YTHDF3 YTH N6-methyladenosine RNA binding protein F3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YTHDF3provided by HGNC
Official Full Name: YTH N6-methyladenosine RNA binding protein F3provided by HGNC
Primary source: HGNC:HGNC:26465
See related: Ensembl:ENSG00000185728 MIM:618669; AllianceGenome:HGNC:26465
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: DF3
Summary: This gene encodes a member of the YTH (YT521-B homology) domain protein family. The YTH domain is common in eukaryotes, is often found in the middle of the protein sequence, and may function in binding to RNA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]
Expression: Ubiquitous expression in bone marrow (RPKM 27.1), colon (RPKM 15.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q12.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (63168553..63212788)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (63593718..63637958)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (64081112..64125346)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

YTHDF3 Regulates the Degradation and Stability of m6A-Enriched Transcripts to Facilitate the Progression of Castration-Resistant Prostate Cancer.
Title: YTHDF3 Regulates the Degradation and Stability of m6A-Enriched Transcripts to Facilitate the Progression of Castration-Resistant Prostate Cancer.
The m[6]A reading protein YTHDF3 potentiates tumorigenicity of cancer stem-like cells in ocular melanoma through facilitating CTNNB1 translation.
Title: The m(6)A reading protein YTHDF3 potentiates tumorigenicity of cancer stem-like cells in ocular melanoma through facilitating CTNNB1 translation.
Knockdown of YAP1 Reduces YTHDF3 to Stabilize SMAD7 and thus Inhibit Bladder Cancer Stem Cell Stemness.
Title: Knockdown of YAP1 Reduces YTHDF3 to Stabilize SMAD7 and thus Inhibit Bladder Cancer Stem Cell Stemness.
ZDHHC20-mediated S-palmitoylation of YTHDF3 stabilizes MYC mRNA to promote pancreatic cancer progression.
Title: ZDHHC20-mediated S-palmitoylation of YTHDF3 stabilizes MYC mRNA to promote pancreatic cancer progression.
The inhibition of YTHDF3/m[6]A/LRP6 reprograms fatty acid metabolism and suppresses lymph node metastasis in cervical cancer.
Title: The inhibition of YTHDF3/m(6)A/LRP6 reprograms fatty acid metabolism and suppresses lymph node metastasis in cervical cancer.
YTHDF3 Modulates EGFR/ATK/ERK/p21 Signaling Axis to Promote Cancer Progression and Osimertinib Resistance of Glioblastoma Cells.
Title: YTHDF3 Modulates EGFR/ATK/ERK/p21 Signaling Axis to Promote Cancer Progression and Osimertinib Resistance of Glioblastoma Cells.
m[6] A reader YTHDF3 triggers the progression of hepatocellular carcinoma through the YTHDF3/m[6] A-EGFR/STAT3 axis and EMT.
Title: m(6) A reader YTHDF3 triggers the progression of hepatocellular carcinoma through the YTHDF3/m(6) A-EGFR/STAT3 axis and EMT.
N[6]-methyladenosine reader YTHDF3 contributes to the aerobic glycolysis of osteosarcoma through stabilizing PGK1 stability.
Title: N(6)-methyladenosine reader YTHDF3 contributes to the aerobic glycolysis of osteosarcoma through stabilizing PGK1 stability.
m[6]A reader YTHDF3 is associated with clinical prognosis, related RNA signatures and immunosuppression in gastric cancer.
Title: m(6)A reader YTHDF3 is associated with clinical prognosis, related RNA signatures and immunosuppression in gastric cancer.
YTHDF3 mediates HNF1alpha regulation of cervical cancer radio-resistance by promoting RAD51D translation in an m6A-dependent manner.
Title: YTHDF3 mediates HNF1α regulation of cervical cancer radio-resistance by promoting RAD51D translation in an m6A-dependent manner.

Submit: New GeneRIF Correction See all GeneRIFs (23)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
nucleocapsid	gag	HIV-1 NC is identified to have a physical interaction with YTH domain family, member 3 (YTHDF3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

A001Y04 (e-PCR)
- UniSTS:17152

SHGC-31794 (e-PCR)
- UniSTS:14123

RH68329 (e-PCR)
- UniSTS:45373

STS-H02876 (e-PCR)
- UniSTS:72266

RH93113 (e-PCR)
- UniSTS:87631

WI-19603 (e-PCR)
- UniSTS:77676

RH80212 (e-PCR)
- UniSTS:92294

D8S1366E (e-PCR)
- UniSTS:151180

G19771 (e-PCR)
- UniSTS:17151

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables N6-methyladenosine-containing RNA reader activity	IBA Inferred from Biological aspect of Ancestor more info
enables N6-methyladenosine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribosome binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA destabilization	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA destabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in mRNA destabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of type I interferon-mediated signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in organelle assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translation	IMP Inferred from Mutant Phenotype more info	PubMed
NOT involved_in positive regulation of translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of translational initiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA stability	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mRNA stability	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of trophoblast cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in stress granule assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: YTH domain-containing family protein 3

Names: YTH N(6)-methyladenosine RNA binding protein 3; YTH N6-methyladenosine RNA binding protein 3; YTH domain family protein 3; YTH domain family, member 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_033226.1 RefSeqGene

Range

5069..49234

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001277813.2 → NP_001264742.1 YTH domain-containing family protein 3 isoform b

See identical proteins and their annotated locations for NP_001264742.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a longer and distinct N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.

Source sequence(s)

AK127574, AL832335, DC419051

Consensus CDS

CCDS75748.1

UniProtKB/TrEMBL

A0A087WY31, B4DPX9

Related

ENSP00000478490.1, ENST00000621413.4

Conserved Domains (1) summary

pfam04146
Location:420 → 553

YTH; YT521-B-like domain
NM_001277814.2 → NP_001264743.1 YTH domain-containing family protein 3 isoform b

See identical proteins and their annotated locations for NP_001264743.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a longer and distinct N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.

Source sequence(s)

AK093081, AK127574, AK298544, AL832335

Consensus CDS

CCDS75748.1

UniProtKB/TrEMBL

A0A087WY31, B4DPX9

Related

ENSP00000481476.1, ENST00000621820.4

Conserved Domains (1) summary

pfam04146
Location:420 → 553

YTH; YT521-B-like domain
NM_001277815.2 → NP_001264744.1 YTH domain-containing family protein 3 isoform c

See identical proteins and their annotated locations for NP_001264744.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.

Source sequence(s)

AK127574, AL832335, BP223018

Consensus CDS

CCDS75749.1

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80

Related

ENSP00000485046.1, ENST00000623280.3

Conserved Domains (1) summary

pfam04146
Location:366 → 499

YTH; YT521-B-like domain
NM_001277816.2 → NP_001264745.1 YTH domain-containing family protein 3 isoform c

See identical proteins and their annotated locations for NP_001264745.1

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.

Source sequence(s)

AK127574, AL832335, AW673093, BP223018

Consensus CDS

CCDS75749.1

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80

Related

ENSP00000481497.1, ENST00000617200.1

Conserved Domains (1) summary

pfam04146
Location:366 → 499

YTH; YT521-B-like domain
NM_001277817.2 → NP_001264746.1 YTH domain-containing family protein 3 isoform c

See identical proteins and their annotated locations for NP_001264746.1

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.

Source sequence(s)

AC011978, AK127574, AL831816, AL832335, BP354748

Consensus CDS

CCDS75749.1

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80

Conserved Domains (1) summary

pfam04146
Location:366 → 499

YTH; YT521-B-like domain
NM_001277818.2 → NP_001264747.1 YTH domain-containing family protein 3 isoform c

See identical proteins and their annotated locations for NP_001264747.1

Status: REVIEWED

Description

Transcript Variant: This variant (7) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.

Source sequence(s)

AK093081, AK127574, AL832335

Consensus CDS

CCDS75749.1

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80

Related

ENSP00000478825.1, ENST00000621890.4

Conserved Domains (1) summary

pfam04146
Location:366 → 499

YTH; YT521-B-like domain
NM_152758.6 → NP_689971.4 YTH domain-containing family protein 3 isoform a

See identical proteins and their annotated locations for NP_689971.4

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform a.

Source sequence(s)

AK127574, AL832335

Consensus CDS

CCDS75747.1

UniProtKB/Swiss-Prot

B3KXL4, Q63Z37, Q659A3, Q7Z739

UniProtKB/TrEMBL

B4DPX9

Related

ENSP00000473496.2, ENST00000539294.6

Conserved Domains (1) summary

pfam04146
Location:417 → 550

YTH; YT521-B-like domain

RNA

NR_102434.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AK127574, AL832335, BC037492, BP223018, CN335163

Related

ENST00000517371.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

63168553..63212788

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011517509.4 → XP_011515811.1 YTH domain-containing family protein 3 isoform X1

See identical proteins and their annotated locations for XP_011515811.1

UniProtKB/TrEMBL

A0A087WY31, B4DPX9

Conserved Domains (1) summary

pfam04146
Location:420 → 553

YTH; YT521-B-like domain
XM_011517510.4 → XP_011515812.1 YTH domain-containing family protein 3 isoform X2

See identical proteins and their annotated locations for XP_011515812.1

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80

Conserved Domains (1) summary

pfam04146
Location:366 → 499

YTH; YT521-B-like domain

Alternate T2T-CHM13v2.0

Genomic

NC_060932.1 Alternate T2T-CHM13v2.0

Range

63593718..63637958

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054360243.1 → XP_054216218.1 YTH domain-containing family protein 3 isoform X1

UniProtKB/TrEMBL

A0A087WY31, B4DPX9
XM_054360244.1 → XP_054216219.1 YTH domain-containing family protein 3 isoform X2

UniProtKB/TrEMBL

A0A024R7W5, A0A024R800, Q8NA80