Phf11 (PHD finger protein 11) - Rat Genome Database

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Gene: Phf11 (PHD finger protein 11) Rattus norvegicus
Analyze
Symbol: Phf11
Name: PHD finger protein 11
RGD ID: 1310853
Description: Predicted to enable zinc ion binding activity. Predicted to be active in nucleus. Orthologous to human PHF11 (PHD finger protein 11); INTERACTS WITH (+)-schisandrin B; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100362408; LOC361051; PHD finger protein 11 family member-like; PHD finger protein 11a; Phf11a
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81537,568,090 - 37,592,490 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1537,568,090 - 37,591,016 (-)EnsemblGRCr8
mRatBN7.21533,390,290 - 33,414,647 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1533,390,292 - 33,413,009 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1535,382,401 - 35,405,147 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01536,533,072 - 36,555,818 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01534,852,690 - 34,875,409 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01538,692,817 - 39,683,417 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1538,647,779 - 38,709,984 (-)Ensemblrn6Rnor6.0
Rnor_5.01542,526,169 - 42,545,873 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41538,443,971 - 38,477,944 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
RGSC_v3.11538,388,421 - 38,580,524 (-)NCBI
Cytogenetic Map15p12NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(-)-demecolcine  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-diaminotoluene  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxynon-2-enal  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrolein  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
benzo[a]pyrene  (ISO)
beta-lapachone  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
diquat  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
ethyl methanesulfonate  (ISO)
flutamide  (EXP)
formaldehyde  (ISO)
fructose  (ISO)
Genipin  (ISO)
gentamycin  (EXP)
glucose  (ISO)
glycidol  (EXP)
herbicide  (ISO)
indometacin  (ISO)
lipopolysaccharide  (ISO)
methyl methanesulfonate  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
nickel atom  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
perfluorohexanesulfonic acid  (ISO)
potassium chromate  (ISO)
raloxifene  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (ISO)
toluene 2,4-diisocyanate  (ISO)
trichostatin A  (ISO)
trovafloxacin  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nuclear membrane  (ISO)
nucleoplasm  (ISO)
nucleus  (IBA,IEA)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Phf11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81537,568,090 - 37,592,490 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1537,568,090 - 37,591,016 (-)EnsemblGRCr8
mRatBN7.21533,390,290 - 33,414,647 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1533,390,292 - 33,413,009 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1535,382,401 - 35,405,147 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01536,533,072 - 36,555,818 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01534,852,690 - 34,875,409 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01538,692,817 - 39,683,417 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1538,647,779 - 38,709,984 (-)Ensemblrn6Rnor6.0
Rnor_5.01542,526,169 - 42,545,873 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41538,443,971 - 38,477,944 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
RGSC_v3.11538,388,421 - 38,580,524 (-)NCBI
Cytogenetic Map15p12NCBI
PHF11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381349,495,953 - 49,528,976 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1349,495,095 - 49,528,981 (+)Ensemblhg38GRCh38
GRCh371350,070,089 - 50,103,112 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361348,967,802 - 49,001,118 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341348,969,249 - 49,001,112NCBI
Celera1331,124,752 - 31,158,072 (+)NCBICelera
Cytogenetic Map13q14.2NCBI
HuRef1330,863,385 - 30,896,419 (+)NCBIHuRef
CHM1_11350,037,327 - 50,070,649 (+)NCBICHM1_1
T2T-CHM13v2.01348,714,592 - 48,747,507 (+)NCBIT2T-CHM13v2.0
Phf11d
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391459,584,646 - 59,608,004 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1459,584,856 - 59,602,919 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381459,347,407 - 59,365,490 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1459,347,407 - 59,365,470 (-)Ensemblmm10GRCm38
MGSCv371459,966,244 - 59,984,327 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361458,302,842 - 58,319,557 (-)NCBIMGSCv36mm8
Celera1457,148,041 - 57,166,125 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1431.48NCBI
Phf11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554312,951,722 - 2,974,131 (+)Ensembl
ChiLan1.0NW_0049554312,945,119 - 2,974,767 (+)NCBIChiLan1.0ChiLan1.0
PHF11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21450,935,190 - 50,969,917 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11349,587,579 - 49,621,614 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01330,636,035 - 30,670,262 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11349,386,374 - 49,419,316 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1349,386,374 - 49,419,310 (+)EnsemblpanPan2panpan1.1
PHF11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1222,235,758 - 2,263,772 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
PHF11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1118,205,078 - 18,251,948 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11118,205,073 - 18,252,082 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21118,519,921 - 18,566,748 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHF11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1327,414,664 - 27,448,814 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl327,414,361 - 27,451,009 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605716,435,793 - 16,471,421 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Phf11
88 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1641913Colcr2Colorectal carcinoma resistance QTL 26.570.0197intestine integrity trait (VT:0010554)poorly differentiated malignant colorectal tumor number (CMO:0002076)15231575947315759Rat
5684946Bss98Bone structure and strength QTL 983.90.0026tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)15139411584Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15144836456Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15231575953331089Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)153185580392671517Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152852773273527732Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152272835342072050Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1525285835104695021Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)152233635152597086Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)1525285835104695021Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151915576287086765Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)15278592347785923Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151492659471614418Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)152233635167336351Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)1525285835104695021Rat

Markers in Region
D15Got232  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01538,704,202 - 38,704,379NCBIRnor6.0
Rnor_5.01542,538,314 - 42,538,491UniSTSRnor5.0
RGSC_v3.41538,463,472 - 38,463,642UniSTSRGSC3.4
RGSC_v3.41538,410,860 - 38,411,034UniSTSRGSC3.4
Cytogenetic Map15p12UniSTS
RH131947  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map15p12UniSTS


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 66 162 91 90 59 92 59 6 355 191 11 140 81 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000074738   ⟹   ENSRNOP00000066769
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1537,568,090 - 37,589,169 (-)Ensembl
mRatBN7.2 Ensembl1533,390,292 - 33,411,371 (-)Ensembl
Rnor_6.0 Ensembl1538,647,779 - 38,709,984 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000114019   ⟹   ENSRNOP00000086591
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1537,568,090 - 37,591,016 (-)Ensembl
mRatBN7.2 Ensembl1533,390,292 - 33,413,009 (-)Ensembl
RefSeq Acc Id: NM_001024272   ⟹   NP_001019443
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81537,568,090 - 37,591,016 (-)NCBI
mRatBN7.21533,390,290 - 33,413,216 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039093501   ⟹   XP_038949429
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81537,568,610 - 37,592,490 (-)NCBI
mRatBN7.21533,390,810 - 33,414,647 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001019443 (Get FASTA)   NCBI Sequence Viewer  
  XP_038949429 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88433 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000086591
  ENSRNOP00000086591.1
GenBank Protein Q5I0E2 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Acc Id: ENSRNOP00000066769   ⟸   ENSRNOT00000074738
RefSeq Acc Id: NP_001019443   ⟸   NM_001024272
- UniProtKB: Q5I0E2 (UniProtKB/Swiss-Prot),   A0A8I6AHQ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038949429   ⟸   XM_039093501
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000086591   ⟸   ENSRNOT00000114019
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-M0RB46-F1-model_v2 AlphaFold M0RB46 1-281 view protein structure
AF-Q5I0E2-F1-model_v2 AlphaFold Q5I0E2 1-336 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310853 AgrOrtholog
BioCyc Gene G2FUF-13559 BioCyc
Ensembl Genes ENSRNOG00000053891 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000114019 ENTREZGENE
  ENSRNOT00000114019.1 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7124805 IMAGE-MGC_LOAD
InterPro EPHD UniProtKB/Swiss-Prot
  PHD-type_Zinc_Finger UniProtKB/Swiss-Prot
  Znf_FYVE_PHD UniProtKB/Swiss-Prot
  Znf_PHD UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
KEGG Report rno:361051 UniProtKB/Swiss-Prot
MGC_CLONE MGC:95064 IMAGE-MGC_LOAD
NCBI Gene 361051 ENTREZGENE
PANTHER PHD FINGER PROTEIN UniProtKB/Swiss-Prot
  PHD FINGER PROTEIN 11 UniProtKB/Swiss-Prot
Pfam zf-HC5HC2H UniProtKB/Swiss-Prot
PhenoGen Phf11 PhenoGen
PROSITE EPHD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000053891 RatGTEx
SMART PHD UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot
UniProt A0A8I6AHQ0 ENTREZGENE, UniProtKB/TrEMBL
  M0RB46_RAT UniProtKB/TrEMBL
  PHF11_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Phf11  PHD finger protein 11  LOC100362408  PHD finger protein 11 family member-like  Data merged from RGD:2318180 737654 PROVISIONAL
2013-01-03 Phf11  PHD finger protein 11  Phf11a  PHD finger protein 11a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100362408  PHD finger protein 11 family member-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-12-06 Phf11  PHD finger protein 11  Phf11_predicted  PHD finger protein 11 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Phf11_predicted  PHD finger protein 11 (predicted)      Symbol and Name status set to approved 70820 APPROVED