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YTHDC2 YTH domain containing 2 [ Homo sapiens (human) ]

Gene ID: 64848, updated on 23-Nov-2021

Summary

Official Symbol
YTHDC2provided by HGNC
Official Full Name
YTH domain containing 2provided by HGNC
Primary source
HGNC:HGNC:24721
See related
Ensembl:ENSG00000047188 MIM:616530
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
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Genomic context

See YTHDC2 in Genome Data Viewer
Location:
5q22.2
Exon count:
32
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (113513683..113595284)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (112849391..112930981)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MCC regulator of WNT signaling pathway Neighboring gene Sharpr-MPRA regulatory region 13961 Neighboring gene RNA, U4atac small nuclear 13, pseudogene Neighboring gene uncharacterized LOC107986441 Neighboring gene uncharacterized LOC105379127

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
GeneReviews: Not available

HIV-1 interactions

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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

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 activity, acting on RNA IDA
Inferred from Direct Assay
more info
PubMed 
enables N6-methyladenosine-containing RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables RNA polymerase binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
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
colocalizes_with endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in intracellular anatomical structure IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
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

Preferred Names
3'-5' RNA helicase YTHDC2
Names
CsA-associated helicase-like protein
probable ATP-dependent RNA helicase YTHDC2
NP_001332904.1
NP_001332905.1
NP_073739.3
XP_011541883.1
XP_011541884.1
XP_011541888.1
XP_016865220.1
XP_016865222.1
XP_016865224.1

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

  1. NG_051594.1 RefSeqGene

    Range
    5012..86602
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001345975.2NP_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
  2. NM_001345976.2NP_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
  3. NM_022828.5NP_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
    Q9H6S0
    Related
    ENSP00000161863.4, ENST00000161863.9
    Conserved Domains (9) summary
    cd06007
    Location:46104
    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:816901
    HA2; Helicase associated domain (HA2) Add an annotation
    cd00046
    Location:210349
    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:487572
    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:610742
    Helicase_C; Helicase conserved C-terminal domain
    pfam04146
    Location:12891419
    YTH; YT521-B-like domain
    pfam07717
    Location:9391066
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
    pfam13857
    Location:491547
    Ank_5; Ankyrin repeats (many copies)
    sd00045
    Location:505537
    ANK; ANK repeat [structural motif]

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

    Range
    113513683..113595284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011543581.1XP_011541883.1  3'-5' RNA helicase YTHDC2 isoform X1

    Conserved Domains (6) summary
    cd06007
    Location:46104
    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:1891016
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:505537
    ANK; ANK repeat [structural motif]
    cd17987
    Location:193368
    DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2
    pfam04146
    Location:12881404
    YTH; YT521-B-like domain
    pfam07717
    Location:9711066
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  2. XM_017009733.1XP_016865222.1  3'-5' RNA helicase YTHDC2 isoform X5

    Conserved Domains (6) summary
    COG1643
    Location:318716
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:205237
    ANK; ANK repeat [structural motif]
    pfam04146
    Location:9881104
    YTH; YT521-B-like domain
    pfam07717
    Location:671766
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
    pfam12796
    Location:211279
    Ank_2; Ankyrin repeats (3 copies)
    cl28899
    Location:168
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  3. XM_011543582.2XP_011541884.1  3'-5' RNA helicase YTHDC2 isoform X2

    Conserved Domains (6) summary
    cd06007
    Location:46104
    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:1891016
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:505537
    ANK; ANK repeat [structural motif]
    cd17987
    Location:193368
    DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2
    pfam04146
    Location:12881404
    YTH; YT521-B-like domain
    pfam07717
    Location:9711066
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  4. XM_011543586.2XP_011541888.1  3'-5' RNA helicase YTHDC2 isoform X4

    Conserved Domains (5) summary
    cd06007
    Location:46104
    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:1891016
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:505537
    ANK; ANK repeat [structural motif]
    cd17987
    Location:193368
    DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2
    pfam07717
    Location:9711066
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  5. XM_017009731.1XP_016865220.1  3'-5' RNA helicase YTHDC2 isoform X3

    Conserved Domains (5) summary
    COG1643
    Location:27854
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:343375
    ANK; ANK repeat [structural motif]
    cd17987
    Location:31206
    DEXHc_YTHDC2; DEXH-box helicase domain of YTH domain containing 2
    pfam04146
    Location:11261242
    YTH; YT521-B-like domain
    pfam07717
    Location:809904
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
  6. XM_017009735.1XP_016865224.1  3'-5' RNA helicase YTHDC2 isoform X6

    Conserved Domains (5) summary
    COG0666
    Location:21105
    ANKYR; Ankyrin repeat [Signal transduction mechanisms]
    COG1643
    Location:150548
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
    sd00045
    Location:3769
    ANK; ANK repeat [structural motif]
    pfam04146
    Location:820936
    YTH; YT521-B-like domain
    pfam07717
    Location:503598
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RNA

  1. XR_001742200.2 RNA Sequence

    Related
    ENST00000515883.5
  2. XR_246540.3 RNA Sequence

  3. XR_948288.2 RNA Sequence

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