Phldb1 (pleckstrin homology-like domain, family B, member 1) - Rat Genome Database
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Gene: Phldb1 (pleckstrin homology-like domain, family B, member 1) Rattus norvegicus
Analyze
Symbol: Phldb1
Name: pleckstrin homology-like domain, family B, member 1
RGD ID: 620878
Description: Predicted to be involved in regulation of embryonic development; regulation of epithelial to mesenchymal transition; and regulation of microtubule cytoskeleton organization. Predicted to localize to basal cortex. Orthologous to human PHLDB1 (pleckstrin homology like domain family B member 1); INTERACTS WITH 2,4-dinitrotoluene; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ll5; pleckstrin homology-like domain family B member 1; protein LL5-alpha
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
mRatBN7.2845,003,538 - 45,051,541 (-)NCBI
Rnor_6.0 Ensembl848,997,184 - 49,045,154 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0848,997,189 - 49,045,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0847,615,937 - 47,666,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4847,645,164 - 47,686,143 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1847,653,935 - 47,682,657 (-)NCBI
Celera844,588,473 - 44,629,442 (-)NCBICelera
Cytogenetic Map8q22NCBI
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

Cellular Component
basal cortex  (IBA,IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:23940118  


Genomics

Comparative Map Data
Phldb1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2845,003,538 - 45,051,541 (-)NCBI
Rnor_6.0 Ensembl848,997,184 - 49,045,154 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0848,997,189 - 49,045,176 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0847,615,937 - 47,666,166 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4847,645,164 - 47,686,143 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1847,653,935 - 47,682,657 (-)NCBI
Celera844,588,473 - 44,629,442 (-)NCBICelera
Cytogenetic Map8q22NCBI
PHLDB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl11118,606,440 - 118,658,031 (+)EnsemblGRCh38hg38GRCh38
GRCh3811118,606,296 - 118,658,028 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3711118,477,151 - 118,528,738 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611117,982,423 - 118,033,951 (+)NCBINCBI36hg18NCBI36
Build 3411117,982,422 - 118,033,951NCBI
Celera11115,637,985 - 115,689,504 (+)NCBI
Cytogenetic Map11q23.3NCBI
HuRef11114,414,710 - 114,466,582 (+)NCBIHuRef
CHM1_111118,363,870 - 118,415,396 (+)NCBICHM1_1
Phldb1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39944,597,605 - 44,649,800 (-)NCBIGRCm39mm39
GRCm39 Ensembl944,597,601 - 44,646,495 (-)Ensembl
GRCm38944,686,308 - 44,735,248 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl944,686,304 - 44,735,198 (-)EnsemblGRCm38mm10GRCm38
MGSCv37944,494,391 - 44,543,277 (-)NCBIGRCm37mm9NCBIm37
MGSCv36944,437,303 - 44,486,189 (-)NCBImm8
Celera941,950,682 - 41,999,929 (-)NCBICelera
Cytogenetic Map9A5.2NCBI
Phldb1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541219,756,379 - 19,800,984 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541219,754,997 - 19,800,984 (+)NCBIChiLan1.0ChiLan1.0
PHLDB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.111117,376,205 - 117,426,391 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl11117,376,205 - 117,426,391 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v011113,446,275 - 113,496,941 (+)NCBIMhudiblu_PPA_v0panPan3
PHLDB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1515,090,823 - 15,138,397 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl515,090,813 - 15,134,784 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha515,143,223 - 15,189,894 (-)NCBI
ROS_Cfam_1.0515,034,008 - 15,080,652 (-)NCBI
UMICH_Zoey_3.1515,172,407 - 15,219,091 (-)NCBI
UNSW_CanFamBas_1.0515,075,943 - 15,122,594 (-)NCBI
UU_Cfam_GSD_1.0515,116,373 - 15,159,865 (-)NCBI
Phldb1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_024404947100,718,559 - 100,766,591 (+)NCBI
SpeTri2.0NW_0049365423,639,992 - 3,688,000 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHLDB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl945,902,105 - 45,949,417 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1945,902,099 - 45,949,415 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2950,924,779 - 50,943,422 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PHLDB1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11110,001,516 - 110,053,166 (+)NCBI
ChlSab1.1 Ensembl1110,002,591 - 110,052,831 (+)Ensembl
Phldb1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478414,016,774 - 14,064,069 (+)NCBI

Position Markers
AU041016  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0848,997,293 - 48,997,456NCBIRnor6.0
Rnor_5.0847,616,041 - 47,616,204UniSTSRnor5.0
RGSC_v3.4847,645,268 - 47,645,431UniSTSRGSC3.4
Celera844,588,577 - 44,588,740UniSTS
Cytogenetic Map8q22UniSTS
BI278154  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0848,997,377 - 48,997,576NCBIRnor6.0
Rnor_5.0847,616,125 - 47,616,324UniSTSRnor5.0
RGSC_v3.4847,645,352 - 47,645,551UniSTSRGSC3.4
Celera844,588,661 - 44,588,860UniSTS
RH 3.4 Map8439.5UniSTS
Cytogenetic Map8q22UniSTS
BE106591  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0849,017,515 - 49,017,667NCBIRnor6.0
Rnor_5.0847,636,263 - 47,636,415UniSTSRnor5.0
RGSC_v3.4847,665,490 - 47,665,642UniSTSRGSC3.4
Celera844,608,787 - 44,608,939UniSTS
RH 3.4 Map8442.8UniSTS
Cytogenetic Map8q22UniSTS
AU047896  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0849,029,258 - 49,029,427NCBIRnor6.0
Rnor_5.0847,648,006 - 47,648,175UniSTSRnor5.0
RGSC_v3.4847,677,232 - 47,677,401UniSTSRGSC3.4
Celera844,620,530 - 44,620,699UniSTS
Cytogenetic Map8q22UniSTS
AU047883  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0849,029,267 - 49,029,512NCBIRnor6.0
Rnor_5.0847,648,015 - 47,648,260UniSTSRnor5.0
RGSC_v3.4847,677,241 - 47,677,486UniSTSRGSC3.4
Celera844,620,539 - 44,620,784UniSTS
Cytogenetic Map8q22UniSTS
RH140559  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0849,002,225 - 49,002,533NCBIRnor6.0
Rnor_5.0847,620,973 - 47,621,281UniSTSRnor5.0
RGSC_v3.4847,650,200 - 47,650,508UniSTSRGSC3.4
Celera844,593,509 - 44,593,817UniSTS
RH 3.4 Map8441.5UniSTS
Cytogenetic Map8q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631216Stl9Serum triglyceride level QTL 94.710.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)84571247575971259Rat
2303564Gluco43Glucose level QTL 433blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)83014480075144800Rat
2303572Insul13Insulin level QTL 132blood insulin amount (VT:0001560)blood insulin level (CMO:0000349)83014480075144800Rat
61464Niddm11Non-insulin dependent diabetes mellitus QTL 113.10.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83995802284958022Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84658843796998640Rat
724514Uae15Urinary albumin excretion QTL 152.9urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)83220198175971421Rat
1331744Bp217Blood pressure QTL 2173.398arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866062857995Rat
1331769Rf39Renal function QTL 393.871urine output (VT:0003620)timed urine volume (CMO:0000260)84571234480003418Rat
737824Hcar10Hepatocarcinoma resistance QTL 102.9liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)84421919789542960Rat
1298065Scl16Serum cholesterol level QTL 163.8blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)83504141480041414Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84571234490712344Rat
631648Stl5Serum triglyceride level QTL 540.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)82986798359908353Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810938911120496129Rat
1331804Cm30Cardiac mass QTL 303.77443heart mass (VT:0007028)heart wet weight (CMO:0000069)83091811258858224Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)839230130106506973Rat
1582222Epfw2Epididymal fat weight QTL 23.20.0005epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)83592559480925594Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)821813070100873963Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)82146491991140553Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)89531047119211942Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81137326757541668Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8873867753738677Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)82784149672841496Rat
1578755Pur5Proteinuria QTL 53.30.0001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)833558660109028082Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)833558660109028082Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)833558660109028082Rat
1300146Rf17Renal function QTL 172.9renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)83091811275918112Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)81038843955388439Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)81038843955388439Rat
1359021Bp271Blood pressure QTL 2711.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82816802350708951Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)832888352101374135Rat
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81766655562666555Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)833558764113580387Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81144825156448251Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8736807652368076Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8736807652368076Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8736807652368076Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81144825156448251Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)844458129118087517Rat
2302278Gluco36Glucose level QTL 364.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)83220198154065241Rat
2313046Bss78Bone structure and strength QTL 783.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)83355866089058369Rat
2313057Bss76Bone structure and strength QTL 7630.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)83355866089058369Rat
2313067Bss77Bone structure and strength QTL 773.10.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)83355866089058369Rat
2313088Bss75Bone structure and strength QTL 753.10.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)83355866089058369Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)829867983106526740Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)829867983106526740Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)844219197100873963Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)829867983106526740Rat
1359033Bp273Blood pressure QTL 273arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
61358Bp39Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83992790184927901Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)82071759265717592Rat
5684993Bmd84Bone mineral density QTL 844.1tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)84658843754065241Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)830918112107206309Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)83355866065717592Rat
61353Bp35Blood pressure QTL 350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)83355866065717592Rat
11556286Cm81Cardiac mass QTL 810.01heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)83355866065717592Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)847200750106394378Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)847200750106394378Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)847200750106394378Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)847200750106394378Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)847200750106394378Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)847200750106394378Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:205
Count of miRNA genes:127
Interacting mature miRNAs:164
Transcripts:ENSRNOT00000047303
Prediction methods: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.


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 3 43 7 4 11 4 6 9 74 35 34 11 6
Low 50 37 8 37 2 2 7 2
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001191578 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595434 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595437 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595438 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595439 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595440 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595441 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595442 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595443 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595444 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595445 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595446 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595447 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080755 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080756 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080758 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080759 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080765 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080769 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080770 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080771 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080772 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080773 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080774 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080775 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001839138 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC095317 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC092599 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC104704 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473975 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220811 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000198 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X74226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000047303   ⟹   ENSRNOP00000046235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl848,997,189 - 49,038,169 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078816   ⟹   ENSRNOP00000068824
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl848,997,195 - 49,025,917 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000088034   ⟹   ENSRNOP00000069330
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl848,997,184 - 49,045,154 (-)Ensembl
RefSeq Acc Id: NM_001191578   ⟹   NP_001178507
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,538 - 45,044,524 (-)NCBI
Rnor_6.0848,997,189 - 49,038,169 (-)NCBI
Rnor_5.0847,615,937 - 47,666,166 (-)NCBI
Celera844,588,473 - 44,629,442 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595434   ⟹   XP_017450923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595435   ⟹   XP_017450924
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595436   ⟹   XP_017450925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595437   ⟹   XP_017450926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595438   ⟹   XP_017450927
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595439   ⟹   XP_017450928
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595440   ⟹   XP_017450929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595441   ⟹   XP_017450930
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595442   ⟹   XP_017450931
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595443   ⟹   XP_017450932
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595444   ⟹   XP_017450933
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595445   ⟹   XP_017450934
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595446   ⟹   XP_017450935
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,175 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595447   ⟹   XP_017450936
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0848,997,194 - 49,045,174 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080755   ⟹   XP_038936683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080756   ⟹   XP_038936684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080758   ⟹   XP_038936686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,051,541 (-)NCBI
RefSeq Acc Id: XM_039080759   ⟹   XP_038936687
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,051,305 (-)NCBI
RefSeq Acc Id: XM_039080760   ⟹   XP_038936688
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080761   ⟹   XP_038936689
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080762   ⟹   XP_038936690
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080763   ⟹   XP_038936691
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080764   ⟹   XP_038936692
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080765   ⟹   XP_038936693
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080766   ⟹   XP_038936694
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080767   ⟹   XP_038936695
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080769   ⟹   XP_038936697
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,038,041 (-)NCBI
RefSeq Acc Id: XM_039080770   ⟹   XP_038936698
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080771   ⟹   XP_038936699
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080772   ⟹   XP_038936700
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080773   ⟹   XP_038936701
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080774   ⟹   XP_038936702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080775   ⟹   XP_038936703
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XM_039080776   ⟹   XP_038936704
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2845,003,543 - 45,044,545 (-)NCBI
RefSeq Acc Id: XR_001839138
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0849,008,813 - 49,045,176 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001178507   ⟸   NM_001191578
- UniProtKB: D3ZNS1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450935   ⟸   XM_017595446
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017450934   ⟸   XM_017595445
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017450933   ⟸   XM_017595444
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017450932   ⟸   XM_017595443
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017450930   ⟸   XM_017595441
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017450931   ⟸   XM_017595442
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017450929   ⟸   XM_017595440
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017450928   ⟸   XM_017595439
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017450926   ⟸   XM_017595437
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017450927   ⟸   XM_017595438
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017450925   ⟸   XM_017595436
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017450924   ⟸   XM_017595435
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017450923   ⟸   XM_017595434
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017450936   ⟸   XM_017595447
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: ENSRNOP00000046235   ⟸   ENSRNOT00000047303
RefSeq Acc Id: ENSRNOP00000068824   ⟸   ENSRNOT00000078816
RefSeq Acc Id: ENSRNOP00000069330   ⟸   ENSRNOT00000088034
RefSeq Acc Id: XP_038936686   ⟸   XM_039080758
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936687   ⟸   XM_039080759
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038936704   ⟸   XM_039080776
- Peptide Label: isoform X19
RefSeq Acc Id: XP_038936703   ⟸   XM_039080775
- Peptide Label: isoform X18
RefSeq Acc Id: XP_038936700   ⟸   XM_039080772
- Peptide Label: isoform X15
RefSeq Acc Id: XP_038936702   ⟸   XM_039080774
- Peptide Label: isoform X17
RefSeq Acc Id: XP_038936691   ⟸   XM_039080763
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038936699   ⟸   XM_039080771
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038936701   ⟸   XM_039080773
- Peptide Label: isoform X16
RefSeq Acc Id: XP_038936698   ⟸   XM_039080770
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038936695   ⟸   XM_039080767
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038936693   ⟸   XM_039080765
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038936694   ⟸   XM_039080766
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038936689   ⟸   XM_039080761
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038936684   ⟸   XM_039080756
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038936692   ⟸   XM_039080764
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038936690   ⟸   XM_039080762
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038936683   ⟸   XM_039080755
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038936688   ⟸   XM_039080760
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038936697   ⟸   XM_039080769
- Peptide Label: isoform X12
Protein Domains
PH

Transcriptome

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

Promoters
RGD ID:13695911
Promoter ID:EPDNEW_R6424
Type:initiation region
Name:Phldb1_1
Description:pleckstrin homology-like domain, family B, member 1
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_6.0849,045,141 - 49,045,201EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
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)
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
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)
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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620878 AgrOrtholog
Ensembl Genes ENSRNOG00000026985 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000046235 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068824 UniProtKB/TrEMBL
  ENSRNOP00000069330 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000047303 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078816 UniProtKB/TrEMBL
  ENSRNOT00000088034 UniProtKB/TrEMBL
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FHA_dom UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PHLDB1/2/3_PH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMAD_FHA_domain UniProtKB/TrEMBL
KEGG Report rno:171434 UniProtKB/TrEMBL
NCBI Gene 171434 ENTREZGENE
Pfam PF00169 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Phldb1 PhenoGen
PROSITE PH_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00233 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SMAD_FHA UniProtKB/TrEMBL
UniProt A0A0G2JTS5_RAT UniProtKB/TrEMBL
  A0A0G2JV32_RAT UniProtKB/TrEMBL
  D3ZNS1 ENTREZGENE, UniProtKB/TrEMBL
  PHLB1_RAT UniProtKB/Swiss-Prot
  Q3SWT3_RAT UniProtKB/TrEMBL
  Q63312 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Phldb1  pleckstrin homology-like domain, family B, member 1  Ll5  LL5 protein  Symbol and Name updated 1299863 APPROVED
2002-08-07 Ll5  LL5 protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_transcript 2.3 kb transcript is detected in pituitary 633318