Ythdc1 YTH N6-methyladenosine RNA binding protein C1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ythdc1provided by RGD
Official Full Name: YTH N6-methyladenosine RNA binding protein C1provided by RGD
Primary source: RGD:621706
See related: EnsemblRapid:ENSRNOG00000001996 AllianceGenome:RGD:621706
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Yt521
Summary: Enables N6-methyladenosine-containing RNA reader activity. Involved in mRNA splicing, via spliceosome. Located in nuclear body. Orthologous to human YTHDC1 (YTH N6-methyladenosine RNA binding protein C1). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 184.9), Lung (RPKM 128.1) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 14p21

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	14	NC_086032.1 (21540276..21570724, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	14	NC_051349.1 (21185438..21215934, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	14	NC_005113.4 (22971834..23002326, complement)

Chromosome 14 - NC_086032.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

METTL3 mediates m6A modification of lncRNA CRNDE to promote ATG10 expression and improve brain ischemia/reperfusion injury through YTHDC1.
Title: METTL3 mediates m6A modification of lncRNA CRNDE to promote ATG10 expression and improve brain ischemia/reperfusion injury through YTHDC1.
Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
Title: Methyltransferase-like 3 modulates visceral hypersensitivity through regulating the nuclear export of circKcnk9 in YTHDC1-dependent manner.
YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA.
Title: YTHDC1 mitigates ischemic stroke by promoting Akt phosphorylation through destabilizing PTEN mRNA.
The YTH domain of YT521-B binds sequence-specifically a GA-containing sequence with a 50-fold affinity increase when the adenine is N6 methylated.
Title: Solution structure of the YTH domain in complex with N6-methyladenosine RNA: a reader of methylated RNA.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

d14rat81 (e-PCR)
- UniSTS:121018

BF388492 (e-PCR)
- UniSTS:244959

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables N6-methyladenosine-containing RNA reader activity	IBA Inferred from Biological aspect of Ancestor more info
enables N6-methyladenosine-containing RNA reader activity	IDA Inferred from Direct Assay more info	PubMed
enables N6-methyladenosine-containing RNA reader activity	IEA Inferred from Electronic Annotation more info
enables N6-methyladenosine-containing RNA reader activity	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in dosage compensation by inactivation of X chromosome	ISO Inferred from Sequence Orthology more info
involved_in dosage compensation by inactivation of X chromosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in mRNA alternative polyadenylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mRNA alternative polyadenylation	ISO Inferred from Sequence Orthology more info
involved_in mRNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in mRNA export from nucleus	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA splice site recognition	ISO Inferred from Sequence Orthology more info
involved_in mRNA splice site recognition	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
involved_in post-transcriptional regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in post-transcriptional regulation of gene expression	ISS Inferred from Sequence or Structural Similarity more info
involved_in primary follicle stage	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within primary follicle stage	ISO Inferred from Sequence Orthology more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of alternative mRNA splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA stability	IEA Inferred from Electronic Annotation more info
involved_in spermatogenesis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within spermatogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nuclear speck	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: YTH domain-containing protein 1

Names: RA301-binding protein; 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)

NM_133423.1 → NP_596914.1 YTH domain-containing protein 1

See identical proteins and their annotated locations for NP_596914.1

Status: PROVISIONAL

Source sequence(s)

AF144731

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Related

ENSRNOP00000095873.1, ENSRNOT00000119155.2

Conserved Domains (1) summary

pfam04146
Location:358 → 495

YTH; YT521-B-like domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086032.1 Reference GRCr8

Range

21540276..21570724 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006250808.4 → XP_006250870.1 YTH domain-containing protein 1 isoform X7

See identical proteins and their annotated locations for XP_006250870.1

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

UniProtKB/TrEMBL

A6JCQ7

Conserved Domains (2) summary

pfam04146
Location:340 → 477

YTH; YT521-B-like domain

cl11266
Location:2 → 98

EssA; WXG100 protein secretion system (Wss), protein EssA
XM_063272837.1 → XP_063128907.1 YTH domain-containing protein 1 isoform X6

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Related

ENSRNOP00000080807.2, ENSRNOT00000110796.2
XM_006250806.4 → XP_006250868.1 YTH domain-containing protein 1 isoform X4

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Conserved Domains (2) summary

pfam04146
Location:358 → 495

YTH; YT521-B-like domain

cl11266
Location:2 → 98

EssA; WXG100 protein secretion system (Wss), protein EssA
XM_039091592.2 → XP_038947520.1 YTH domain-containing protein 1 isoform X5

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Conserved Domains (1) summary

cd21134
Location:353 → 489

YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily
XM_039091591.2 → XP_038947519.1 YTH domain-containing protein 1 isoform X3

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Conserved Domains (1) summary

cd21134
Location:353 → 489

YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily
XM_039091590.2 → XP_038947518.1 YTH domain-containing protein 1 isoform X2

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Conserved Domains (1) summary

cd21134
Location:371 → 507

YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily
XM_063272838.1 → XP_063128908.1 YTH domain-containing protein 1 isoform X9

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02
XM_006250805.5 → XP_006250867.1 YTH domain-containing protein 1 isoform X1

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

UniProtKB/TrEMBL

A0A8I6GG56

Related

ENSRNOP00000087598.1, ENSRNOT00000118221.2

Conserved Domains (1) summary

pfam04146
Location:370 → 507

YTH; YT521-B-like domain
XM_008769990.4 → XP_008768212.2 YTH domain-containing protein 1 isoform X8

UniProtKB/Swiss-Prot

G3V690, O54729, Q9QY02

Conserved Domains (1) summary

cd21134
Location:371 → 507

YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily
XM_039091594.2 → XP_038947522.1 YTH domain-containing protein 1 isoform X10

Conserved Domains (1) summary

cd21134
Location:371 → 507

YTH; YTH (YT521-B homology) domains are RNA-binding domains that belong to the PUA superfamily