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YTHDF3 Gene

protein-coding GIFtS: 50

GC08P064243

YTH domain family, member 3
(Previous name: YTH domain family 3 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
FLJ31657 ^¹, ²

Descriptions
YTH domain family 3 ^¹, ²
YTH domain family, member 3 ^²

External Ids
HGNC: 26465¹
Entrez Gene: 253943²
UniProtKB: Q7Z739³
Ensembl: ENSG00000185728⁷

Search outside databases for aliases for YTHDF3 gene

Previous GC identifer: GC08P064132

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Gene Wiki entry for YTHDF3

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the YTHDF3 gene

Entrez Gene cytogenetic band: 8q12.3 Ensembl cytogenetic band: 8q12.3 HGNC cytogenetic band: 8q12.2

YTHDF3 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 8 GeneLoc Exon Structure

GeneLoc location for GC08P064243: (about GC identifiers)

Start:	64,243,675 bp from pter
End:	64,287,900 bp from pter
Size:	44,226 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000008.9 NT_008183.18

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: YTHD3_HUMAN, Q7Z739 (See protein sequence)

Recommended Name: YTH domain family protein 3

Size: 585 amino acids; 63861 Da

Secondary accessions: Q63Z37 Q659A3

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_689971.4

ENSEMBL proteins:

ENSP00000368753

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Recombinant Proteins from Abcam (YTHDF3)
	Human Recombinant Proteins from Abnova (YTHDF3)

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

1 Gene Ontology (GO) cellular component term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005737	cytoplasm	IDA	11256614

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Antibodies for YTHDF3:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Browse Antibodies at Sigma-Aldrich
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (YTHDF3), each with their Abpromise^SM
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for YTHDF3

Assays for YTHDF3:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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Graphical View of Domain Structure for InterPro Entry Q7Z739

ProtoNet protein and cluster: Q7Z739

1 Blocks protein family: IPB007275 YT521-B-like protein

UniProtKB/Swiss-Prot: YTHD3_HUMAN, Q7Z739

Similarity: Contains 1 YTH domain

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (YTHDF3)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_152758

Applied Biosystems Silencer® siRNAs for YTHDF3

Sigma-Aldrich siRNA for YTHDF3

Sigma-Aldrich shRNA for YTHDF3

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for YTHDF3
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_152758
Myc/DDK tagged cDNA clone in CMV expression vector: NM_152758
untagged cDNA clones in CMV expression vector (see all 2): NM_152758

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_152758

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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(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 drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for YTHDF3

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
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 Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (YTHDF3)
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_152758

Sigma-Aldrich siRNA for YTHDF3

Sigma-Aldrich shRNA for YTHDF3

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_152758

REFSEQ mRNAs for YTHDF3 gene:

NM_152758.4

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_152758

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_152758
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_152758
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_152758

Additional cDNA sequence:

AK002173.1 AK056219.1 AK093081.1 AK127574.1 AK298544.1 AL050081.1 AL831816.1 AL832005.1

AL832335.1 AL832369.1 BC037492.1 BC052970.1 BX537996.2

11 DOTS entries:

DT.102825847 DT.91749167 DT.100652083 DT.95268981 DT.100652089 DT.102825850 DT.95355192 DT.100666742

DT.95260348 DT.95268980 DT.91808969

24/285 AceView cDNA sequences (see all 285 ):

CK904693 AA908355 AA284518 BM477044 AA371224 BM985066 BX390013 CB046550

AI967934 AW196318 BE466725 BM981239 AA418619 AA128191 AA633148 CD675986

AW169433 AI582541 AI918717 AI363820 BQ637880 CB105178 BM454875 AA706607

highest scoring ESTs for YTHDF3:

AL050081 R52179 AA018525 AA021637 AA033680 AA040544 AA040545 AA126698 AA234532 AA248084

Unigene Cluster for YTHDF3:

YTH domain family, member 3

Hs.491861 [show with all ESTs]

Unigene Representative Sequence: NM_152758

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000339066

(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 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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YTHDF3 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for YTHDF3

¹ / ² / ³

5 probe-sets matching YTHDF3 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
35290_at²^{, 3}	U95-A	1	1.00	1.00	0.71	0.92	AL050081	1.00	1.00	1.00	1
60824_at²^{, 3}	U95-C	1	1.00	1.00	0.70	1.08	R52179	1.00	1.00	1.00	1
221749_at²^{, 3}	U133-A	1	1.00	1.00	--	--	AU157915	0.60	1.00	0.82	1
1564053_a_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
221749_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

GeneDecks YTHDF3 for binary patterns associated with the probe-sets selected above

About GeneDecksing

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Data from

(Publications) and GNF BioGPS
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CGAP SAGE TAG: AGAATTTGAA

SOURCE GeneReport for Unigene cluster: Hs.491861
Expression variation in blood from EXPOLDB for YTHDF3

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for YTHDF3 gene from 5/10 species (see all 10 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	YTHDF3¹	--	YTH domain family, member 3	97.83(n) 99.49(a)	486970 XM_852818.1 XP_857911.1
cow (Bos taurus)	YTHDF3¹	--	YTH domain family, member 3	95.32(n) 98.61(a)	519708 XM_597933.3 XP_597933.3
rat (Rattus norvegicus)	Ythdf3¹	--	YTH domain family, member 3	96.24(n) 98.63(a)	361920 XM_342217.3 XP_342218.2
mouse (Mus musculus)	Ythdf3^{1, 5}	3⁵	YTH domain family 3^{1, 5}	96.35(n)¹ 98.63(a)¹	229096¹ NM_172677.2¹ NP_766265.2¹ AA692431⁵ AA816120⁵ (see all 24)
chicken (Gallus gallus)	YTHDF3¹	--	YTH domain family, member 3	90.39(n) 96.4(a)	421145 NM_001006391.1 NP_001006391.1

About this table Species with no ortholog for YTHDF3

ENSEMBL Gene Tree for YTHDF3

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
About This Section

Paralogs for YTHDF3 gene

YTHDF2² YTHDF1²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/166 NCBI SNPs in YTHDF3 are shown (see all 166 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 45)

AB	SNP ID	Valid	Chr 8 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs2241754^1,2	A,C,F,H	64243387(+)	`GCACTA/GCTATC`	1	--	ng5¹		5		EA EU WA	1720
	rs7464^1,2	A,C,F,H	64287510(+)	`ATACCA/GTGCAT`	1	--	ut3¹		13		MN EU EA WA NA	1234
	rs1836635^1,2	A,C,F,H	64242491(+)	`TAAAAC/TGGTCT`	1	--	ng5¹		8		NA EA EU WA	724
	rs2241753^1,2	C,F,H	64243040(+)	`TCAGAG/ACGGAG`	1	--	ng5¹		9		EA EU WA	2114
--	rs9657033^1,2	A,C	64241738(+)	`gtctcA/Gggtat`	1	--	ng5¹		0	--	--	--	--
	rs13274195^1,2	C,H	64284812(+)	`AACAAA/CCAATA`	1	K/N	mis¹		4		EU EA WA	418
--	rs13255987^1,2	H	64261698(+)	`CATGAC/GTGGAC`	1	T/S	mis¹ ese³		4		EU EA WA	418
	rs2043525^1,2	A,C,F,H,O	64270401(+)	`GAAGCG/TGTAAT`	1	--	int¹		6		EU EA WA	598
	rs1435458^1,2	A,C,F,H	64246942(+)	`AACACG/ATAATC`	1	--	int¹		9		NA EA EU WA	839
--	rs7016339^1,2	A,C,F,H	64284284(+)	`CTCATC/GTTACT`	1	--	int¹		4		EU EA WA	416

About this table

HapMap Linkage Disequilibrium images for YTHDF3 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
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(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

10 PubMed articles for YTHDF3 gene:

The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)^{2, 3} Strausberg R.L....Marra M.A. (2002)
The full-ORF clone resource of the German cDNA Consortium. (PubMed id 17974005)⁴ Bechtel S....Schupp I. (2007)
The LIFEdb database in 2006. (PubMed id 16381901)³ Mehrle A....Wiemann S. (2006)
Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. (PubMed id 15342556)³ Suzuki Y.... Sugano S. (2004)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)³ Ota T....Sugano S. (2004)
From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)³ Wiemann S....Poustka A. (2004)
Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)³ Wiemann S.... Poustka A. (2001)
Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing. (PubMed id 11256614)³ Simpson J.C.... Wiemann S. (2000)
DNA cloning using in vitro site-specific recombination. (PubMed id 11076863)³ Hartley J.L....Brasch M.A. (2000)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
About This Section

Entrez Gene: 253943	HGNC: 26465	AceView: YTHDF3	Ensembl:ENSG00000185728	euGenes: HUgn253943
ECgene: YTHDF3	H-InvDB: YTHDF3

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for YTHDF3
(Available from WIS Yeda, Salk, Tufts)

About This Section

(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section

Products for YTHDF3:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for YTHDF3-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for YTHDF3		Browse antibodies at Sigma-Aldrich
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for YTHDF3		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

	Antibodies		Primer Pairs
	Cell Culture Products		ELISAs
	Flow Cytometry Kits		Protease Activity Assays & Reagents
	Cell Selection/Detection Kits & Reagents		ELISA/Assay Development Kits & Reagents
	Multiplex/Array Assay Kits & Reagents		ELISpot Kits & Development Modules
	Recombinant & Natural Proteins

	Recombinant Proteins (YTHDF3)
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	Custom Service for Rabbit Pab from Full-length Protein

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Search Tocris compounds for YTHDF3

Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

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YTHDF3 Gene

protein-coding GIFtS: 50

Aliases &
Descriptions
for YTHDF3

Summaries
for YTHDF3

Genomic Location
for YTHDF3

Proteins
for YTHDF3

Protein Domains/
Families
for YTHDF3

Gene Function
for YTHDF3

Pathways & Interactions
for YTHDF3

Drugs & Compounds
for YTHDF3

Transcripts
for YTHDF3

Expression
for YTHDF3

Orthologs
for YTHDF3

Paralogs
for YTHDF3

SNPs/Variants
for YTHDF3

Disorders & Mutations
for YTHDF3

Medical News
for YTHDF3

Publications
for YTHDF3

Search for YTHDF3

Genome Databases showing YTHDF3

Other Databases showing YTHDF3

Specialized Databases showing YTHDF3

Licensable Technologies
for YTHDF3

Services
for YTHDF3

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

YTHDF3 Gene

protein-coding GIFtS: 50

Aliases & Descriptionsfor YTHDF3

Summariesfor YTHDF3

Genomic Locationfor YTHDF3

Proteinsfor YTHDF3

Protein Domains/Familiesfor YTHDF3

Gene Functionfor YTHDF3

Pathways & Interactionsfor YTHDF3

Drugs & Compoundsfor YTHDF3

Transcriptsfor YTHDF3

Expression for YTHDF3

Orthologsfor YTHDF3

Paralogsfor YTHDF3

SNPs/Variantsfor YTHDF3

Disorders & Mutationsfor YTHDF3

Medical Newsfor YTHDF3

Publicationsfor YTHDF3

Search for YTHDF3

Genome Databases showing YTHDF3

Other Databases showing YTHDF3

Specialized Databases showing YTHDF3

Licensable Technologiesfor YTHDF3

Servicesfor YTHDF3

Gene Index: 3 5 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

Aliases &
Descriptions
for YTHDF3

Summaries
for YTHDF3

Genomic Location
for YTHDF3

Proteins
for YTHDF3

Protein Domains/
Families
for YTHDF3

Gene Function
for YTHDF3

Pathways & Interactions
for YTHDF3

Drugs & Compounds
for YTHDF3

Transcripts
for YTHDF3

Expression
for YTHDF3

Orthologs
for YTHDF3

Paralogs
for YTHDF3

SNPs/Variants
for YTHDF3

Disorders & Mutations
for YTHDF3

Medical News
for YTHDF3

Publications
for YTHDF3

Licensable Technologies
for YTHDF3

Services
for YTHDF3