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YTHDC1 YTH domain containing 1 [ Homo sapiens (human) ]

Gene ID: 91746, updated on 4-Nov-2018

Summary

Official Symbol
YTHDC1provided by HGNC
Official Full Name
YTH domain containing 1provided by HGNC
Primary source
HGNC:HGNC:30626
See related
Ensembl:ENSG00000083896 MIM:617283; Vega:OTTHUMG00000129306
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
Expression
Ubiquitous expression in bone marrow (RPKM 22.7), ovary (RPKM 15.2) and 25 other tissues See more
Orthologs

Genomic context

See YTHDC1 in Genome Data Viewer
Location:
4q13.2
Exon count:
17
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (68310387..68350117, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (69176105..69215824, 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 metallothionein 2 pseudogene 1 Neighboring gene transmembrane serine protease 11E

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
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
NHGRI GWA 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
N6-methyladenosine-containing RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
dosage compensation by inactivation of X chromosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splice site selection IDA
Inferred from Direct Assay
more info
PubMed 
posttranscriptional regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

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

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.

mRNA and Protein(s)

  1. NM_001031732.3NP_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, AL157447, BC041119, DA214087
    Consensus CDS
    CCDS33992.1
    UniProtKB/Swiss-Prot
    Q96MU7
    Related
    ENSP00000339245.4, OTTHUMP00000159642, ENST00000344157.8, OTTHUMT00000251437
    Conserved Domains (1) summary
    pfam04146
    Location:355493
    YTH; YT521-B-like domain
  2. NM_001330698.1NP_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, AL157447, BC041119, BU509020, DA214087
    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_133370.3NP_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, AL157447, BC053863, DA214087
    Consensus CDS
    CCDS3522.2
    UniProtKB/Swiss-Prot
    Q96MU7
    Related
    ENSP00000347888.3, OTTHUMP00000159643, ENST00000355665.7, OTTHUMT00000251438
    Conserved Domains (1) summary
    pfam04146
    Location:337474
    YTH; YT521-B-like domain

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_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    68310387..68350117 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265707.3XP_005265764.1  YTH domain-containing protein 1 isoform X1

    See identical proteins and their annotated locations for XP_005265764.1

    Conserved Domains (1) summary
    pfam04146
    Location:340477
    YTH; YT521-B-like domain
  2. XM_005265708.3XP_005265765.1  YTH domain-containing protein 1 isoform X2

    See identical proteins and their annotated locations for XP_005265765.1

    Conserved Domains (1) summary
    pfam04146
    Location:337474
    YTH; YT521-B-like domain
  3. XM_017008833.2XP_016864322.1  YTH domain-containing protein 1 isoform X4

  4. XM_017008832.2XP_016864321.1  YTH domain-containing protein 1 isoform X3

RNA

  1. XR_001741348.2 RNA Sequence

  2. XR_001741346.2 RNA Sequence

  3. XR_001741347.2 RNA Sequence

Reference GRCh38.p12 ALT_REF_LOCI_1

Genomic

  1. NT_167250.2 Reference GRCh38.p12 ALT_REF_LOCI_1

    Range
    4029..43759 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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