Nepn (nephrocan) - Rat Genome Database

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Gene: Nepn (nephrocan) Mus musculus
Analyze
Symbol: Nepn
Name: nephrocan
RGD ID: 1317129
MGI Page MGI
Description: Acts 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. Located in extracellular space and interstitial matrix. Is expressed in several structures, including embryo endoderm; genitourinary system; gut; humerus; and musculature. Orthologous to human NEPNP (nephrocan, pseudogene).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5730521E12Rik; Npn; p; periolin
RGD Orthologs
Human
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391052,264,961 - 52,280,707 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1052,265,068 - 52,280,721 (+)EnsemblGRCm39 Ensembl
GRCm381052,388,864 - 52,404,611 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1052,388,972 - 52,404,625 (+)EnsemblGRCm38mm10GRCm38
MGSCv371052,111,414 - 52,124,410 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361052,080,023 - 52,093,019 (+)NCBIMGSCv36mm8
Celera1053,229,342 - 53,242,318 (+)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1026.6NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:16141072   PMID:16141073   PMID:16990280   PMID:17328885   PMID:17683524   PMID:18757743   PMID:19877272   PMID:19896480  
PMID:20003319   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22008794   PMID:23824574   PMID:24194600   PMID:24390927   PMID:24449834   PMID:24633704   PMID:25209250   PMID:30959515  
PMID:31861348   PMID:34439790   PMID:35794642   PMID:36123357   PMID:38355793  


Genomics

Comparative Map Data
Nepn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391052,264,961 - 52,280,707 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1052,265,068 - 52,280,721 (+)EnsemblGRCm39 Ensembl
GRCm381052,388,864 - 52,404,611 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1052,388,972 - 52,404,625 (+)EnsemblGRCm38mm10GRCm38
MGSCv371052,111,414 - 52,124,410 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361052,080,023 - 52,093,019 (+)NCBIMGSCv36mm8
Celera1053,229,342 - 53,242,318 (+)NCBICelera
Cytogenetic Map10B3NCBI
cM Map1026.6NCBI
NEPNP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386117,602,928 - 117,645,087 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6117,633,706 - 117,645,087 (+)EnsemblGRCh38hg38GRCh38
GRCh376117,924,091 - 117,966,250 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366118,030,784 - 118,072,943 (+)NCBINCBI36Build 36hg18NCBI36
Celera6118,666,992 - 118,709,154 (+)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6115,504,735 - 115,547,424 (+)NCBIHuRef
CHM1_16118,188,033 - 118,230,144 (+)NCBICHM1_1
T2T-CHM13v2.06118,787,169 - 118,829,325 (+)NCBIT2T-CHM13v2.0

Variants

.
Variants in Nepn
618 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:181
Count of miRNA genes:165
Interacting mature miRNAs:175
Transcripts:ENSMUST00000067085, ENSMUST00000160539
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300882Ath17_matherosclerosis 17 (mouse)Not determined105109149085091639Mouse
39128215Lwq17_mliver weight QTL 17 (mouse)101270405184079784Mouse
1302160Mbis2_mMycobacterium bovis-induced systemic lupus erythematosus 2 (mouse)Not determined102028318556031223Mouse
4141943W6q6_mweight 6 weeks QTL 6 (mouse)Not determined1270405184079784Mouse
27226772Tibl13_mtibia length 13, 10 week (mouse)1018875748129635869Mouse
21079434Bdym5_mbody mass QTL 5 (mouse)104054599654836096Mouse
14697707Stsl2_mSalmonella typhimurium susceptibility locus 2 (mouse)104627609653876096Mouse
1357656Hrtq3_mheart weight QTL 3 (mouse)Not determined101270405184079784Mouse
14746991Manh68_mmandible shape 68 (mouse)105228049786280497Mouse
26884426Cvht1_mcranial vault height 1, 5 week (mouse)1024675898121035905Mouse
10045641Jckm3_mjuvenile cystic kidney modifier 3 (mouse)Not determined104984818783848412Mouse
4142380W3q11_mweight 3 weeks QTL 11 (mouse)Not determined1270405184079784Mouse
27226764Tibl19_mtibia length 19, 16 week (mouse)1039175996129635869Mouse
1357825Kidpq2_mkidney weight percentage QTL 2 (mouse)Not determined101270405184079784Mouse
1302150Bbaa18_mB.burgdorferi-associated arthritis 18 (mouse)Not determined104933801283338157Mouse
4142313Angvq1_mangiogenesis by VEGF QTL 1 (mouse)Not determined4672040382491121Mouse
1301380Cia8_mcollagen induced arthritis QTL 8 (mouse)Not determined105149340082491121Mouse
1301003Lmblgq4_mlimb length QTL 4 (mouse)Not determined102159119268091639Mouse
4141159Phl2_mprogressive hearing loss 2 (mouse)Not determined104797449970112651Mouse
1301386Sysbp1_msystolic blood pressure 1 (mouse)Not determined101010826587401095Mouse
10045632Heal16_mwound healing/regeneration 16 (mouse)Not determined103097449964974630Mouse
10755518Chol16_mcholesterol 16 (mouse)101891504352915043Mouse
1301966Lifespan2_mlife span 2 (mouse)Not determined104984822283848397Mouse
1302092Ath11_matherosclerosis 11 (mouse)Not determined10615194558693521Mouse
26884421Cvht5_mcranial vault height 5, 10 week (mouse)104557609669135830Mouse
1302067Scc9_mcolon tumor susceptibility 9 (mouse)Not determined1018259333125575232Mouse
26884411Bzwq8_mbi-zygomatic width QTL 8, 10 week (mouse)1044876096115935905Mouse
1357558Bmch4_mbone mechanical trait 4 (mouse)Not determined103157713665577284Mouse
1300597Skull14_mskull morphology 14 (mouse)Not determined104984818783848412Mouse
4142169Pbwg16_mpostnatal body weight growth 16 (mouse)Not determined104984818783848412Mouse
26884403Cvht8_mcranial vault height 8, 16 week (mouse)102287589991035862Mouse
26884400Huml5_mhumerus length 5, 16 week (mouse)104627609669235830Mouse
27095920Pglq9_mpelvic girdle length QTL 9, 10 week (mouse)103377599670835830Mouse
26884407Bzwq14_mbi-zygomatic width QTL 14, 16 wee (mouse)1045476096120635905Mouse
1301502Eae17_msusceptibility to experimental allergic encephalomyelitis 17 (mouse)Not determined105109149085091639Mouse
1300898Cfid_mcystic fibrosis intestinal distress (mouse)Not determined102972040363720483Mouse
4141070Ltgq1_mliver triglyceride QTL 1 (mouse)Not determined4123732675237326Mouse
1558757Eae34_mexperimental allergic encephalomyelitis susceptibility 34 (mouse)Not determined1021408154114217230Mouse
1357740Obsty3_mobesity 3 (mouse)Not determined108235478116190980Mouse
27095911Pglq15_mpelvic girdle length QTL 15, 16 week (mouse)1039175996129635869Mouse
4141956Egq7_mearly growth QTL 7 (mouse)Not determined1270405184079784Mouse
1357864Scfpq1_msubcutaneous fat pad percentage QTL 1 (mouse)Not determined101270405184079784Mouse
1357737Hpcr2_mhepatocarcinogen resistance 2 (mouse)Not determined104984822283848397Mouse
4142272W10q5_mweight 10 weeks QTL 5 (mouse)Not determined1270405184079784Mouse

Markers in Region
Nepn  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map10B3UniSTS
cM Map10 UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000067085   ⟹   ENSMUSP00000070130
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1052,267,704 - 52,280,721 (+)Ensembl
GRCm38.p6 Ensembl1052,391,608 - 52,404,625 (+)Ensembl
Ensembl Acc Id: ENSMUST00000219730   ⟹   ENSMUSP00000151395
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1052,265,068 - 52,277,052 (+)Ensembl
GRCm38.p6 Ensembl1052,388,972 - 52,400,956 (+)Ensembl
RefSeq Acc Id: NM_025684   ⟹   NP_079960
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391052,267,705 - 52,280,707 (+)NCBI
GRCm381052,391,608 - 52,404,604 (+)NCBI
MGSCv371052,111,414 - 52,124,410 (+)RGD
Celera1053,229,342 - 53,242,318 (+)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006512818   ⟹   XP_006512881
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391052,264,961 - 52,280,707 (+)NCBI
GRCm381052,388,864 - 52,404,611 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006512819   ⟹   XP_006512882
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391052,264,963 - 52,280,707 (+)NCBI
GRCm381052,388,866 - 52,404,611 (+)NCBI
Sequence:
RefSeq Acc Id: NP_079960   ⟸   NM_025684
- Peptide Label: precursor
- UniProtKB: Q9CQ76 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006512881   ⟸   XM_006512818
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006512882   ⟸   XM_006512819
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSMUSP00000151395   ⟸   ENSMUST00000219730
Ensembl Acc Id: ENSMUSP00000070130   ⟸   ENSMUST00000067085
Protein Domains
LRRNT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9CQ76-F1-model_v2 AlphaFold Q9CQ76 1-512 view protein structure

Promoters
RGD ID:6819660
Promoter ID:MM_KWN:4125
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Kidney
Transcripts:OTTMUST00000069226
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361052,108,701 - 52,109,201 (+)MPROMDB
RGD ID:8671966
Promoter ID:EPDNEW_M14014
Type:single initiation site
Name:Nepn_1
Description:Mus musculus nephrocan , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381052,391,609 - 52,391,669EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913900 AgrOrtholog
Ensembl Genes ENSMUSG00000038624 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000067085 ENTREZGENE
  ENSMUST00000067085.7 UniProtKB/Swiss-Prot
  ENSMUST00000219730.2 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt_4 UniProtKB/Swiss-Prot
  Leu-rich_rpt_typical-subtyp UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_TM_domain-containing UniProtKB/Swiss-Prot
  SLRP UniProtKB/TrEMBL
KEGG Report mmu:66650 UniProtKB/Swiss-Prot
MGD MGI:1913900 ENTREZGENE
NCBI Gene 66650 ENTREZGENE
PANTHER AGAP008170-PA UniProtKB/TrEMBL
  ANTIGEN BSP, PUTATIVE-RELATED UniProtKB/Swiss-Prot
  INSULIN LIKE GROWTH FACTOR BINDING PROTEIN ACID LABILE SUBUNIT UniProtKB/Swiss-Prot
  INSULIN-LIKE GROWTH FACTOR-BINDING PROTEIN COMPLEX ACID LABILE SUBUNIT UniProtKB/TrEMBL
  NEPHROCAN UniProtKB/TrEMBL
Pfam LRR_1 UniProtKB/TrEMBL
  LRR_4 UniProtKB/Swiss-Prot
  LRR_8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Nepn PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LRR_SD22 UniProtKB/Swiss-Prot
  LRR_TYP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP L domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A1W2P6T1_MOUSE UniProtKB/TrEMBL
  NEPN_MOUSE UniProtKB/Swiss-Prot
  Q8BMW1_MOUSE UniProtKB/TrEMBL
  Q9CQ76 ENTREZGENE