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YTHDF3 YTH N6-methyladenosine RNA binding protein 3 [ Homo sapiens (human) ]

Gene ID: 253943, updated on 17-Oct-2021

Summary

Official Symbol
YTHDF3provided by HGNC
Official Full Name
YTH N6-methyladenosine RNA binding protein 3provided by HGNC
Primary source
HGNC:HGNC:26465
See related
Ensembl:ENSG00000185728 MIM:618669
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
DF3
Summary
This gene encodes a member of the YTH (YT521-B homology) domain protein family. The YTH domain is common in eukaryotes, is often found in the middle of the protein sequence, and may function in binding to RNA. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]
Expression
Ubiquitous expression in bone marrow (RPKM 27.1), colon (RPKM 15.4) and 25 other tissues See more
Orthologs
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Genomic context

See YTHDF3 in Genome Data Viewer
Location:
8q12.3
Exon count:
8
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (63168553..63212788)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (64081112..64125346)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14742 Neighboring gene YTHDF3 divergent transcript Neighboring gene RNA, 7SL, cytoplasmic 135, pseudogene Neighboring gene uncharacterized LOC105375873

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?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
nucleocapsid gag HIV-1 NC is identified to have a physical interaction with YTH domain family, member 3 (YTHDF3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ31657

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 
enables ribosome binding IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in P-body IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytoplasmic stress granule IDA
Inferred from Direct Assay
more info
PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
YTH domain-containing family protein 3
Names
YTH N(6)-methyladenosine RNA binding protein 3
YTH domain family protein 3
YTH domain family, member 3

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_033226.1 RefSeqGene

    Range
    5001..49236
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001277813.2NP_001264742.1  YTH domain-containing family protein 3 isoform b

    See identical proteins and their annotated locations for NP_001264742.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a longer and distinct N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AK127574, AL832335, DC419051
    Consensus CDS
    CCDS75748.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A087WY31, Q658Z6
    Related
    ENSP00000478490.1, ENST00000621413.4
    Conserved Domains (1) summary
    pfam04146
    Location:420553
    YTH; YT521-B-like domain
  2. NM_001277814.2NP_001264743.1  YTH domain-containing family protein 3 isoform b

    See identical proteins and their annotated locations for NP_001264743.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (b) has a longer and distinct N-terminus, compared to isoform a. Both variants 2 and 3 encode the same isoform.
    Source sequence(s)
    AK093081, AK127574, AK298544, AL832335
    Consensus CDS
    CCDS75748.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A087WY31, B4DPX9, Q658Z6, Q8NA80
    Related
    ENSP00000481476.1, ENST00000621820.4
    Conserved Domains (1) summary
    pfam04146
    Location:420553
    YTH; YT521-B-like domain
  3. NM_001277815.2NP_001264744.1  YTH domain-containing family protein 3 isoform c

    See identical proteins and their annotated locations for NP_001264744.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.
    Source sequence(s)
    AK127574, AL832335, BP223018
    Consensus CDS
    CCDS75749.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A024R7W5, Q658Z6
    Related
    ENSP00000485046.1, ENST00000623280.3
    Conserved Domains (1) summary
    pfam04146
    Location:366499
    YTH; YT521-B-like domain
  4. NM_001277816.2NP_001264745.1  YTH domain-containing family protein 3 isoform c

    See identical proteins and their annotated locations for NP_001264745.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.
    Source sequence(s)
    AK127574, AL832335, AW673093, BP223018
    Consensus CDS
    CCDS75749.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A024R7W5, Q658Z6
    Related
    ENSP00000481497.1, ENST00000617200.1
    Conserved Domains (1) summary
    pfam04146
    Location:366499
    YTH; YT521-B-like domain
  5. NM_001277817.2NP_001264746.1  YTH domain-containing family protein 3 isoform c

    See identical proteins and their annotated locations for NP_001264746.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (6) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.
    Source sequence(s)
    AC011978, AK127574, AL831816, AL832335, BP354748
    Consensus CDS
    CCDS75749.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A024R7W5, Q658Z6, Q8N3V9
    Conserved Domains (1) summary
    pfam04146
    Location:366499
    YTH; YT521-B-like domain
  6. NM_001277818.2NP_001264747.1  YTH domain-containing family protein 3 isoform c

    See identical proteins and their annotated locations for NP_001264747.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (7) differs in its 5' UTR and uses a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus, compared to isoform a. Variants 4, 5, 6, and 7 encode the same isoform.
    Source sequence(s)
    AK093081, AK127574, AL832335
    Consensus CDS
    CCDS75749.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    A0A024R7W5, Q658Z6, Q8NA80
    Related
    ENSP00000478825.1, ENST00000621890.4
    Conserved Domains (1) summary
    pfam04146
    Location:366499
    YTH; YT521-B-like domain
  7. NM_152758.6NP_689971.4  YTH domain-containing family protein 3 isoform a

    See identical proteins and their annotated locations for NP_689971.4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a.
    Source sequence(s)
    AK127574, AL832335
    Consensus CDS
    CCDS75747.1
    UniProtKB/Swiss-Prot
    Q7Z739
    UniProtKB/TrEMBL
    Q658Z6
    Related
    ENSP00000473496.2, ENST00000539294.6
    Conserved Domains (1) summary
    pfam04146
    Location:417550
    YTH; YT521-B-like domain

RNA

  1. NR_102434.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AK127574, AL832335, BC037492, BP223018, CN335163
    Related
    ENST00000517371.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    63168553..63212788
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011517509.3XP_011515811.1  YTH domain-containing family protein 3 isoform X1

    See identical proteins and their annotated locations for XP_011515811.1

    UniProtKB/TrEMBL
    A0A087WY31
    Conserved Domains (1) summary
    pfam04146
    Location:420553
    YTH; YT521-B-like domain
  2. XM_011517510.3XP_011515812.1  YTH domain-containing family protein 3 isoform X2

    See identical proteins and their annotated locations for XP_011515812.1

    UniProtKB/TrEMBL
    A0A024R7W5
    Conserved Domains (1) summary
    pfam04146
    Location:366499
    YTH; YT521-B-like domain
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