YTHDC2 YTH N6-methyladenosine RNA binding protein C2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: YTHDC2provided by HGNC
Official Full Name: YTH N6-methyladenosine RNA binding protein C2provided by HGNC
Primary source: HGNC:HGNC:24721
See related: Ensembl:ENSG00000047188 MIM:616530; AllianceGenome:HGNC:24721
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: CAHL; hYTHDC2
Summary: This gene encodes a member of the DEAH (Asp-Glu-Ala-His) subfamily of proteins, part of the DEAD (Asp-Glu-Ala-Asp) box family of RNA helicases. The encoded protein binds to N6-methyladenosine, a common modified RNA nucleotide that is enriched in the stop codons and 3' UTRs of eukaryotic messenger RNAs. Binding of proteins to this modified nucleotide may regulate mRNA translation and stability. This gene may be associated with susceptibility to pancreatic cancer in human patients, and knockdown of this gene resulted in reduced proliferation in a human liver cancer cell line. [provided by RefSeq, Sep 2016]
Expression: Ubiquitous expression in testis (RPKM 9.0), lymph node (RPKM 7.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q22.2

Exon count:: 32

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (113513694..113595284)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (114026401..114108085)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (112849391..112930981)

Chromosome 5 - NC_000005.10 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: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A homozygous missense variant in YTHDC2 induces azoospermia in two siblings.
Title: A homozygous missense variant in YTHDC2 induces azoospermia in two siblings.
The m[6]A reader YTHDC2 regulates UVB-induced DNA damage repair and histone modification.
Title: The m(6)A reader YTHDC2 regulates UVB-induced DNA damage repair and histone modification.
The m6A Reader YTHDC2 Suppresses Lung Adenocarcinoma Tumorigenesis by Destabilizing MRPL12.
Title: The m6A Reader YTHDC2 Suppresses Lung Adenocarcinoma Tumorigenesis by Destabilizing MRPL12.
YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling.
Title: YTHDC2 Retards Cell Proliferation and Triggers Apoptosis in Papillary Thyroid Cancer by Regulating CYLD-Mediated Inactivation of Akt Signaling.
Crosstalk between RNA m[6]A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells.
Title: Crosstalk between RNA m(6)A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells.
Overexpression of YTHDC2 contributes to the progression of prostate cancer and predicts poor outcomes in patients with prostate cancer.
Title: Overexpression of YTHDC2 contributes to the progression of prostate cancer and predicts poor outcomes in patients with prostate cancer.
lncRNA ZNRD1-AS1 promotes malignant lung cell proliferation, migration, and angiogenesis via the miR-942/TNS1 axis and is positively regulated by the m[6]A reader YTHDC2.
Title: lncRNA ZNRD1-AS1 promotes malignant lung cell proliferation, migration, and angiogenesis via the miR-942/TNS1 axis and is positively regulated by the m(6)A reader YTHDC2.
Construction and clinical evaluation of N6-methyladenosine risk signature of YTHDC2, IGF2BP2, and HNRNPC in head and neck squamous cell carcinoma.
Title: Construction and clinical evaluation of N6-methyladenosine risk signature of YTHDC2, IGF2BP2, and HNRNPC in head and neck squamous cell carcinoma.
Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.
Title: Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.
The m(6)A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay.
Title: The m(6)A reader YTHDC2 is essential for escape from KSHV SOX-induced RNA decay.

Submit: New GeneRIF Correction See all GeneRIFs (26)

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

EBI GWAS Catalog

Description
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients. EBI GWAS Catalog EBI GWAS CatalogPubMed

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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Replication interactions

Interaction	Pubs
Knockdown of YTH domain containing 2 (YTHDC2) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	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

NoName (e-PCR)
- UniSTS:482319

STS-H71891 (e-PCR)
- UniSTS:19235

D5S421 (e-PCR), detects polymorphism
- UniSTS:72747

RH121291 (e-PCR)
- UniSTS:138557

RH66654 (e-PCR)
- UniSTS:80964

CDR1 (e-PCR)
- UniSTS:98895

YTHDC2 (e-PCR)
- UniSTS:504924

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5' RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on RNA	IDA Inferred from Direct Assay more info	PubMed
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation 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	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase binding	IPI Inferred from Physical Interaction more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in germline cell cycle switching, mitotic to meiotic cell cycle	ISS Inferred from Sequence or Structural Similarity more info
involved_in meiotic cell cycle	IEA Inferred from Electronic Annotation more info
involved_in oocyte development	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation by host of viral genome replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to interleukin-1	IDA Inferred from Direct Assay more info	PubMed
involved_in response to tumor necrosis factor	IDA Inferred from Direct Assay more info	PubMed
involved_in spermatid development	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in ribonucleoprotein granule	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: 3'-5' RNA helicase YTHDC2

Names: CsA-associated helicase-like protein; YTH domain containing 2; probable ATP-dependent RNA helicase YTHDC2

NP_001332904.1

EC 3.6.4.13

NP_001332905.1

EC 3.6.4.13

NP_073739.3

EC 3.6.4.13

XP_011541883.1

EC 3.6.4.13

XP_011541884.1

EC 3.6.4.13

XP_011541888.1

EC 3.6.4.13

XP_047273483.1

EC 3.6.4.13

XP_047273484.1

EC 3.6.4.13

XP_047273485.1

EC 3.6.4.13

XP_054209127.1

EC 3.6.4.13

XP_054209128.1

EC 3.6.4.13

XP_054209129.1

EC 3.6.4.13

XP_054209130.1

EC 3.6.4.13

XP_054209131.1

EC 3.6.4.13

XP_054209132.1

EC 3.6.4.13

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_051594.1 RefSeqGene

Range

5012..86602

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001345975.2 → NP_001332904.1 3'-5' RNA helicase YTHDC2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start site compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.

Source sequence(s)

AC010389, AC093208

UniProtKB/TrEMBL

Q6ZMY0
NM_001345976.2 → NP_001332905.1 3'-5' RNA helicase YTHDC2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start site compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.

Source sequence(s)

AC010389, AC093208

UniProtKB/TrEMBL

Q6ZMY0
NM_022828.5 → NP_073739.3 3'-5' RNA helicase YTHDC2 isoform 1

See identical proteins and their annotated locations for NP_073739.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AC010389, AK096486, BC137285

Consensus CDS

CCDS4113.1

UniProtKB/Swiss-Prot

B2RP66, Q9H6S0

UniProtKB/TrEMBL

Q6ZMY0

Related

ENSP00000161863.4, ENST00000161863.9

Conserved Domains (9) summary

cd06007
Location:46 → 104

R3H_DEXH_helicase; R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine ...

smart00847
Location:816 → 901

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:210 → 349

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00204
Location:487 → 572

ANK; ankyrin repeats; ankyrin repeats mediate protein-protein interactions in very diverse families of proteins. The number of ANK repeats in a protein can range from 2 to over 20 (ankyrins, for example). ANK repeats may occur in combinations with other ...

pfam00271
Location:610 → 742

Helicase_C; Helicase conserved C-terminal domain

pfam04146
Location:1289 → 1419

YTH; YT521-B-like domain

pfam07717
Location:939 → 1066

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

pfam13857
Location:491 → 547

Ank_5; Ankyrin repeats (many copies)

sd00045
Location:505 → 537

ANK; ANK repeat [structural motif]

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_000005.10 Reference GRCh38.p14 Primary Assembly

Range

113513694..113595284

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417527.1 → XP_047273483.1 3'-5' RNA helicase YTHDC2 isoform X2

UniProtKB/Swiss-Prot

B2RP66, Q9H6S0
XM_011543582.3 → XP_011541884.1 3'-5' RNA helicase YTHDC2 isoform X3

UniProtKB/TrEMBL

Q6ZMY0

Conserved Domains (6) summary

cd06007
Location:46 → 104

R3H_DEXH_helicase; R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine ...

COG1643
Location:189 → 1016

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

sd00045
Location:505 → 537

ANK; ANK repeat [structural motif]

cd17987
Location:193 → 368

DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2

pfam04146
Location:1288 → 1404

YTH; YT521-B-like domain

pfam07717
Location:971 → 1066

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
XM_011543581.2 → XP_011541883.1 3'-5' RNA helicase YTHDC2 isoform X1

UniProtKB/TrEMBL

Q6ZMY0

Conserved Domains (6) summary

cd06007
Location:46 → 104

R3H_DEXH_helicase; R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine ...

COG1643
Location:189 → 1016

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

sd00045
Location:505 → 537

ANK; ANK repeat [structural motif]

cd17987
Location:193 → 368

DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2

pfam04146
Location:1288 → 1404

YTH; YT521-B-like domain

pfam07717
Location:971 → 1066

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
XM_011543586.3 → XP_011541888.1 3'-5' RNA helicase YTHDC2 isoform X5

Conserved Domains (5) summary

cd06007
Location:46 → 104

R3H_DEXH_helicase; R3H domain of a group of proteins which also contain a DEXH-box helicase domain, and may function as ATP-dependent DNA or RNA helicases. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine ...

COG1643
Location:189 → 1016

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

sd00045
Location:505 → 537

ANK; ANK repeat [structural motif]

cd17987
Location:193 → 368

DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2

pfam07717
Location:971 → 1066

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
XM_047417529.1 → XP_047273485.1 3'-5' RNA helicase YTHDC2 isoform X6
XM_047417528.1 → XP_047273484.1 3'-5' RNA helicase YTHDC2 isoform X4