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

    Gene ID: 64848, updated on 30-Sep-2018

    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; Vega:OTTHUMG00000128837
    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

    Genomic context

    See YTHDC2 in Genome Data Viewer
    Location:
    5q22.2
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (113513662..113595287)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (112849391..112930984)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene MCC, WNT signaling pathway regulator Neighboring gene uncharacterized LOC107986366 Neighboring gene testis specific serine kinase 1B 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    NHGRI GWAS Catalog

    Description
    Genome-wide association study identifies genetic variants influencing F-cell levels in sickle-cell patients.
    NHGRI GWA Catalog

    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
    3'-5' RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    ATP-dependent 3'-5' RNA helicase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    N6-methyladenosine-containing RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    N6-methyladenosine-containing RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA binding HDA PubMed 
    RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA polymerase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    RNA-dependent ATPase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    germline cell cycle switching, mitotic to meiotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    meiotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    oocyte development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    positive regulation by host of viral genome replication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    response to interleukin-1 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    response to tumor necrosis factor IDA
    Inferred from Direct Assay
    more info
    PubMed 
    spermatid development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    colocalizes_with endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ribonucleoprotein granule ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    3'-5' RNA helicase YTHDC2; probable ATP-dependent RNA helicase YTHDC2
    Names
    CsA-associated helicase-like protein
    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)

    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
      4980..86605
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001345975.1NP_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_001345976.1NP_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_022828.4NP_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, AC093208, AK096486, BC137285
      Consensus CDS
      CCDS4113.1
      UniProtKB/Swiss-Prot
      Q9H6S0
      Related
      ENSP00000161863.4, OTTHUMP00000159057, ENST00000161863.8, OTTHUMT00000250776
      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 Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

      Range
      113513662..113595287
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011543581.1XP_011541883.1  probable ATP-dependent RNA helicase YTHDC2 isoform X1

      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:12891404
      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]
    2. XM_017009733.1XP_016865222.1  probable ATP-dependent RNA helicase YTHDC2 isoform X5

    3. XM_011543582.2XP_011541884.1  probable ATP-dependent RNA helicase YTHDC2 isoform X2

      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:12891404
      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]
    4. XM_011543586.2XP_011541888.1  probable ATP-dependent RNA helicase YTHDC2 isoform X4

      Conserved Domains (8) 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
      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]
    5. XM_017009731.1XP_016865220.1  probable ATP-dependent RNA helicase YTHDC2 isoform X3

      Conserved Domains (8) summary
      smart00847
      Location:654739
      HA2; Helicase associated domain (HA2) Add an annotation
      cd00046
      Location:48187
      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:325410
      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:448580
      Helicase_C; Helicase conserved C-terminal domain
      pfam04146
      Location:11271242
      YTH; YT521-B-like domain
      pfam07717
      Location:777904
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
      pfam13857
      Location:329385
      Ank_5; Ankyrin repeats (many copies)
      sd00045
      Location:343375
      ANK; ANK repeat [structural motif]
    6. XM_017009735.1XP_016865224.1  probable ATP-dependent RNA helicase YTHDC2 isoform X6

      Conserved Domains (8) summary
      smart00847
      Location:348433
      HA2; Helicase associated domain (HA2) Add an annotation
      COG1643
      Location:150548
      HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]
      cd00204
      Location:19104
      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:142274
      Helicase_C; Helicase conserved C-terminal domain
      pfam04146
      Location:821936
      YTH; YT521-B-like domain
      pfam07717
      Location:471598
      OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold
      pfam13857
      Location:2379
      Ank_5; Ankyrin repeats (many copies)
      sd00045
      Location:3769
      ANK; ANK repeat [structural motif]

    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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