Phf21a (PHD finger protein 21A) - Rat Genome Database

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Gene: Phf21a (PHD finger protein 21A) Rattus norvegicus
Analyze
Symbol: Phf21a
Name: PHD finger protein 21A
RGD ID: 1560612
Description: Enables chromatin binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within suckling behavior. Located in nucleus. Orthologous to human PHF21A (PHD finger protein 21A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; fenvalerate.
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC362166; RGD1560612; similar to PHF21A protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2378,158,760 - 78,331,903 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl378,194,549 - 78,331,865 (+)Ensembl
Rnor_6.0381,099,765 - 81,271,841 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl381,134,505 - 81,271,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0387,803,380 - 87,979,083 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4376,583,850 - 76,759,238 (+)NCBIRGSC3.4rn4RGSC3.4
Celera377,360,760 - 77,537,633 (+)NCBICelera
Cytogenetic Map3q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. The rest repression of the neurosecretory phenotype is negatively modulated by BHC80, a protein of the BRAF/HDAC complex. Klajn A, etal., J Neurosci. 2009 May 13;29(19):6296-307. doi: 10.1523/JNEUROSCI.5943-08.2009.
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:15325272   PMID:16684532   PMID:24217620  


Genomics

Comparative Map Data
Phf21a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2378,158,760 - 78,331,903 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl378,194,549 - 78,331,865 (+)Ensembl
Rnor_6.0381,099,765 - 81,271,841 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl381,134,505 - 81,271,849 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0387,803,380 - 87,979,083 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4376,583,850 - 76,759,238 (+)NCBIRGSC3.4rn4RGSC3.4
Celera377,360,760 - 77,537,633 (+)NCBICelera
Cytogenetic Map3q24NCBI
PHF21A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381145,929,319 - 46,121,454 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1145,929,319 - 46,121,454 (-)EnsemblGRCh38hg38GRCh38
GRCh371145,950,870 - 46,143,005 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361145,907,446 - 46,099,561 (-)NCBINCBI36hg18NCBI36
Build 341145,910,692 - 46,099,561NCBI
Celera1146,098,473 - 46,290,814 (-)NCBI
Cytogenetic Map11p11.2NCBI
HuRef1145,657,507 - 45,849,706 (-)NCBIHuRef
CHM1_11145,949,282 - 46,141,198 (-)NCBICHM1_1
T2T-CHM13v2.01146,085,233 - 46,277,451 (-)NCBI
Phf21a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39292,014,096 - 92,195,011 (+)NCBIGRCm39mm39
GRCm39 Ensembl291,923,462 - 92,195,011 (+)Ensembl
GRCm38292,183,751 - 92,364,667 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl292,093,117 - 92,364,666 (+)EnsemblGRCm38mm10GRCm38
MGSCv37292,024,339 - 92,204,823 (+)NCBIGRCm37mm9NCBIm37
MGSCv36292,014,888 - 92,161,749 (+)NCBImm8
Celera293,578,000 - 93,757,795 (+)NCBICelera
Cytogenetic Map2E1NCBI
Phf21a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554221,857,335 - 2,045,816 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554221,857,335 - 2,045,816 (+)NCBIChiLan1.0ChiLan1.0
PHF21A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11146,374,675 - 46,627,242 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1146,374,675 - 46,564,358 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01145,883,122 - 46,074,805 (-)NCBIMhudiblu_PPA_v0panPan3
PHF21A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11843,300,426 - 43,493,956 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1843,335,986 - 43,492,828 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1842,028,422 - 42,221,992 (+)NCBI
ROS_Cfam_1.01843,956,093 - 44,149,924 (+)NCBI
ROS_Cfam_1.0 Ensembl1843,956,161 - 44,149,010 (+)Ensembl
UMICH_Zoey_3.11843,440,642 - 43,634,184 (+)NCBI
UNSW_CanFamBas_1.01842,993,830 - 43,187,352 (+)NCBI
UU_Cfam_GSD_1.01843,725,813 - 43,919,410 (+)NCBI
Phf21a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494720,795,602 - 20,981,802 (+)NCBI
SpeTri2.0NW_0049365622,920,254 - 3,093,444 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHF21A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl216,344,322 - 16,545,272 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1216,341,964 - 16,544,127 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2217,688,605 - 17,803,280 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHF21A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1119,219,067 - 19,409,474 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl119,248,427 - 19,406,918 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666038116,496,495 - 116,686,491 (+)NCBIVero_WHO_p1.0
Phf21a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247672,388,093 - 2,584,033 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_0046247672,388,111 - 2,584,033 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat31  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2378,196,030 - 78,196,190 (+)MAPPERmRatBN7.2
Rnor_6.0381,136,068 - 81,136,227NCBIRnor6.0
Rnor_5.0387,839,283 - 87,839,442UniSTSRnor5.0
RGSC_v3.4376,620,759 - 76,620,918UniSTSRGSC3.4
RGSC_v3.4376,620,663 - 76,620,970RGDRGSC3.4
RGSC_v3.1376,517,187 - 76,517,346RGD
Celera377,398,290 - 77,398,449UniSTS
RH 3.4 Map31018.5RGD
RH 3.4 Map31018.5UniSTS
RH 2.0 Map3698.6RGD
SHRSP x BN Map342.8698RGD
Cytogenetic Map3q24UniSTS
BE109327  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2378,335,413 - 78,335,593 (+)MAPPERmRatBN7.2
Rnor_6.0381,275,387 - 81,275,566NCBIRnor6.0
Rnor_5.0387,978,856 - 87,979,035UniSTSRnor5.0
RGSC_v3.4376,761,869 - 76,762,048UniSTSRGSC3.4
Celera377,537,406 - 77,537,585UniSTS
RH 3.4 Map3685.09UniSTS
Cytogenetic Map3q24UniSTS
RH130596  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2378,332,254 - 78,332,442 (+)MAPPERmRatBN7.2
Rnor_6.0381,272,228 - 81,272,415NCBIRnor6.0
Rnor_5.0387,975,697 - 87,975,884UniSTSRnor5.0
RGSC_v3.4376,758,710 - 76,758,897UniSTSRGSC3.4
Celera377,534,247 - 77,534,434UniSTS
Cytogenetic Map3q24UniSTS
AI407863  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2378,262,535 - 78,262,682 (+)MAPPERmRatBN7.2
Rnor_6.0381,202,606 - 81,202,752NCBIRnor6.0
Rnor_5.0387,905,759 - 87,905,905UniSTSRnor5.0
RGSC_v3.4376,687,299 - 76,687,445UniSTSRGSC3.4
Celera377,464,837 - 77,464,983UniSTS
Cytogenetic Map3q24UniSTS
BE107484  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2378,263,795 - 78,263,948 (+)MAPPERmRatBN7.2
Rnor_6.0381,203,866 - 81,204,018NCBIRnor6.0
Rnor_5.0387,907,019 - 87,907,171UniSTSRnor5.0
RGSC_v3.4376,688,559 - 76,688,711UniSTSRGSC3.4
Celera377,466,105 - 77,466,257UniSTS
RH 3.4 Map3706.9UniSTS
Cytogenetic Map3q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
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
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)35378111291609953Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)361017749121056321Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)36113434889115068Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)364655305115665732Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)364655305115665732Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)370348525121056321Rat
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)370653097121056321Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)373376539118376539Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:512
Count of miRNA genes:185
Interacting mature miRNAs:208
Transcripts:ENSRNOT00000008061, ENSRNOT00000008241, ENSRNOT00000066219, ENSRNOT00000067664
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 36 22 6 19 6 2 2 74 34 41 11 2
Low 7 35 35 35 6 9 1 6
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_001070000 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762045 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762051 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762052 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762053 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762054 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775453 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775454 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775456 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775457 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592176 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592177 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592178 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602554 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602555 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602556 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602557 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602558 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602559 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602560 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106451 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC129036 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY724487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000118 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000067664   ⟹   ENSRNOP00000061099
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl378,194,549 - 78,331,865 (+)Ensembl
Rnor_6.0 Ensembl381,134,505 - 81,271,849 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000095030   ⟹   ENSRNOP00000078574
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl378,194,549 - 78,331,865 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000113738   ⟹   ENSRNOP00000088965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl378,194,549 - 78,331,865 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114898   ⟹   ENSRNOP00000093848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl378,202,266 - 78,331,865 (+)Ensembl
RefSeq Acc Id: XM_039106451   ⟹   XP_038962379
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2378,158,760 - 78,331,903 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038962379 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL79559 (Get FASTA)   NCBI Sequence Viewer  
  EDL79560 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: ENSRNOP00000061099   ⟸   ENSRNOT00000067664
RefSeq Acc Id: XP_038962379   ⟸   XM_039106451
RefSeq Acc Id: ENSRNOP00000078574   ⟸   ENSRNOT00000095030
RefSeq Acc Id: ENSRNOP00000093848   ⟸   ENSRNOT00000114898
RefSeq Acc Id: ENSRNOP00000088965   ⟸   ENSRNOT00000113738

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M6K4-F1-model_v2 AlphaFold F1M6K4 1-694 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560612 AgrOrtholog
BioCyc Gene G2FUF-48707 BioCyc
Ensembl Genes ENSRNOG00000006063 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061099 ENTREZGENE
  ENSRNOP00000061099.4 UniProtKB/TrEMBL
  ENSRNOP00000078574.1 UniProtKB/TrEMBL
  ENSRNOP00000088965.1 UniProtKB/TrEMBL
  ENSRNOP00000093848.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000067664 ENTREZGENE
  ENSRNOT00000067664.5 UniProtKB/TrEMBL
  ENSRNOT00000095030.1 UniProtKB/TrEMBL
  ENSRNOT00000113738.1 UniProtKB/TrEMBL
  ENSRNOT00000114898.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro 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
NCBI Gene 362166 ENTREZGENE
Pfam PHD UniProtKB/TrEMBL
PhenoGen Phf21a PhenoGen
PROSITE ZF_PHD_1 UniProtKB/TrEMBL
  ZF_PHD_2 UniProtKB/TrEMBL
SMART PHD UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0A8I5ZL73_RAT UniProtKB/TrEMBL
  A0A8I6A676_RAT UniProtKB/TrEMBL
  A0A8I6AXM6_RAT UniProtKB/TrEMBL
  F1M6K4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-05-26 Phf21a  PHD finger protein 21A  RGD1560612  similar to PHF21A protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1560612  similar to PHF21A protein   RGD1560612_predicted  similar to PHF21A protein (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1560612_predicted  similar to PHF21A protein (predicted)  LOC362166  similar to PHF21A protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC362166  similar to PHF21A protein      Symbol and Name status set to provisional 70820 PROVISIONAL