Phldb3 (pleckstrin homology-like domain, family B, member 3) - Rat Genome Database

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Gene: Phldb3 (pleckstrin homology-like domain, family B, member 3) Rattus norvegicus
Analyze
Symbol: Phldb3
Name: pleckstrin homology-like domain, family B, member 3
RGD ID: 1561121
Description: Predicted to enable enzyme binding activity. Orthologous to human PHLDB3 (pleckstrin homology like domain family B member 3); INTERACTS WITH (S)-nicotine; 17beta-estradiol; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC308431; pleckstrin homology-like domain family B member 3; RGD1561121; similar to pleckstrin homology-like domain, family B, member 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Candidate Gene For: Scl82
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8189,328,991 - 89,347,446 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl189,328,819 - 89,347,436 (+)EnsemblGRCr8
mRatBN7.2180,201,083 - 80,219,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx185,593,421 - 85,612,010 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0194,144,522 - 94,162,978 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0187,349,166 - 87,367,759 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0181,474,553 - 81,492,631 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)Ensemblrn6Rnor6.0
Rnor_5.0182,733,955 - 82,750,033 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4179,893,173 - 79,910,727 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera174,654,454 - 74,671,763 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse:




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

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:23382074  


Genomics

Comparative Map Data
Phldb3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8189,328,991 - 89,347,446 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl189,328,819 - 89,347,436 (+)EnsemblGRCr8
mRatBN7.2180,201,083 - 80,219,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx185,593,421 - 85,612,010 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0194,144,522 - 94,162,978 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0187,349,166 - 87,367,759 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0181,474,553 - 81,492,631 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)Ensemblrn6Rnor6.0
Rnor_5.0182,733,955 - 82,750,033 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4179,893,173 - 79,910,727 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera174,654,454 - 74,671,763 (+)NCBICelera
Cytogenetic Map1q21NCBI
PHLDB3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381943,475,103 - 43,504,746 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1943,473,625 - 43,505,301 (-)Ensemblhg38GRCh38
GRCh371943,979,255 - 44,008,898 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361948,671,095 - 48,700,825 (-)NCBIBuild 36Build 36hg18NCBI36
Build 341948,692,027 - 48,700,927NCBI
Celera1940,779,982 - 40,809,738 (-)NCBICelera
Cytogenetic Map19q13.31NCBI
HuRef1940,409,110 - 40,438,880 (-)NCBIHuRef
CHM1_11943,980,918 - 44,010,647 (-)NCBICHM1_1
T2T-CHM13v2.01946,295,450 - 46,325,619 (-)NCBIT2T-CHM13v2.0
Phldb3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39724,309,731 - 24,328,722 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl724,310,188 - 24,328,722 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38724,610,294 - 24,629,297 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl724,610,763 - 24,629,297 (+)Ensemblmm10GRCm38
MGSCv37725,396,347 - 25,414,316 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36724,320,088 - 24,338,057 (+)NCBIMGSCv36mm8
Celera719,225,235 - 19,243,204 (+)NCBICelera
Cytogenetic Map7A3NCBI
cM Map711.8NCBI
Phldb3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555551,241,202 - 1,260,935 (-)Ensembl
ChiLan1.0NW_0049555551,241,728 - 1,261,531 (-)NCBIChiLan1.0ChiLan1.0
PHLDB3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22049,632,590 - 49,664,470 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11951,499,656 - 51,533,410 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01940,414,313 - 40,447,076 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11949,025,015 - 49,053,979 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1949,025,015 - 49,053,979 (-)EnsemblpanPan2panpan1.1
PHLDB3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11111,608,742 - 111,628,899 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1111,609,379 - 111,628,627 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1111,088,456 - 111,108,603 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01112,218,902 - 112,239,054 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1112,219,678 - 112,239,045 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11111,807,048 - 111,827,170 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01111,440,782 - 111,460,948 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01112,324,954 - 112,345,187 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Phldb3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934916,354,899 - 16,377,730 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936706703,881 - 718,280 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936706702,252 - 724,396 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHLDB3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl650,346,830 - 50,373,982 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1650,349,561 - 50,374,841 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2646,234,054 - 46,258,719 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHLDB3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1636,991,411 - 37,022,658 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607316,529,164 - 16,561,976 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phldb3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249071,033,750 - 1,055,867 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249071,034,760 - 1,056,559 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Phldb3
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12170,087,131 - 170,105,575 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Phldb3
154 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:60
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000034460
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)151940904101229020Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)187889942132889942Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)151941022208479811Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)139728272132889942Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14630261591302615Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)14630261591302615Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)151940904168768703Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
1331800Scl25Serum cholesterol level QTL 253.013blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)187785026142582336Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)183019780128019780Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)166404680111404680Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134184556172281316Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)14630261591302615Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)18126986099645535Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)166009857160501508Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134565911208798288Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)14630261591302615Rat
1302788Scl19Serum cholesterol QTL 194.60.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)166400974132889942Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)184107164115183752Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)151511344153680016Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16540563796805205Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15190920691302615Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)186622262131622262Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)158769992103769992Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)166077886111077886Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)14630261591302615Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)14630261591302615Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)186993904131993904Rat
152025249Scl82Serum cholesterol level QTL 824.77blood cholesterol amount (VT:0000180)152891222109116986Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)187558587132558587Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)14630261591302615Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 159 91 90 59 92 59 6 356 192 10 138 81 91 31 16 16

Sequence


Ensembl Acc Id: ENSRNOT00000083493   ⟹   ENSRNOP00000075680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl189,328,819 - 89,347,436 (+)Ensembl
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)Ensembl
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000138307   ⟹   ENSRNOP00000099025
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl189,328,819 - 89,347,436 (+)Ensembl
RefSeq Acc Id: NM_001395091   ⟹   NP_001382020
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8189,328,991 - 89,347,446 (+)NCBI
mRatBN7.2180,201,083 - 80,219,541 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001382020 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM08080 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000075680
  ENSRNOP00000075680.2
  ENSRNOP00000099025.1
Ensembl Acc Id: ENSRNOP00000075680   ⟸   ENSRNOT00000083493
RefSeq Acc Id: NP_001382020   ⟸   NM_001395091
- UniProtKB: A0A0G2KB72 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000099025   ⟸   ENSRNOT00000138307
Protein Domains
PH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2KB72-F1-model_v2 AlphaFold A0A0G2KB72 1-638 view protein structure

Transcriptome

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

Promoters
RGD ID:13689802
Promoter ID:EPDNEW_R326
Type:initiation region
Name:Phldb3_1
Description:pleckstrin homology-like domain, family B, member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0181,474,534 - 81,474,594EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561121 AgrOrtholog
BioCyc Gene G2FUF-60435 BioCyc
Ensembl Genes ENSRNOG00000055259 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000083493 ENTREZGENE
  ENSRNOT00000083493.3 UniProtKB/TrEMBL
  ENSRNOT00000138307.1 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro PH-like_domain UniProtKB/TrEMBL
  PH_type UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
NCBI Gene 308431 ENTREZGENE
PANTHER PLECKSTRIN HOMOLOGY-LIKE DOMAIN FAMILY B MEMBER 3 UniProtKB/TrEMBL
  PLECKSTRIN HOMOLOGY-LIKE DOMAIN, FAMILY B, MEMBER 3 UniProtKB/TrEMBL
Pfam PF00169 UniProtKB/TrEMBL
PhenoGen Phldb3 PhenoGen
PROSITE PH_DOMAIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055259 RatGTEx
SMART SM00233 UniProtKB/TrEMBL
Superfamily-SCOP PH domain-like UniProtKB/TrEMBL
UniProt A0A0G2KB72 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LCU3_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Phldb3  pleckstrin homology-like domain, family B, member 3  RGD1561121_predicted  similar to pleckstrin homology-like domain, family B, member 3 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1561121_predicted  similar to pleckstrin homology-like domain, family B, member 3 (predicted)  LOC308431  similar to pleckstrin homology-like domain, family B, member 3  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC308431  similar to pleckstrin homology-like domain, family B, member 3      Symbol and Name status set to provisional 70820 PROVISIONAL