Nepn (nephrocan) - Rat Genome Database

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Gene: Nepn (nephrocan) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Nepn
Name: nephrocan
RGD ID: 1307755
Description: Predicted to act upstream of or within extracellular matrix organization; negative regulation of transcription by RNA polymerase II; and negative regulation of transforming growth factor beta receptor signaling pathway. Predicted to be located in interstitial matrix. Predicted to be active in extracellular space; INTERACTS WITH amitrole; bisphenol A; methimazole.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC309775; RGD1307755; similar to RIKEN cDNA 5730521E12
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82032,329,314 - 32,342,162 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl2032,320,625 - 32,342,162 (+)EnsemblGRCr8
mRatBN7.22031,786,607 - 31,799,458 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2031,783,526 - 31,799,446 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx2032,788,320 - 32,804,264 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02032,179,229 - 32,195,173 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02032,909,499 - 32,925,415 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.02033,527,932 - 33,543,860 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,527,932 - 33,543,848 (+)Ensemblrn6Rnor6.0
Rnor_5.02035,306,004 - 35,321,932 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.42031,112,352 - 31,128,229 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera2033,181,453 - 33,197,265 (+)NCBICelera
RGSC_v3.12031,126,079 - 31,141,773 (+)NCBI
Cytogenetic Map20q11NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Nepn
80 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:60
Count of miRNA genes:53
Interacting mature miRNAs:53
Transcripts:ENSRNOT00000066492
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)20418947649189476Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202668936256021148Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20133724594Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600300Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20153308346533083Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20134066551Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202074558556021148Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202668936256021148Rat
1598870Bp289Blood pressure QTL 2892.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)20821635953216359Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203215696745978663Rat
1598858Cm61Cardiac mass QTL 613.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)20821635953216359Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202679235356021148Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)201224324249189476Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202668936256021148Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578510Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600300Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202668936256021148Rat

Markers in Region
RH133020  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22031,799,161 - 31,799,381 (+)MAPPERmRatBN7.2
Rnor_6.02033,543,564 - 33,543,783NCBIRnor6.0
Rnor_5.02035,321,636 - 35,321,855UniSTSRnor5.0
RGSC_v3.42031,127,945 - 31,128,164UniSTSRGSC3.4
Celera2033,196,981 - 33,197,200UniSTS
RH 3.4 Map20317.4UniSTS
Cytogenetic Map20q11UniSTS


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
6 7 44 71 37 38 22 21 22 6 150 88 8 51 29 58 16

Sequence


Ensembl Acc Id: ENSRNOT00000066492   ⟹   ENSRNOP00000060467
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2032,320,625 - 32,342,162 (+)Ensembl
mRatBN7.2 Ensembl2031,783,526 - 31,799,446 (+)Ensembl
Rnor_6.0 Ensembl2033,527,932 - 33,543,848 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099270   ⟹   ENSRNOP00000093322
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl2032,329,314 - 32,342,162 (+)Ensembl
mRatBN7.2 Ensembl2031,786,639 - 31,799,446 (+)Ensembl
RefSeq Acc Id: NM_001414970   ⟹   NP_001401899
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82032,329,314 - 32,342,162 (+)NCBI
mRatBN7.22031,786,607 - 31,799,458 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001401899 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92938 (Get FASTA)   NCBI Sequence Viewer  
  EDL92939 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000060467.2
  ENSRNOP00000093322
  ENSRNOP00000093322.1
Ensembl Acc Id: ENSRNOP00000060467   ⟸   ENSRNOT00000066492
Ensembl Acc Id: ENSRNOP00000093322   ⟸   ENSRNOT00000099270
RefSeq Acc Id: NP_001401899   ⟸   NM_001414970
- Peptide Label: precursor
- UniProtKB: A0A8I6AJL1 (UniProtKB/TrEMBL),   A6K484 (UniProtKB/TrEMBL),   A6K483 (UniProtKB/TrEMBL),   D3ZHG5 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZHG5-F1-model_v2 AlphaFold D3ZHG5 1-471 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:1307755 AgrOrtholog
BioCyc Gene G2FUF-3645 BioCyc
Ensembl Genes ENSRNOG00000000410 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066492.3 UniProtKB/TrEMBL
  ENSRNOT00000099270 ENTREZGENE
  ENSRNOT00000099270.2 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
  LRR_TM_domain-containing UniProtKB/TrEMBL
  SLRP UniProtKB/TrEMBL
NCBI Gene 309775 ENTREZGENE
PANTHER AGAP008170-PA UniProtKB/TrEMBL
  ANTIGEN BSP, PUTATIVE-RELATED UniProtKB/TrEMBL
  CHAOPTIN-RELATED UniProtKB/TrEMBL
  LEUCINE RICH REPEAT FAMILY PROTEIN UniProtKB/TrEMBL
Pfam LRR_8 UniProtKB/TrEMBL
PhenoGen Nepn PhenoGen
PROSITE LRR UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000410 RatGTEx
SMART LRR_SD22 UniProtKB/TrEMBL
  LRR_TYP UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/TrEMBL
UniProt A0A8I6AJL1 ENTREZGENE, UniProtKB/TrEMBL
  A6K483 ENTREZGENE, UniProtKB/TrEMBL
  A6K484 ENTREZGENE, UniProtKB/TrEMBL
  D3ZHG5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Nepn  nephrocan  RGD1307755_predicted  similar to RIKEN cDNA 5730521E12 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307755_predicted  similar to RIKEN cDNA 5730521E12 (predicted)  LOC309775_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC309775_predicted  similar to RIKEN cDNA 5730521E12 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL