Ythdf3 MGI Mouse Gene Detail - MGI:1918850 - YTH N6-methyladenosine RNA binding protein 3

Symbol

Ythdf3
Name

YTH N6-methyladenosine RNA binding protein 3
Synonyms

9130022A11Rik

Feature Type

protein coding gene
IDs

MGI:1918850
NCBI Gene: 229096
Alliance

gene page
Transcription Start Sites

6 TSS

Sequence Map

Chr3:16237376-16271201 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 4.04 cM
Mapping Data

1 experiment

SNPs within 2kb

736 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1918850	protein coding gene	Chr3:16237309-16271201 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027085	protein coding gene	Chr3:13423144-13461869 (+)
A/J	MGP_AJ_G0027046	protein coding gene	Chr3:13326724-13360457 (+)
AKR/J	MGP_AKRJ_G0027015	protein coding gene	Chr3:13354492-13389038 (+)
BALB/cJ	MGP_BALBcJ_G0027058	protein coding gene	Chr3:13070403-13105617 (+)
C3H/HeJ	MGP_C3HHeJ_G0026798	protein coding gene	Chr3:13456222-13490507 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0027502	protein coding gene	Chr3:14246443-14283117 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0024863	protein coding gene	Chr3:11675800-11705499 (+)
CAST/EiJ	MGP_CASTEiJ_G0026254	protein coding gene	Chr3:13459672-13495229 (+)
CBA/J	MGP_CBAJ_G0026776	protein coding gene	Chr3:14515998-14551591 (+)
DBA/2J	MGP_DBA2J_G0026910	protein coding gene	Chr3:12907591-12942522 (+)
FVB/NJ	MGP_FVBNJ_G0026879	protein coding gene	Chr3:12650378-12684261 (+)
LP/J	MGP_LPJ_G0027022	protein coding gene	Chr3:13971898-14011022 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0026899	protein coding gene	Chr3:16257496-16298965 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0027561	protein coding gene	Chr3:13182587-13217860 (+)
PWK/PhJ	MGP_PWKPhJ_G0025987	protein coding gene	Chr3:12754769-12788527 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0025794	protein coding gene	Chr3:12996110-13032080 (+)
WSB/EiJ	MGP_WSBEiJ_G0026327	protein coding gene	Chr3:13218362-13261903 (+)

Human Ortholog

YTHDF3, YTH N6-methyladenosine RNA binding protein F3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

YTHDF3, YTH N6-methyladenosine RNA binding protein F3
Synonyms

DF3
Links

HGNC:26465

NCBI Gene ID: 253943

neXtProt AC: NX_Q7Z739

UniProt: Q7Z739
Chr Location

8q12.3; chr8:63168553-63212788 (+) GRCh38

MGI Vertebrate Homology

Ythdf3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: YTHDF3
Gene Tree

Ythdf3

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References

1 with disease annotations

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Phenotype Summary

12 phenotypes from 3 alleles in 3 genetic backgrounds
3 phenotypes from multigenic genotypes
16 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

34
Endonuclease-mediated

7
Gene trapped

23
Radiation induced

1
Targeted

3
Genomic Mutations

1 involving Ythdf3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

55 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit decreased susceptibility to vesicular stomatitis virus (VSV) infection. Homozygous KO does not affect viability or fertility.

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All GO Annotations

33
GO References

7

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

714
Tissues

5
cDNA Data

173
Literature Summary

6

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase ythdf3

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All Sequences

72
RefSeq

18
UniProt

4
CCDS

CCDS38396.1, CCDS50869.1, CCDS89615.1

Ensembl

ENSMUSG00000047213 (Evidence)
NCBI Gene

229096

			Length	Strain/Species	Flank
genomic	ENSMUSG00000047213	Ensembl Gene Model \| MGI Sequence Detail	33826	C57BL/6J	± kb
transcript	ENSMUST00000108346	Ensembl \| MGI Sequence Detail	4929	Not Applicable
polypeptide	ENSMUSP00000103983	Ensembl \| MGI Sequence Detail	596	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000029879 YTH domain-containing family protein 3

(term hierarchy)
InterPro Domains

IPR007275 YTH domain

IPR045168 YTH domain containing protein
GlyGen

Q8BYK6 9 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (7 sites)

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All nucleic 175

cDNA 173

Primer pair 1

Other 1

Microarray probesets 8

Summaries

All 46

Developmental Gene Expression 6

Diseases 1

Gene Ontology 7

Phenotypes 16
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:355331 Mao Y, et al., Advanced paternal age exacerbates neuroinflammation in offspring via m6A modification-mediated intergenerational inheritance. J Neuroinflammation. 2024 Oct 4;21(1):249

TSS for Ythdf3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr28473	Chr3:16237341-16237370 (+)	-20 bp
Tssr28474	Chr3:16237372-16237444 (+)	32 bp
Tssr28475	Chr3:16237461-16237472 (+)	91 bp
Tssr28476	Chr3:16238028-16238041 (+)	659 bp
Tssr28477	Chr3:16250680-16250699 (+)	13,314 bp
Tssr28478	Chr3:16268855-16268869 (+)	31,486 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24