Phf1 (PHD finger protein 1) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Phf1 (PHD finger protein 1) Rattus norvegicus
Analyze
Symbol: Phf1
Name: PHD finger protein 1
RGD ID: 1303205
Description: Enables chromatin binding activity. Predicted to be involved in DNA repair-dependent chromatin remodeling and negative regulation of gene expression, epigenetic. Predicted to be located in centrosome and site of double-strand break. Predicted to be part of ESC/E(Z) complex. Predicted to be active in nucleus. Orthologous to human PHF1 (PHD finger protein 1); PARTICIPATES IN histone modification pathway; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: MGC94975; polycomb-like 1; T-complex testis-expressed 3; Tctex3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8205,019,650 - 5,024,732 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl205,019,673 - 5,024,731 (+)EnsemblGRCr8
mRatBN7.2205,017,765 - 5,022,872 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,017,893 - 5,022,871 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx205,743,511 - 5,748,256 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,105,248 - 5,109,993 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,583,678 - 5,588,429 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,526,926 - 5,531,940 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,526,961 - 5,531,941 (+)Ensemblrn6Rnor6.0
Rnor_5.0207,585,909 - 7,590,953 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4205,170,270 - 5,175,027 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera206,600,534 - 6,605,292 (+)NCBICelera
RGSC_v3.1205,170,496 - 5,175,254 (+)NCBI
Cytogenetic Map20p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
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. SET for life: biochemical activities and biological functions of SET domain-containing proteins. Herz HM, etal., Trends Biochem Sci. 2013 Dec;38(12):621-39. doi: 10.1016/j.tibs.2013.09.004. Epub 2013 Oct 20.
3. Tctex3, related to Drosophila polycomblike, is expressed in male germ cells and mapped to the mouse t-complex. Kawakami S, etal., Mamm Genome 1998 Nov;9(11):874-80.
4. Tudor: a versatile family of histone methylation 'readers'. Lu R and Wang GG, Trends Biochem Sci. 2013 Nov;38(11):546-55. doi: 10.1016/j.tibs.2013.08.002. Epub 2013 Sep 10.
5. Readout of epigenetic modifications. Patel DJ and Wang Z, Annu Rev Biochem. 2013;82:81-118. doi: 10.1146/annurev-biochem-072711-165700.
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. Polycomblike protein PHF1b: a transcriptional sensor for GABA receptor activity. Saha S, etal., BMC Pharmacol Toxicol. 2013 Jul 23;14:37. doi: 10.1186/2050-6511-14-37.
10. Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Simon JA and Kingston RE, Mol Cell. 2013 Mar 7;49(5):808-24. doi: 10.1016/j.molcel.2013.02.013.
Additional References at PubMed
PMID:12477932   PMID:18286210   PMID:20873783   PMID:23104054   PMID:23142980   PMID:23273982   PMID:31451685  


Genomics

Comparative Map Data
Phf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8205,019,650 - 5,024,732 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl205,019,673 - 5,024,731 (+)EnsemblGRCr8
mRatBN7.2205,017,765 - 5,022,872 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl205,017,893 - 5,022,871 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx205,743,511 - 5,748,256 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0205,105,248 - 5,109,993 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0205,583,678 - 5,588,429 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0205,526,926 - 5,531,940 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl205,526,961 - 5,531,941 (+)Ensemblrn6Rnor6.0
Rnor_5.0207,585,909 - 7,590,953 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4205,170,270 - 5,175,027 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera206,600,534 - 6,605,292 (+)NCBICelera
RGSC_v3.1205,170,496 - 5,175,254 (+)NCBI
Cytogenetic Map20p12NCBI
PHF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38633,410,412 - 33,416,439 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl633,410,382 - 33,416,453 (+)Ensemblhg38GRCh38
GRCh37633,378,791 - 33,384,216 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36633,486,772 - 33,492,194 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34633,486,771 - 33,492,194NCBI
Celera634,933,196 - 34,938,653 (+)NCBICelera
Cytogenetic Map6p21.32NCBI
HuRef633,120,927 - 33,126,379 (+)NCBIHuRef
CHM1_1633,380,668 - 33,386,125 (+)NCBICHM1_1
T2T-CHM13v2.0633,231,158 - 33,237,801 (+)NCBIT2T-CHM13v2.0
Phf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391727,152,101 - 27,156,882 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1727,152,026 - 27,156,882 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381726,933,127 - 26,937,908 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1726,933,052 - 26,937,908 (+)Ensemblmm10GRCm38
MGSCv371727,070,072 - 27,074,835 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361726,660,921 - 26,665,478 (+)NCBIMGSCv36mm8
Celera1727,469,737 - 27,474,613 (+)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1713.6NCBI
Phf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554371,943,065 - 1,946,705 (+)Ensembl
ChiLan1.0NW_0049554371,943,049 - 1,947,027 (+)NCBIChiLan1.0ChiLan1.0
PHF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2547,895,593 - 47,901,452 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1643,762,809 - 43,768,624 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0632,990,080 - 32,995,785 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1634,101,057 - 34,107,124 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl634,101,371 - 34,107,124 (+)EnsemblpanPan2panpan1.1
PHF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1122,822,372 - 2,827,406 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl122,822,295 - 2,827,413 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha122,903,174 - 2,908,215 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0123,154,008 - 3,159,051 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl123,153,480 - 3,159,051 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1122,821,133 - 2,826,172 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0122,902,441 - 2,907,279 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0123,000,352 - 3,005,393 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Phf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494638,472,973 - 38,478,329 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647625,479,953 - 25,487,403 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647625,481,938 - 25,487,026 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl729,714,293 - 29,719,987 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1729,714,295 - 29,719,996 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2734,375,137 - 34,380,844 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11738,650,013 - 38,655,458 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1738,648,140 - 38,655,420 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604433,259,392 - 33,265,130 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475423,400,664 - 23,404,212 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475423,400,338 - 23,405,370 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Phf1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1186,866,496 - 6,871,459 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Phf1
34 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:81
Interacting mature miRNAs:83
Transcripts:ENSRNOT00000059548
Prediction methods:Microtar, Miranda, Rnahybrid
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
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015332005306452Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124164241Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)2016693431Rat
4889857Pur27Proteinuria QTL 2712.20.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20127341128Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129193376Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129193376Rat
7175096Tcs1T cell selection QTL 1T cell selection trait (VT:0004917)expression2047282825026446Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
61474Eae1Experimental allergic encephalomyelitis QTL 13nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)2016693431Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20126925056Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20126128279Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
1331772Cdexp2CD45RC expression in CD8 T cells QTL 25.7CD8-positive T cell quantity (VT:0008077)blood CD45RC(high) CD8 T cell count to CD45RC(low) CD8 T cell count ratio (CMO:0001990)20362632310078622Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129193376Rat
1300152Bp195Blood pressure QTL 1953.46arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2036263239244918Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129193376Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129193376Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20114100378Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127341128Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat

Markers in Region
RH128947  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8205,024,504 - 5,024,707 (+)Marker Load Pipeline
mRatBN7.2205,022,644 - 5,022,847 (+)MAPPERmRatBN7.2
Rnor_6.0205,531,713 - 5,531,915NCBIRnor6.0
Rnor_5.0207,590,726 - 7,590,928UniSTSRnor5.0
RGSC_v3.4205,174,802 - 5,175,004UniSTSRGSC3.4
Celera206,605,065 - 6,605,269UniSTS
RH 3.4 Map2055.53UniSTS
Cytogenetic Map20p12UniSTS


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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 160 91 90 59 92 59 6 356 192 11 139 81 92 31 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001414742 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_212538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601587 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601588 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017601589 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039098511 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063279027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001842414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005497188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010060636 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC128962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC083843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BX883042 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000020 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000059548   ⟹   ENSRNOP00000056303
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,020,675 - 5,022,871 (+)Ensembl
Rnor_6.0 Ensembl205,526,975 - 5,531,939 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000091364   ⟹   ENSRNOP00000073301
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,018,113 - 5,022,870 (+)Ensembl
Rnor_6.0 Ensembl205,527,181 - 5,531,938 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092247   ⟹   ENSRNOP00000075915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl205,017,893 - 5,022,871 (+)Ensembl
Rnor_6.0 Ensembl205,526,961 - 5,531,940 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,529,662 - 5,531,131 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092650
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,526,998 - 5,531,938 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092667
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,526,999 - 5,531,941 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000092668
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl205,526,979 - 5,531,939 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120945   ⟹   ENSRNOP00000098528
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl205,019,673 - 5,024,731 (+)Ensembl
RefSeq Acc Id: NM_001414742   ⟹   NP_001401671
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,975 - 5,024,732 (+)NCBI
mRatBN7.2205,018,115 - 5,022,872 (+)NCBI
RefSeq Acc Id: NM_212538   ⟹   NP_997703
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,975 - 5,024,732 (+)NCBI
mRatBN7.2205,018,115 - 5,022,872 (+)NCBI
Rnor_6.0205,527,181 - 5,531,938 (+)NCBI
Rnor_5.0207,585,909 - 7,590,953 (+)NCBI
RGSC_v3.4205,170,270 - 5,175,027 (+)RGD
Celera206,600,534 - 6,605,292 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601587   ⟹   XP_017457076
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,673 - 5,024,732 (+)NCBI
mRatBN7.2205,017,786 - 5,022,872 (+)NCBI
Rnor_6.0205,526,928 - 5,531,940 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601588   ⟹   XP_017457077
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,699 - 5,024,732 (+)NCBI
mRatBN7.2205,017,892 - 5,022,872 (+)NCBI
Rnor_6.0205,527,005 - 5,531,940 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017601589   ⟹   XP_017457078
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,658 - 5,024,732 (+)NCBI
mRatBN7.2205,017,771 - 5,022,872 (+)NCBI
Rnor_6.0205,526,926 - 5,531,940 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039098510   ⟹   XP_038954438
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,661 - 5,024,732 (+)NCBI
mRatBN7.2205,017,774 - 5,022,872 (+)NCBI
RefSeq Acc Id: XM_039098511   ⟹   XP_038954439
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,650 - 5,024,732 (+)NCBI
mRatBN7.2205,017,765 - 5,022,872 (+)NCBI
RefSeq Acc Id: XM_063279026   ⟹   XP_063135096
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,699 - 5,024,732 (+)NCBI
RefSeq Acc Id: XM_063279027   ⟹   XP_063135097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,699 - 5,024,732 (+)NCBI
RefSeq Acc Id: XR_001842414
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,668 - 5,023,965 (+)NCBI
mRatBN7.2205,017,779 - 5,022,872 (+)NCBI
Rnor_6.0205,526,926 - 5,531,940 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005497188
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,664 - 5,023,948 (+)NCBI
mRatBN7.2205,017,775 - 5,022,089 (+)NCBI
RefSeq Acc Id: XR_010060636
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8205,019,699 - 5,023,965 (+)NCBI
RefSeq Acc Id: NP_997703   ⟸   NM_212538
- UniProtKB: Q6MGC9 (UniProtKB/TrEMBL),   A6JJJ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457078   ⟸   XM_017601589
- Peptide Label: isoform X5
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457076   ⟸   XM_017601587
- Peptide Label: isoform X1
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017457077   ⟸   XM_017601588
- Peptide Label: isoform X3
- UniProtKB: Q6MGC9 (UniProtKB/TrEMBL),   A6JJJ4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000075915   ⟸   ENSRNOT00000092247
Ensembl Acc Id: ENSRNOP00000056303   ⟸   ENSRNOT00000059548
Ensembl Acc Id: ENSRNOP00000073301   ⟸   ENSRNOT00000091364
RefSeq Acc Id: XP_038954439   ⟸   XM_039098511
- Peptide Label: isoform X6
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038954438   ⟸   XM_039098510
- Peptide Label: isoform X2
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001401671   ⟸   NM_001414742
- UniProtKB: Q6MGC9 (UniProtKB/TrEMBL),   A6JJJ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135097   ⟸   XM_063279027
- Peptide Label: isoform X7
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063135096   ⟸   XM_063279026
- Peptide Label: isoform X4
- UniProtKB: A6JJJ4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000098528   ⟸   ENSRNOT00000120945
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6MGC9-F1-model_v2 AlphaFold Q6MGC9 1-560 view protein structure

Transcriptome

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

Promoters
RGD ID:13701420
Promoter ID:EPDNEW_R11942
Type:initiation region
Name:Phf1_2
Description:PHD finger protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11943  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,526,983 - 5,527,043EPDNEW
RGD ID:13701421
Promoter ID:EPDNEW_R11943
Type:initiation region
Name:Phf1_1
Description:PHD finger protein 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R11942  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0205,527,183 - 5,527,243EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303205 AgrOrtholog
BioCyc Gene G2FUF-4505 BioCyc
Ensembl Genes ENSRNOG00000000480 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000120945 ENTREZGENE
  ENSRNOT00000120945.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.140 UniProtKB/TrEMBL
  3.30.40.10 UniProtKB/TrEMBL
  3.90.980.20 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7114670 IMAGE-MGC_LOAD
InterPro KDM4_Tudor_2 UniProtKB/TrEMBL
  Mtf2_C_dom UniProtKB/TrEMBL
  PHF1 UniProtKB/TrEMBL
  PHF1_PHD-finger2 UniProtKB/TrEMBL
  Tudor UniProtKB/TrEMBL
  Tudor_PHF1 UniProtKB/TrEMBL
  Zinc_finger_PHD-type_CS UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
MGC_CLONE MGC:94975 IMAGE-MGC_LOAD
NCBI Gene 294287 ENTREZGENE
PANTHER POLYCOMB-LIKE TRANSCRIPTION FACTOR UniProtKB/TrEMBL
  PTHR12628:SF11 UniProtKB/TrEMBL
Pfam Mtf2_C UniProtKB/TrEMBL
  PHD UniProtKB/TrEMBL
  Tudor_2 UniProtKB/TrEMBL
PhenoGen Phf1 PhenoGen
PROSITE ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000480 RatGTEx
SMART PHD UniProtKB/TrEMBL
  TUDOR UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
  Tudor/PWWP/MBT UniProtKB/TrEMBL
UniProt A0ABK0KW73_RAT UniProtKB/TrEMBL
  A6JJJ4 ENTREZGENE, UniProtKB/TrEMBL
  Q5XI49_RAT UniProtKB/TrEMBL
  Q6MGC9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Phf1  PHD finger protein 1      Symbol and Name status set to approved 1299863 APPROVED
2005-07-14 Phf1  PHD finger protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL