1 |
| 240459_at2, 3
|
U133-B |
1 |
0.82 |
1.00 |
-- |
-- |
AW467048 |
0.40 |
1.00 |
0.76 |
1 |
| 212455_at2
|
U133Plus2 |
1 |
1.00 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 228556_at2
|
U133Plus2 |
1 |
0.91 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
| 240459_at2
|
U133Plus2 |
1 |
0.82 |
1.00 |
-- |
-- |
-- |
-- |
-- |
-- |
-- |
About this table
YTHDC1 for expression About GeneDecksing
Data from
Genenote
(Publications) and GNF BioGPS
About these images
About these images
CGAP SAGE TAG: TAGTTGCACA
SOURCE GeneReport for Unigene cluster: Hs.175955
SABiosciences Custom PCR Arrays for YTHDC1
|
Orthologs
for YTHDC1 gene
(Orthologs according to
1,2HomoloGene (2older version, for species not in 1newer version),
3euGenes,
4SGD
and/or
5MGI Dec 24 2010,
with possible further links to
Flybase
and/or
WormBase,
Gene Trees according to Ensembl)
About This Section
|
Orthologs for YTHDC1 gene from 5/12 species (see all 12)
About this table Species with no ortholog for YTHDC1
ENSEMBL Gene Tree for YTHDC1 (if available) |
Paralogs
for YTHDC1 gene(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section
| Paralogs for YTHDC1 gene
- ENSG000002360372 PELP12 ENSG000002296242 ENSG000002376952 ENSG000002275722 ENSG000002316932 ENSG000002340452 ENSG000002349082
- ENSG000002329042 ENSG000002308082 ENSG000002278912 ENSG000002285582 ENSG000002293192 ENSG000002313602 ENSG000002355172 ENSG000002411542
- ENSG000002302222 ENSG000002432592 ENSG000002286322 ENSG000002372012 ENSG000002378782 ENSG000002273772 ENSG000002234112 ENSG000002377662
- ENSG000002278202 ENSG000002281012 ENSG000002376922
YTHDC1 for paralogs About GeneDecksing
|
Genomic Variants
for YTHDC1 gene(SNPs according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Resequencing Primers from Qiagen)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Chr 4 pos | Sequence | Recs | AA
Chg | Type | More | Recs | Allele
freq | Pop | Total
sample | More |
|---|
About this tableHapMap Linkage Disequilibrium images for YTHDC1 (up to first 250kb)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 1 variation for YTHDC1
1 CNV: 3499 | | QIAGEN SeqTarget long-range PCR primers for resequencing YTHDC1 |
|
Disorders & Mutations
for YTHDC1 gene
(in which this Gene is Involved, According to
OMIM, UniProtKB,
PharmGKB,
Genatlas, GeneTests,
Blood group antigen gene mutations by BGMUT,
LSDB, HGMD, GAD,
HuGE Navigator,
and/or TGDB.)
About This Section
| -- |
Medical News
for YTHDC1 gene(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications
for YTHDC1 gene (in
PubMed.
Associations of this gene to articles via
1Entrez Gene,
2UniProtKB/Swiss-Prot,
3HGNC,
4GAD,
5PharmGKB,
6UniProtKB/TrEMBL, and/or
7Novoseek)
About This Section
|
10/25 PubMed articles for YTHDC1 gene, integrated from 7 sources (see all 25):
(articles sorted by number of sources associating them with YTHDC1)- Emerin interacts in vitro with the splicing-associated factor, YT521- B. (PubMed id 12755701)1, 2, 7 Wilkinson F.L.... Morris G.E. (2003)
- YTH: a new domain in nuclear proteins. (PubMed id 12368078)1, 3, 7 Stoilov P....Stamm S. (2002)
- Phosphoproteome analysis of the human mitotic spindle. (PubMed id 16565220)1, 2 Nousiainen M.... Koerner R. (2006)
- A probability-based approach for high-throughput protein phosphorylation analysis and site localization. (PubMed id 16964243)1, 2 Beausoleil S.A.... Gygi S.P. (2006)
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (2006)
- Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)1, 2 Hillier L.W....Wilson R.K. (2005)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
- Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
- Large-scale characterization of HeLa cell nuclear phosphoproteins. (PubMed id 15302935)1, 2 Beausoleil S.A....Gygi S.P. (2004)
- Prediction of the coding sequences of unidentified human genes. XXII. The complete sequences of 50 new cDNA clones which code for large proteins. (PubMed id 11853319)1, 2 Nagase T.... Ohara O. (2001)
|
External Searches for YTHDC1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing YTHDC1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing YTHDC1 gene
(According to HUGE)
About This Section
| |
Specialized Databases showing YTHDC1 gene(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
|
About This Section
| Patent Information for YTHDC1 gene:
Search GeneIP for patents involving YTHDC1
GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search
|
Products
for YTHDC1 gene(Antibodies, recombinant proteins, and assays by Millipore, Sigma-Aldrich, R&D Systems, Qiagen, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Epitomics, ProSpec, Uscn,
Clones available from Millipore, Sigma-Aldrich, OriGene, GenScript, Sino Biological, PCR Arrays from SABiosciences, Drugs and/or compounds by Sigma-Aldrich, Tocris Bioscience, and/or
Enzo Life Sciences)
About This Section
|
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| |  | Search Tocris compounds for YTHDC1 |
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