Ythdf1 (YTH N6-methyladenosine RNA binding protein F1) - Rat Genome Database

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Gene: Ythdf1 (YTH N6-methyladenosine RNA binding protein F1) Rattus norvegicus
Analyze
Symbol: Ythdf1
Name: YTH N6-methyladenosine RNA binding protein F1
RGD ID: 1308932
Description: Predicted to enable N6-methyladenosine-containing RNA reader activity; mRNA binding activity; and ribosome binding activity. Predicted to be involved in several processes, including learning or memory; post-transcriptional regulation of gene expression; and stress granule assembly. Predicted to be located in P-body and cytoplasmic stress granule. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in colorectal cancer. Orthologous to human YTHDF1 (YTH N6-methyladenosine RNA binding protein F1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC296467; YTH domain family 1; YTH domain family protein 1; YTH domain family, member 1; YTH domain-containing family protein 1; YTH N(6)-methyladenosine RNA binding protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,402,228 - 188,417,740 (-)NCBIGRCr8
mRatBN7.23168,024,660 - 168,040,172 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,024,663 - 168,040,172 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,404,856 - 172,420,353 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,363,946 - 181,379,443 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,025,619 - 178,041,133 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03176,415,911 - 176,431,423 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,415,914 - 176,431,423 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,125,831 - 180,141,407 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,014,277 - 170,029,789 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13169,920,315 - 169,935,825 (-)NCBI
Celera3164,544,900 - 164,560,398 (+)NCBICelera
Cytogenetic Map3q43NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Circular RNA protein tyrosine kinase 2 (circPTK2) promotes colorectal cancer proliferation, migration, invasion and chemoresistance. Jiang Z, etal., Bioengineered. 2022 Jan;13(1):810-823. doi: 10.1080/21655979.2021.2012952.
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22658674   PMID:22681889   PMID:24284625   PMID:26046440   PMID:26318451   PMID:28106072   PMID:28106076   PMID:30401835   PMID:30728504   PMID:30843071   PMID:34015275  
PMID:34310344   PMID:36894806   PMID:37572160  


Genomics

Comparative Map Data
Ythdf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83188,402,228 - 188,417,740 (-)NCBIGRCr8
mRatBN7.23168,024,660 - 168,040,172 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3168,024,663 - 168,040,172 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3172,404,856 - 172,420,353 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03181,363,946 - 181,379,443 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03178,025,619 - 178,041,133 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03176,415,911 - 176,431,423 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3176,415,914 - 176,431,423 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03180,125,831 - 180,141,407 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43170,014,277 - 170,029,789 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13169,920,315 - 169,935,825 (-)NCBI
Celera3164,544,900 - 164,560,398 (+)NCBICelera
Cytogenetic Map3q43NCBI
YTHDF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382063,195,429 - 63,216,131 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2063,195,429 - 63,216,139 (-)EnsemblGRCh38hg38GRCh38
GRCh372061,826,781 - 61,847,483 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362061,297,226 - 61,317,983 (-)NCBINCBI36Build 36hg18NCBI36
Build 342061,297,228 - 61,317,983NCBI
Celera2058,504,268 - 58,525,021 (-)NCBICelera
Cytogenetic Map20q13.33NCBI
HuRef2058,551,559 - 58,578,606 (-)NCBIHuRef
CHM1_12061,727,941 - 61,748,702 (-)NCBICHM1_1
T2T-CHM13v2.02065,000,752 - 65,021,443 (-)NCBIT2T-CHM13v2.0
Ythdf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392180,546,170 - 180,562,729 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2180,546,170 - 180,562,742 (-)EnsemblGRCm39 Ensembl
GRCm382180,904,377 - 180,920,936 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2180,904,377 - 180,920,949 (-)EnsemblGRCm38mm10GRCm38
MGSCv372180,639,082 - 180,655,641 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362180,833,785 - 180,850,344 (-)NCBIMGSCv36mm8
Celera2184,990,626 - 185,007,152 (-)NCBICelera
Cytogenetic Map2H4NCBI
cM Map2103.5NCBI
Ythdf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955528935,182 - 951,722 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955528935,182 - 951,722 (+)NCBIChiLan1.0ChiLan1.0
YTHDF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22168,978,501 - 68,999,192 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12068,970,507 - 68,991,196 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02059,575,703 - 59,596,447 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12061,115,366 - 61,135,639 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2061,116,645 - 61,135,769 (-)Ensemblpanpan1.1panPan2
YTHDF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12446,927,218 - 46,940,015 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2446,927,848 - 46,951,949 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2446,111,317 - 46,124,326 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02447,881,084 - 47,894,120 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2447,799,759 - 47,894,081 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12446,896,564 - 46,909,548 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02447,020,531 - 47,033,541 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02447,776,866 - 47,789,883 (-)NCBIUU_Cfam_GSD_1.0
Ythdf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640195,134,237 - 195,149,728 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651410,587,222 - 10,603,478 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651410,587,877 - 10,603,373 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YTHDF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1762,329,302 - 62,341,413 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11762,329,302 - 62,341,312 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
YTHDF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12985,373 - 1,010,533 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2985,425 - 1,012,091 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605048,723,072 - 48,745,291 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ythdf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474128,917,942 - 28,933,599 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474128,918,466 - 28,933,593 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ythdf1
30 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:644
Count of miRNA genes:267
Interacting mature miRNAs:342
Transcripts:ENSRNOT00000037271
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3141074471169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3149040888168026850Rat
1300161Rf10Renal function QTL 103.57renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)3161192952169034231Rat
8552791Vie2Viral induced encephalitis QTL 24.1brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)3145956084169034231Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
2317883Alcrsp26Alcohol response QTL 261.80.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)3145526770169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat

Markers in Region
D3Rat1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23168,026,691 - 168,026,850 (+)MAPPERmRatBN7.2
Rnor_6.03176,417,943 - 176,418,101NCBIRnor6.0
Rnor_5.03180,127,863 - 180,128,021UniSTSRnor5.0
RGSC_v3.43170,016,309 - 170,016,467UniSTSRGSC3.4
RGSC_v3.43170,016,252 - 170,016,653RGDRGSC3.4
RGSC_v3.13169,922,345 - 169,922,503RGD
Celera3164,558,222 - 164,558,366UniSTS
RH 3.4 Map31533.2RGD
RH 3.4 Map31533.2UniSTS
RH 2.0 Map31027.1RGD
SHRSP x BN Map391.5299RGD
FHH x ACI Map3104.89RGD
Cytogenetic Map3q43UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000037271   ⟹   ENSRNOP00000037700
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,024,663 - 168,040,172 (-)Ensembl
Rnor_6.0 Ensembl3176,415,914 - 176,431,423 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000098734   ⟹   ENSRNOP00000078758
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,024,663 - 168,039,862 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000111765   ⟹   ENSRNOP00000093829
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3168,024,663 - 168,039,878 (-)Ensembl
RefSeq Acc Id: NM_001024756   ⟹   NP_001019927
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83188,402,228 - 188,417,740 (-)NCBI
mRatBN7.23168,024,660 - 168,040,172 (-)NCBI
Rnor_6.03176,415,911 - 176,431,423 (-)NCBI
Rnor_5.03180,125,831 - 180,141,407 (-)NCBI
RGSC_v3.43170,014,277 - 170,029,789 (-)RGD
Celera3164,544,900 - 164,560,398 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001019927 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97360 (Get FASTA)   NCBI Sequence Viewer  
  EDL88782 (Get FASTA)   NCBI Sequence Viewer  
  EDL88783 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037700.5
  ENSRNOP00000078758.1
  ENSRNOP00000093829.1
RefSeq Acc Id: NP_001019927   ⟸   NM_001024756
- UniProtKB: A0A8I6AL56 (UniProtKB/TrEMBL),   Q4V8J6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037700   ⟸   ENSRNOT00000037271
Ensembl Acc Id: ENSRNOP00000093829   ⟸   ENSRNOT00000111765
Ensembl Acc Id: ENSRNOP00000078758   ⟸   ENSRNOT00000098734
Protein Domains
YTH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4V8J6-F1-model_v2 AlphaFold Q4V8J6 1-559 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692742
Promoter ID:EPDNEW_R3267
Type:initiation region
Name:Ythdf1_1
Description:YTH N-methyladenosine RNA binding protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03176,431,505 - 176,431,565EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308932 AgrOrtholog
BioCyc Gene G2FUF-46313 BioCyc
Ensembl Genes ENSRNOG00000027015 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037271.5 UniProtKB/TrEMBL
  ENSRNOT00000098734.1 UniProtKB/TrEMBL
  ENSRNOT00000111765.1 UniProtKB/TrEMBL
Gene3D-CATH ph1033 like domains UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442371 IMAGE-MGC_LOAD
InterPro YTH_domain UniProtKB/TrEMBL
  YTH_prot UniProtKB/TrEMBL
KEGG Report rno:296467 UniProtKB/TrEMBL
MGC_CLONE MGC:114393 IMAGE-MGC_LOAD
NCBI Gene 296467 ENTREZGENE
PANTHER PTHR12357 UniProtKB/TrEMBL
  YTH DOMAIN-CONTAINING FAMILY PROTEIN 1 UniProtKB/TrEMBL
Pfam YTH UniProtKB/TrEMBL
PhenoGen Ythdf1 PhenoGen
PROSITE YTH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000027015 RatGTEx
UniProt A0A8I5ZLF0_RAT UniProtKB/TrEMBL
  A0A8I6AL56 ENTREZGENE, UniProtKB/TrEMBL
  A6KM74_RAT UniProtKB/TrEMBL
  F7F2Q6_RAT UniProtKB/TrEMBL
  Q4V8J6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-03-09 Ythdf1  YTH N6-methyladenosine RNA binding protein F1  Ythdf1  YTH N(6)-methyladenosine RNA binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-12-01 Ythdf1  YTH N(6)-methyladenosine RNA binding protein 1  Ythdf1  YTH domain family, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-10-23 Ythdf1  YTH domain family, member 1  Ythdf1  YTH domain family 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ythdf1  YTH domain family 1  Ythdf1_predicted  YTH domain family 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ythdf1_predicted  YTH domain family 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED