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YTHDC1 YTH N6-methyladenosine RNA binding protein C1 [ Homo sapiens (human) ]

Gene ID: 91746, updated on 27-Jan-2023

Summary

Official Symbol
YTHDC1provided by HGNC
Official Full Name
YTH N6-methyladenosine RNA binding protein C1provided by HGNC
Primary source
HGNC:HGNC:30626
See related
Ensembl:ENSG00000083896 MIM:617283; AllianceGenome:HGNC:30626
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
YT521; YT521-B
Summary
Enables N6-methyladenosine-containing RNA binding activity. Involved in mRNA export from nucleus; mRNA splice site selection; and regulation of gene expression. Located in nuclear speck and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 22.7), ovary (RPKM 15.2) and 25 other tissues See more
Orthologs
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Genomic context

See YTHDC1 in Genome Data Viewer
Location:
4q13.2
Exon count:
17
Annotation release Status Assembly Chr Location
110 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (68310387..68350090, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (71751442..71791158, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (69176105..69215808, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene UDP glucuronosyltransferase family 2 member B11 pseudogene Neighboring gene apolipoprotein O pseudogene 4 Neighboring gene U2 spliceosomal RNA Neighboring gene metallothionein 2 pseudogene 1

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

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2019-04-24)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2019-04-24)

ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1966

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables N6-methyladenosine-containing RNA binding IBA
Inferred from Biological aspect of Ancestor
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 IDA
Inferred from Direct Assay
more info
PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
YTH domain-containing protein 1
Names
YTH domain containing 1
putative splicing factor YT521
splicing factor YT521
splicing factor YT521-B

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.

mRNA and Protein(s)

  1. NM_001031732.4NP_001026902.1  YTH domain-containing protein 1 isoform 1

    See identical proteins and their annotated locations for NP_001026902.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS33992.1
    UniProtKB/Swiss-Prot
    Q8TF35, Q96MU7
    Related
    ENSP00000339245.4, ENST00000344157.9
    Conserved Domains (1) summary
    pfam04146
    Location:355493
    YTH; YT521-B-like domain
  2. NM_001330698.2NP_001317627.1  YTH domain-containing protein 1 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is longer compared to isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS82929.1
    UniProtKB/Swiss-Prot
    Q96MU7
    UniProtKB/TrEMBL
    J3QR07
    Related
    ENSP00000463982.1, ENST00000579690.5
    Conserved Domains (1) summary
    pfam04146
    Location:355492
    YTH; YT521-B-like domain
  3. NM_133370.4NP_588611.2  YTH domain-containing protein 1 isoform 2

    See identical proteins and their annotated locations for NP_588611.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC074378
    Consensus CDS
    CCDS3522.2
    UniProtKB/Swiss-Prot
    Q96MU7
    Related
    ENSP00000347888.3, ENST00000355665.7
    Conserved Domains (1) summary
    pfam04146
    Location:337474
    YTH; YT521-B-like domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    68310387..68350090 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265708.4XP_005265765.1  YTH domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005265765.1

    Conserved Domains (1) summary
    pfam04146
    Location:337474
    YTH; YT521-B-like domain

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167250.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    4029..43732 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    71751442..71791158 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)