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; amitrole.
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
Alliance Genes
More Info more info ...
Candidate Gene For: Scl82
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8189,328,991 - 89,347,446 (+)NCBIGRCr8
mRatBN7.2180,201,083 - 80,219,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx185,593,421 - 85,612,010 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0194,144,522 - 94,162,978 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0187,349,166 - 87,367,759 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0181,474,553 - 81,492,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,733,955 - 82,750,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4179,893,173 - 79,910,727 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera174,654,454 - 74,671,763 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease 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 (+)NCBIGRCr8
mRatBN7.2180,201,083 - 80,219,541 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx185,593,421 - 85,612,010 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0194,144,522 - 94,162,978 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0187,349,166 - 87,367,759 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0181,474,553 - 81,492,631 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0182,733,955 - 82,750,033 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4179,893,173 - 79,910,727 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 Ensembl1943,474,954 - 43,504,935 (-)EnsemblGRCh38hg38GRCh38
GRCh371943,979,255 - 44,008,898 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361948,671,095 - 48,700,825 (-)NCBINCBI36Build 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 Ensembl
GRCm38724,610,294 - 24,629,297 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl724,610,763 - 24,629,297 (+)EnsemblGRCm38mm10GRCm38
MGSCv37725,396,347 - 25,414,316 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
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 (-)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1111,088,456 - 111,108,603 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01112,218,902 - 112,239,054 (+)NCBIROS_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_1.0
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
SpeTri2.0NW_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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249071,034,760 - 1,056,559 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Phldb3
118 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat
1358192Ept13Estrogen-induced pituitary tumorigenesis QTL 133.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)177494165122494165Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)177857876122857876Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)177876254106047988Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)178350581123350581Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)178430536123430536Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17843075491209302Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)178479925123479925Rat


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 2 2 1 1
Low 1 8 56 41 17 41 8 11 44 35 35 10 8
Below cutoff 35 1 30 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083493   ⟹   ENSRNOP00000075680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl180,201,578 - 80,219,534 (+)Ensembl
Rnor_6.0 Ensembl181,474,553 - 81,492,631 (+)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
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000075680   ⟸   ENSRNOT00000083493
RefSeq Acc Id: NP_001382020   ⟸   NM_001395091
- UniProtKB: A0A0G2KB72 (UniProtKB/TrEMBL)
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
  ENSRNOT00000083493.2 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/TrEMBL
InterPro 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


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