Podnl1 (podocan-like 1) - Rat Genome Database

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Gene: Podnl1 (podocan-like 1) Rattus norvegicus
Analyze
Symbol: Podnl1
Name: podocan-like 1
RGD ID: 1307753
Description: Predicted to be located in collagen-containing extracellular matrix. Predicted to be active in extracellular space. Orthologous to human PODNL1 (podocan like 1); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: INFERRED
Previously known as: LOC288907; podocan-like protein 1; RGD1307753; similar to podocan protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81940,932,026 - 40,938,760 (-)NCBIGRCr8
mRatBN7.21924,027,261 - 24,033,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,027,297 - 24,033,846 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1930,848,103 - 30,854,713 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01931,502,513 - 31,509,125 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01933,725,285 - 33,731,895 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01925,240,001 - 25,246,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,239,674 - 25,246,525 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,217,189 - 36,223,683 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,711,112 - 25,718,223 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11925,716,193 - 25,722,205 (-)NCBI
Celera1923,575,604 - 23,582,182 (-)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21672516  


Genomics

Comparative Map Data
Podnl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81940,932,026 - 40,938,760 (-)NCBIGRCr8
mRatBN7.21924,027,261 - 24,033,867 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1924,027,297 - 24,033,846 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1930,848,103 - 30,854,713 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01931,502,513 - 31,509,125 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01933,725,285 - 33,731,895 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01925,240,001 - 25,246,583 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1925,239,674 - 25,246,525 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01936,217,189 - 36,223,683 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41925,711,112 - 25,718,223 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11925,716,193 - 25,722,205 (-)NCBI
Celera1923,575,604 - 23,582,182 (-)NCBICelera
Cytogenetic Map19q11NCBI
PODNL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381913,931,187 - 13,953,383 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1913,931,187 - 13,953,392 (-)EnsemblGRCh38hg38GRCh38
GRCh371914,042,000 - 14,064,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361913,904,167 - 13,910,289 (-)NCBINCBI36Build 36hg18NCBI36
Celera1913,935,745 - 13,957,830 (-)NCBICelera
Cytogenetic Map19p13.12NCBI
HuRef1913,613,296 - 13,635,472 (-)NCBIHuRef
CHM1_11914,042,604 - 14,064,744 (-)NCBICHM1_1
T2T-CHM13v2.01914,057,347 - 14,079,667 (-)NCBIT2T-CHM13v2.0
Podnl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39884,852,552 - 84,869,620 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl884,852,618 - 84,859,156 (+)EnsemblGRCm39 Ensembl
GRCm38884,125,928 - 84,142,991 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl884,125,989 - 84,132,527 (+)EnsemblGRCm38mm10GRCm38
MGSCv37886,649,888 - 86,656,416 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36887,016,094 - 87,022,672 (+)NCBIMGSCv36mm8
Celera888,426,410 - 88,432,912 (+)NCBICelera
Cytogenetic Map8C2NCBI
cM Map840.31NCBI
Podnl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541532,683,414 - 32,688,586 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541532,683,256 - 32,688,736 (-)NCBIChiLan1.0ChiLan1.0
PODNL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22018,860,573 - 18,868,406 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11917,861,279 - 17,868,395 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01913,493,464 - 13,500,577 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11914,223,455 - 14,244,705 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1914,224,233 - 14,244,705 (-)Ensemblpanpan1.1panPan2
PODNL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12048,543,572 - 48,548,689 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2048,526,786 - 48,548,689 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2048,417,642 - 48,422,750 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02049,061,764 - 49,066,871 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2049,044,531 - 49,066,877 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12048,272,306 - 48,277,413 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02048,698,788 - 48,703,895 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02048,942,095 - 48,947,203 (+)NCBIUU_Cfam_GSD_1.0
Podnl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118207,722,336 - 207,727,304 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366592,627,741 - 2,632,344 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366592,627,229 - 2,632,251 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PODNL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl265,230,031 - 65,235,302 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1265,229,987 - 65,235,319 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2265,503,713 - 65,509,033 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PODNL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1612,589,983 - 12,599,647 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660747,063,558 - 7,070,423 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Podnl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249011,205,184 - 1,210,174 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249011,204,688 - 1,211,892 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Podnl1
22 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:95
Interacting mature miRNAs:103
Transcripts:ENSRNOT00000037453
Prediction methods:Microtar, Miranda, Rnahybrid
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
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61407Scl12Serum cholesterol level QTL 120.001blood HDL cholesterol amount (VT:0000184)serum high density lipoprotein cholesterol level (CMO:0000361)191392640130303727Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat

Markers in Region
RH132148  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21924,027,376 - 24,027,593 (-)MAPPERmRatBN7.2
Rnor_6.01925,246,256 - 25,246,472NCBIRnor6.0
Rnor_5.01936,223,356 - 36,223,572UniSTSRnor5.0
RGSC_v3.41925,711,223 - 25,711,439UniSTSRGSC3.4
Celera1923,575,715 - 23,575,931UniSTS
Cytogenetic Map19q11UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 10 33 106 84 83 52 25 52 6 194 80 86 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000037453   ⟹   ENSRNOP00000037510
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1924,027,297 - 24,033,846 (-)Ensembl
Rnor_6.0 Ensembl1925,239,674 - 25,246,525 (+)Ensembl
RefSeq Acc Id: NM_001400940   ⟹   NP_001387869
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81940,932,026 - 40,938,631 (-)NCBI
mRatBN7.21924,027,261 - 24,033,867 (-)NCBI
RefSeq Acc Id: NM_001400941   ⟹   NP_001387870
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81940,932,026 - 40,938,631 (-)NCBI
mRatBN7.21924,027,261 - 24,033,867 (-)NCBI
RefSeq Acc Id: NM_001400942   ⟹   NP_001387871
RefSeq Status: INFERRED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81940,932,026 - 40,938,631 (-)NCBI
mRatBN7.21924,027,261 - 24,033,867 (-)NCBI
RefSeq Acc Id: XM_063277828   ⟹   XP_063133898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81940,935,412 - 40,938,760 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001387869 (Get FASTA)   NCBI Sequence Viewer  
  NP_001387870 (Get FASTA)   NCBI Sequence Viewer  
  NP_001387871 (Get FASTA)   NCBI Sequence Viewer  
  XP_063133898 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037510.5
Ensembl Acc Id: ENSRNOP00000037510   ⟸   ENSRNOT00000037453
RefSeq Acc Id: NP_001387871   ⟸   NM_001400942
- Peptide Label: isoform 3
RefSeq Acc Id: NP_001387870   ⟸   NM_001400941
- Peptide Label: isoform 2 precursor
RefSeq Acc Id: NP_001387869   ⟸   NM_001400940
- Peptide Label: isoform 1 precursor
- UniProtKB: D3ZY32 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063133898   ⟸   XM_063277828
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZY32-F1-model_v2 AlphaFold D3ZY32 1-582 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:1307753 AgrOrtholog
BioCyc Gene G2FUF-6064 BioCyc
Ensembl Genes ENSRNOG00000006741 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037453.7 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/TrEMBL
InterPro L_dom-like UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/TrEMBL
  Leu-rich_rpt_typical-subtyp UniProtKB/TrEMBL
  SLRP UniProtKB/TrEMBL
NCBI Gene 288907 ENTREZGENE
PANTHER AGAP008170-PA UniProtKB/TrEMBL
  PODOCAN UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/TrEMBL
  LRR_8 UniProtKB/TrEMBL
PhenoGen Podnl1 PhenoGen
PRINTS LEURICHRPT UniProtKB/TrEMBL
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006741 RatGTEx
SMART LRR_BAC UniProtKB/TrEMBL
  LRR_SD22 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt D3ZY32 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Podnl1  podocan-like 1  RGD1307753_predicted  similar to podocan protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307753_predicted  similar to podocan protein (predicted)  LOC288907_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC288907_predicted  similar to podocan protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL