Phf11b (PHD finger protein 11B) - Rat Genome Database

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Gene: Phf11b (PHD finger protein 11B) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Phf11b
Name: PHD finger protein 11B
RGD ID: 1359377
Description: Predicted to enable zinc ion binding activity. Predicted to be active in nucleus. Orthologous to human PHF11 (PHD finger protein 11); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC100362359; LOC102551046; LOC364393; PHD finger protein 11-like; Phf11l; similar to RIKEN cDNA 4933417L10
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81537,478,888 - 37,496,535 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21533,363,389 - 33,380,418 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1533,363,395 - 33,378,606 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1535,355,640 - 35,372,563 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01536,506,314 - 36,523,237 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01534,763,483 - 34,780,403 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01539,666,750 - 39,705,094 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01543,484,829 - 43,522,980 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41538,372,722 - 38,391,822 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1533,057,710 - 33,258,879 (-)NCBICelera
RGSC_v3.11538,396,511 - 38,407,535 (-)NCBI
Cytogenetic Map15p12NCBI
JBrowse:




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

Cellular Component
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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.

Genomics

Variants

.
Variants in Phf11b
108 total Variants

QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
10755503Bp391Blood pressure QTL 3912.37arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)152024860037896129Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
152025253Hrtrt24Heart rate QTL 243.82heart pumping trait (VT:2000009)152788577486257085Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat

Markers in Region
D15Arb1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21533,442,908 - 33,443,032 (+)MAPPERmRatBN7.2
mRatBN7.21533,503,823 - 33,503,945 (+)MAPPERmRatBN7.2
Rnor_6.01538,682,232 - 38,682,351NCBIRnor6.0
Rnor_6.01538,662,195 - 38,662,316NCBIRnor6.0
Rnor_5.01542,515,581 - 42,515,700UniSTSRnor5.0
RGSC_v3.41538,390,592 - 38,390,709UniSTSRGSC3.4
Celera1518,253,121 - 18,253,242UniSTS
RGSC_v3.11538,406,291 - 38,406,409RGD
SHRSP x BN Map1527.8899RGD
SHRSP x BN Map1527.8899UniSTS
FHH x ACI Map1529.96RGD
Cytogenetic Map15p12UniSTS
D15Rat142  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81537,734,148 - 37,734,295 (+)Marker Load Pipeline
mRatBN7.21533,557,950 - 33,558,097 (+)MAPPERmRatBN7.2
Rnor_6.01539,696,476 - 39,696,622NCBIRnor6.0
Rnor_5.01543,517,491 - 43,517,637UniSTSRnor5.0
RGSC_v3.41538,488,925 - 38,489,070RGDRGSC3.4
RGSC_v3.41538,488,924 - 38,489,070UniSTSRGSC3.4
Celera1533,264,391 - 33,264,537UniSTS
RGSC_v3.11538,504,625 - 38,504,770RGD
SHRSP x BN Map1527.8098UniSTS
SHRSP x BN Map1527.8098RGD
Cytogenetic Map15p12UniSTS
D15Got34  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21533,442,853 - 33,443,019 (+)MAPPERmRatBN7.2
mRatBN7.21533,503,768 - 33,503,932 (+)MAPPERmRatBN7.2
Rnor_6.01538,682,177 - 38,682,338NCBIRnor6.0
Rnor_6.01538,662,140 - 38,662,303NCBIRnor6.0
Rnor_5.01542,515,526 - 42,515,687UniSTSRnor5.0
RGSC_v3.41538,390,537 - 38,390,696RGDRGSC3.4
RGSC_v3.41538,390,537 - 38,390,696UniSTSRGSC3.4
Celera1518,253,066 - 18,253,229UniSTS
RGSC_v3.11538,406,237 - 38,406,396RGD
RH 3.4 Map15216.18RGD
RH 3.4 Map15216.18UniSTS
RH 2.0 Map15196.6RGD
Cytogenetic Map15p12UniSTS
RH131947  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map15p12UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 17 50 67 137 94 11 47 36 32 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000116009   ⟹   ENSRNOP00000089162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1533,363,395 - 33,378,606 (-)Ensembl
RefSeq Acc Id: NM_001014235   ⟹   NP_001014257
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81537,478,888 - 37,495,805 (-)NCBI
mRatBN7.21533,363,389 - 33,380,418 (-)NCBI
RefSeq Acc Id: XM_063274479   ⟹   XP_063130549
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81537,478,888 - 37,496,535 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001014257 (Get FASTA)   NCBI Sequence Viewer  
  XP_063130549 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH88253 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000076409
  ENSRNOP00000077108
GenBank Protein Q5I0J8 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001014257   ⟸   NM_001014235
- UniProtKB: Q5I0J8 (UniProtKB/Swiss-Prot),   A0A8I5XZW0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000089162   ⟸   ENSRNOT00000116009
RefSeq Acc Id: XP_063130549   ⟸   XM_063274479
- Peptide Label: isoform X1
- UniProtKB: A0A8I5XZW0 (UniProtKB/TrEMBL)
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5I0J8-F1-model_v2 AlphaFold Q5I0J8 1-293 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:1359377 AgrOrtholog
BioCyc Gene G2FUF-13560 BioCyc
Ensembl Genes ENSRNOG00000064184 Ensembl
  ENSRNOG00000084041 ENTREZGENE
Ensembl Transcript ENSRNOT00000095639 ENTREZGENE
  ENSRNOT00000116879 ENTREZGENE
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7374374 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:364393 UniProtKB/Swiss-Prot
MGC_CLONE MGC:109066 IMAGE-MGC_LOAD
NCBI Gene 364393 ENTREZGENE
PANTHER PHD FINGER PROTEIN UniProtKB/Swiss-Prot
  PHD FINGER PROTEIN 11 UniProtKB/Swiss-Prot
Pfam zf-HC5HC2H UniProtKB/Swiss-Prot
PhenoGen Phf11b PhenoGen
PROSITE EPHD UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000064184 RatGTEx
  ENSRNOG00000084041 RatGTEx
SMART PHD UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot
UniProt A0A8I5XZW0 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A989_RAT UniProtKB/TrEMBL
  PH11L_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Phf11b  PHD finger protein 11B  LOC102551046  PHD finger protein 11-like  Data merged from RGD:7640685 737654 PROVISIONAL
2015-07-29 Phf11b  PHD finger protein 11B  LOC100362359  PHD finger protein 11-like  Data merged from RGD:2318327 737654 PROVISIONAL
2013-12-18 LOC102551046  PHD finger protein 11-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2013-01-02 Phf11b  PHD finger protein 11B  Phf11l  PHD finger protein 11-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100362359  PHD finger protein 11-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-03-13 Phf11l  PHD finger protein 11-like  LOC364393  similar to RIKEN cDNA 4933417L10  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-29 LOC364393  similar to RIKEN cDNA 4933417L10      Symbol and Name status set to provisional 70820 PROVISIONAL