Phc1 (polyhomeotic homolog 1) - Rat Genome Database
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Gene: Phc1 (polyhomeotic homolog 1) Rattus norvegicus
Analyze
Symbol: Phc1
Name: polyhomeotic homolog 1
RGD ID: 1309203
Description: Predicted to have chromatin binding activity. Predicted to be involved in cellular response to leukemia inhibitory factor; cellular response to retinoic acid; and histone ubiquitination. Predicted to localize to PRC1 complex; nuclear body; and sex chromatin. Human ortholog(s) of this gene implicated in primary autosomal recessive microcephaly 11. Orthologous to human PHC1 (polyhomeotic homolog 1); PARTICIPATES IN histone modification pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC312690; polyhomeotic homolog 1 (Drosophila); polyhomeotic-like 1; polyhomeotic-like 1 (Drosophila); polyhomeotic-like protein 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24155,510,274 - 155,532,636 (-)NCBI
Rnor_6.0 Ensembl4155,093,949 - 155,116,154 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04155,093,947 - 155,118,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04222,121,134 - 222,143,635 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44158,736,736 - 158,759,429 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14158,982,409 - 159,004,315 (-)NCBI
Celera4144,331,497 - 144,353,650 (-)NCBICelera
Cytogenetic Map4q42NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8070621   PMID:12167701   PMID:12183370   PMID:14557078   PMID:15525528   PMID:16687444   PMID:19636380   PMID:20439489   PMID:21282530   PMID:23418308  


Genomics

Comparative Map Data
Phc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24155,510,274 - 155,532,636 (-)NCBI
Rnor_6.0 Ensembl4155,093,949 - 155,116,154 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04155,093,947 - 155,118,838 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04222,121,134 - 222,143,635 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44158,736,736 - 158,759,429 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14158,982,409 - 159,004,315 (-)NCBI
Celera4144,331,497 - 144,353,650 (-)NCBICelera
Cytogenetic Map4q42NCBI
PHC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl128,913,896 - 8,941,467 (+)EnsemblGRCh38hg38GRCh38
GRCh38128,914,509 - 8,941,467 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37129,067,105 - 9,094,063 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36128,958,583 - 8,985,330 (+)NCBINCBI36hg18NCBI36
Build 34128,958,532 - 8,984,156NCBI
Celera1210,604,723 - 10,631,471 (+)NCBI
Cytogenetic Map12p13.31NCBI
HuRef128,847,980 - 8,874,662 (+)NCBIHuRef
CHM1_1129,036,292 - 9,063,026 (+)NCBICHM1_1
Phc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm396122,294,690 - 122,317,946 (-)NCBIGRCm39mm39
GRCm39 Ensembl6122,294,690 - 122,317,520 (-)Ensembl
GRCm386122,317,731 - 122,340,227 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl6122,317,731 - 122,340,561 (-)EnsemblGRCm38mm10GRCm38
MGSCv376122,267,749 - 122,287,033 (-)NCBIGRCm37mm9NCBIm37
MGSCv366122,283,350 - 122,302,616 (-)NCBImm8
Celera6124,111,949 - 124,131,254 (-)NCBICelera
Cytogenetic Map6F1NCBI
cM Map657.52NCBI
Phc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554136,156,934 - 6,176,460 (-)NCBIChiLan1.0ChiLan1.0
PHC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1129,230,801 - 9,257,811 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl129,231,394 - 9,257,806 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0128,999,018 - 9,025,900 (+)NCBIMhudiblu_PPA_v0panPan3
PHC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2736,797,927 - 36,819,386 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12736,797,327 - 36,816,726 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Phc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936870275,764 - 300,460 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl562,557,756 - 62,580,651 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1562,557,774 - 62,580,640 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2565,355,682 - 65,378,586 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHC1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1118,733,769 - 8,759,430 (+)NCBI
ChlSab1.1 Ensembl118,733,988 - 8,758,600 (+)Ensembl
Phc1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248604,720,722 - 4,747,456 (-)NCBI

Position Markers
AA955967  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04155,094,019 - 155,094,152NCBIRnor6.0
Rnor_5.04222,121,295 - 222,121,428UniSTSRnor5.0
RGSC_v3.44158,736,806 - 158,736,939UniSTSRGSC3.4
Celera4144,331,567 - 144,331,700UniSTS
RH 3.4 Map4997.0UniSTS
Cytogenetic Map4q42UniSTS
RH143857  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.04155,113,470 - 155,113,579NCBIRnor6.0
Rnor_5.04222,140,656 - 222,140,765UniSTSRnor5.0
RGSC_v3.44158,756,745 - 158,756,854UniSTSRGSC3.4
Celera4144,350,966 - 144,351,075UniSTS
RH 3.4 Map4995.1UniSTS
Cytogenetic Map4q42UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61446Coreg2Compensatory renal growth QTL 23.5kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)4147274055157294090Rat
61451Ciaa4CIA Autoantibody QTL 43.1blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)4125884464168047091Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4117926139162926139Rat
724558Plsm2Polydactyly-luxate syndrome (PLS) morphotypes QTL 20.0003hindlimb integrity trait (VT:0010563)hind foot phalanges count (CMO:0001949)4131834282176834282Rat
1331738Bp209Blood pressure QTL 2092.979arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)4136351734180689124Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4108876717169215811Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4105971071168047091Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)463537179157286626Rat
631683Bp116Blood pressure QTL 1160.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)4123111827168111827Rat
737978Pia23Pristane induced arthritis QTL 235.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4116726724157291438Rat
1582237Kidm34Kidney mass QTL 3440.0001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)4146942075168998263Rat
1298524Oia8Oil induced arthritis QTL 8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
631511Pia7Pristane induced arthritis QTL 74.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4131532269168047091Rat
1581574Eae20Experimental allergic encephalomyelitis QTL 207.8nervous system integrity trait (VT:0010566)percentage of study population developing experimental autoimmune encephalomyelitis during a period of time (CMO:0001047)4152482121158564471Rat
2293659Bmd35Bone mineral density QTL 354.50.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)4136908430182878540Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)494893247168046938Rat
634342Cia24Collagen induced arthritis QTL 244.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4145373934176509907Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123478354168478354Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)443414605155469929Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)484475257178931073Rat
1578674Bmd12Bone mineral density QTL 123.8femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)4137171018182171018Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)47850904182171018Rat
1358364Sradr4Stress Responsive Adrenal Weight QTL 44.92adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)4128602727173602727Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)486438317168047091Rat
2303623Vencon2Ventilatory control QTL 23.8respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)4134917642179917642Rat
1549827Scl46Serum cholesterol level QTL 463.5blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)4131864442176864442Rat
61362Oia2Oil induced arthritis QTL 20.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4136351734174694858Rat
61422Cia13Collagen induced arthritis QTL 134.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4132455408168047091Rat
6478718Anxrr34Anxiety related response QTL 340.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478748Anxrr42Anxiety related response QTL 420.28008locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
6478754Anxrr43Anxiety related response QTL 430.14035locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4145547014184226339Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110702761155702761Rat
6478778Anxrr51Anxiety related response QTL 510.25384locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4123587009168587009Rat
6478693Anxrr32Anxiety related response QTL 320.00092locomotor behavior trait (VT:0001392)measurement of voluntary locomotion into, out of or within a discrete space in an experimental apparatus (CMO:0000957)4145547014184226339Rat
6478700Anxrr33Anxiety related response QTL 330.00896locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4145547014184226339Rat
7411558Bw133Body weight QTL 13313.840.001body mass (VT:0001259)body weight gain (CMO:0000420)4124442168169442168Rat
10401796Kidm48Kidney mass QTL 48kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)4146497452184226339Rat
10755501Bp390Blood pressure QTL 3902.5arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)423850384169318094Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4112807675157807675Rat
12798525Anxrr57Anxiety related response QTL 573.210.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4146086918168047091Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:86
Count of miRNA genes:71
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000020529
Prediction methods: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.


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 1 28 19 6 8 6 3 70 28 41 10
Low 2 15 38 35 11 35 8 8 4 7 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020529   ⟹   ENSRNOP00000020529
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl4155,093,949 - 155,116,154 (-)Ensembl
RefSeq Acc Id: NM_001107886   ⟹   NP_001101356
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,274 - 155,532,488 (-)NCBI
Rnor_6.04155,093,949 - 155,116,154 (-)NCBI
Rnor_5.04222,121,134 - 222,143,635 (-)NCBI
RGSC_v3.44158,736,736 - 158,759,429 (-)RGD
Celera4144,331,497 - 144,353,650 (-)RGD
Sequence:
RefSeq Acc Id: XM_006237300   ⟹   XP_006237362
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,513 (-)NCBI
Rnor_6.04155,093,947 - 155,116,164 (-)NCBI
Rnor_5.04222,121,134 - 222,143,635 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237302   ⟹   XP_006237364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.04155,093,947 - 155,118,838 (-)NCBI
Rnor_5.04222,121,134 - 222,143,635 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006237303   ⟹   XP_006237365
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,512 (-)NCBI
Rnor_6.04155,093,947 - 155,116,164 (-)NCBI
Rnor_5.04222,121,134 - 222,143,635 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039107668   ⟹   XP_038963596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,513 (-)NCBI
RefSeq Acc Id: XM_039107669   ⟹   XP_038963597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,629 (-)NCBI
RefSeq Acc Id: XM_039107670   ⟹   XP_038963598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,636 (-)NCBI
RefSeq Acc Id: XM_039107671   ⟹   XP_038963599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.24155,510,279 - 155,532,512 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001101356   ⟸   NM_001107886
- UniProtKB: D3ZVD1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006237364   ⟸   XM_006237302
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006237365   ⟸   XM_006237303
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006237362   ⟸   XM_006237300
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000020529   ⟸   ENSRNOT00000020529
RefSeq Acc Id: XP_038963598   ⟸   XM_039107670
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038963597   ⟸   XM_039107669
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038963596   ⟸   XM_039107668
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038963599   ⟸   XM_039107671
- Peptide Label: isoform X6
Protein Domains
FCS-type   SAM

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 222128902 222128903 G A snv DOB/Oda (KyushuU)
4 222129014 222129015 C A snv IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)
4 222138187 222138188 T C snv BBDP/WorN (KNAW), SBH/Ygl (KNAW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), BUF/N (KNAW), GK/Ox (KNAW), LEW/Crl (KNAW), LEW/NCrl (KNAW), MNS/Gib (KNAW), BUF/MNa (KyushuU), NIG-III/Hok (KyushuU), HTX/Kyo (KyushuU), ZF (KyushuU), WAG/Rij (KNAW), ZFDM (KyushuU), SBH/Ygl (MCW), MR/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 155111001 155111002 T C snv SBH/Ygl (MCW), WKY/NHsd (RGD), CDS, Buf/N (MCW), MR/N (MCW), WKY/N (MCW), BBDP/Wor (RGD), GK/Ox (RGD), LEW/Crl (RGD), LEW/NCrlBR (RGD), MNS/Gib (RGD), SBH/Ygl (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), WAG/Rij (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), CDR


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
4 158754276 158754277 T C snv SHR/OlaIpcv (ICL), LCR/2Mco (UMich), BUF/N (KNAW), MR/N (KNAW), WKY/N (KNAW), SHR/OlaIpcv (KNAW), SHRSP/Gcrc (MDC), BBDP/WorN (ICL), GK/Ox (ICL), LEW/Crl (ICL), LEW/NCrl (ICL), MNS/Gib (ICL), SBH/Ygl (ICL), SHR/OlaIpcv (ICL), SHR/NHsd (ICL), SHRSP/Gcrc (ICL), WAG/Rij (ICL), WKY/Gcrc (ICL), WKY/NHsd (ICL), WKY/NCrl (ICL), LCR/1Mco (UMich)
4 158755127 158755128 C T snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309203 AgrOrtholog
Ensembl Genes ENSRNOG00000015191 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020529 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020529 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.10.150.50 UniProtKB/TrEMBL
  3.30.60.160 UniProtKB/TrEMBL
InterPro SAM UniProtKB/TrEMBL
  SAM/pointed UniProtKB/TrEMBL
  Znf_FCS UniProtKB/TrEMBL
  Znf_FCS_sf UniProtKB/TrEMBL
KEGG Report rno:312690 UniProtKB/TrEMBL
NCBI Gene 312690 ENTREZGENE
Pfam SAM_1 UniProtKB/TrEMBL
PhenoGen Phc1 PhenoGen
PROSITE SAM_DOMAIN UniProtKB/TrEMBL
  ZF_FCS UniProtKB/TrEMBL
SMART SAM UniProtKB/TrEMBL
Superfamily-SCOP SAM_homology UniProtKB/TrEMBL
UniProt D3ZVD1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Phc1  polyhomeotic homolog 1  Phc1  polyhomeotic homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-04-29 Phc1  polyhomeotic homolog 1 (Drosophila)  Phc1  polyhomeotic-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Phc1  polyhomeotic-like 1 (Drosophila)   Phc1_predicted  polyhomeotic-like 1 (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Phc1_predicted  polyhomeotic-like 1 (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED