Cldn9 (claudin 9) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cldn9 (claudin 9) Mus musculus
Analyze
Symbol: Cldn9
Name: claudin 9
RGD ID: 1319097
MGI Page MGI
Description: Predicted to enable virus receptor activity. Acts upstream of or within tight junction organization. Located in bicellular tight junction and plasma membrane. Is expressed in several structures, including alimentary system; forelimb bud; pituitary gland; sensory organ; and yolk sac. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 116. Orthologous to human CLDN9 (claudin 9).
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: claudin-9; nmf32; nmf329
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391723,901,558 - 23,903,000 (-)NCBIGRCm39mm39
GRCm39 Ensembl1723,901,558 - 23,903,000 (-)Ensembl
GRCm381723,682,584 - 23,684,026 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1723,682,584 - 23,684,026 (-)EnsemblGRCm38mm10GRCm38
MGSCv371723,819,551 - 23,820,985 (-)NCBIGRCm37mm9NCBIm37
MGSCv361723,410,206 - 23,411,640 (-)NCBImm8
Celera1724,188,801 - 24,190,235 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
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

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10225958   PMID:11923212   PMID:12477932   PMID:14698084   PMID:15366020   PMID:16774906   PMID:17075866   PMID:17130295   PMID:17683524   PMID:18036336   PMID:18480174   PMID:19696885  
PMID:19706201   PMID:21267068   PMID:21677750   PMID:21873635   PMID:22155109   PMID:22275141   PMID:24952082   PMID:26238476   PMID:26669782   PMID:30850599  


Genomics

Comparative Map Data
Cldn9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391723,901,558 - 23,903,000 (-)NCBIGRCm39mm39
GRCm39 Ensembl1723,901,558 - 23,903,000 (-)Ensembl
GRCm381723,682,584 - 23,684,026 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1723,682,584 - 23,684,026 (-)EnsemblGRCm38mm10GRCm38
MGSCv371723,819,551 - 23,820,985 (-)NCBIGRCm37mm9NCBIm37
MGSCv361723,410,206 - 23,411,640 (-)NCBImm8
Celera1724,188,801 - 24,190,235 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
CLDN9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl163,012,923 - 3,014,505 (+)EnsemblGRCh38hg38GRCh38
GRCh38163,012,923 - 3,014,505 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37163,062,924 - 3,064,506 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36163,002,207 - 3,004,507 (+)NCBINCBI36hg18NCBI36
Build 34163,002,206 - 3,004,507NCBI
Celera163,268,017 - 3,270,066 (+)NCBI
Cytogenetic Map16p13.3NCBI
HuRef163,034,306 - 3,036,355 (+)NCBIHuRef
CHM1_1163,062,331 - 3,064,380 (+)NCBICHM1_1
Cldn9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21012,714,137 - 12,715,568 (-)NCBImRatBN7.2
Rnor_6.01013,003,010 - 13,004,441 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1013,003,011 - 13,004,441 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01012,826,055 - 12,827,486 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41012,947,423 - 12,948,854 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11012,947,422 - 12,948,854 (-)NCBI
Celera1012,409,464 - 12,410,895 (-)NCBICelera
Cytogenetic Map10q12NCBI
Cldn9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544214,327,140 - 14,327,793 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544214,326,705 - 14,328,150 (-)NCBIChiLan1.0ChiLan1.0
CLDN9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1163,125,922 - 3,128,744 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl163,127,610 - 3,128,263 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0161,953,439 - 1,956,349 (+)NCBIMhudiblu_PPA_v0panPan3
CLDN9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1638,172,035 - 38,174,089 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl638,172,550 - 38,173,203 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha639,412,579 - 39,414,588 (-)NCBI
ROS_Cfam_1.0638,482,646 - 38,484,655 (-)NCBI
UMICH_Zoey_3.1638,168,431 - 38,170,439 (-)NCBI
UNSW_CanFamBas_1.0638,140,919 - 38,142,928 (-)NCBI
UU_Cfam_GSD_1.0638,616,706 - 38,618,715 (-)NCBI
Cldn9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,552,854 - 105,554,643 (+)NCBI
SpeTri2.0NW_0049366941,155,252 - 1,156,007 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLDN9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl339,172,853 - 39,174,354 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1339,172,731 - 39,181,827 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2340,525,809 - 40,526,986 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLDN9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.152,755,023 - 2,757,879 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl52,756,747 - 2,757,400 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366606828,074,953 - 28,076,622 (-)NCBIVero_WHO_p1.0
Cldn9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624824757,962 - 759,818 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
Cldn9  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381723,682,996 - 23,683,649UniSTSGRCm38
MGSCv371723,819,963 - 23,820,616UniSTSGRCm37
Celera1724,189,213 - 24,189,866UniSTS
Cytogenetic Map17A3.3UniSTS
cM Map17 UniSTS
UniSTS:237588  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381723,682,157 - 23,682,358UniSTSGRCm38
MGSCv371723,819,124 - 23,819,325UniSTSGRCm37
Celera1724,188,374 - 24,188,575UniSTS
Cytogenetic Map17A3.3UniSTS
Cldn9  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381723,683,032 - 23,683,848UniSTSGRCm38
MGSCv371723,819,999 - 23,820,815UniSTSGRCm37
Celera1724,189,249 - 24,190,065UniSTS
Cytogenetic Map17A3.3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357902Obq19_mobesity QTL 19 (mouse)Not determined17125443244Mouse
12910982Pifs2_mpeptide-induced fatal syndrome 2 (mouse)17125970523Mouse
1357743Lith3_mlithogenic gene 3 (mouse)Not determined17125975624Mouse
1300613Pcyts4_mplasmacytoma susceptibility 4 (mouse)Not determined17126862710Mouse
1301615Cfld3_mcystic fibrosis lung disease 3 (mouse)Not determined17126862710Mouse
1302100Circp2_mcircadian photosensitivity 2 (mouse)Not determined17128979566Mouse
12910527Nrq1a_mnoise-induced hearing loss resistant QTL 1a (mouse)17128979566Mouse
12910528Nrq1_mnoise-induced hearing loss resistant QTL 1 (mouse)17128979566Mouse
13524851Asrq8_macoustic startle response 8 (mouse)17130809908Mouse
10412276Leci2_mleukocyte endothelial cell interactions 2 (mouse)Not determined17312791337128037Mouse
1357680Idd23_minsulin dependent diabetes susceptibility 23 (mouse)Not determined17392461526182159Mouse
1300890Bhr3_mbronchial hyperresponsiveness 3 (mouse)Not determined17392461548559063Mouse
1301327Lmr7_mleishmaniasis resistance 7 (mouse)Not determined17480447727496965Mouse
4141215Mnic1_mmacronutrient intake, carbohydrate 1 (mouse)Not determined480447745359340Mouse
1300706Alan1_malloantigen response 1 (mouse)Not determined17480447746158776Mouse
1357789Kdnw3_mkidney weight 3 (mouse)Not determined17480447747574740Mouse
4141272Tfv1_mtotal food volume 1 (mouse)Not determined480447765330362Mouse
10043949Pbft7_mpercent body fat 7 (mouse)Not determined17667496240674962Mouse
4141608Phl1_mprogressive hearing loss 1 (mouse)Not determined17765701129268449Mouse
1301935Skull24_mskull morphology 24 (mouse)Not determined17836594042366175Mouse
1300787Cd8mts5_mCD8 memory T cell subset 5 (mouse)Not determined17836594042366175Mouse
1301338Lmr1_mleishmaniasis resistance 1 (mouse)Not determined17986241186688972Mouse
1302028Asbb3_mautoimmune susceptibility in C57BL/6J and BALB/c 3 (mouse)Not determined171065914544659245Mouse
4142342Lfnq4_mlung function QTL 4 (mouse)Not determined1098759739053168Mouse
4141067Hbnr2_mHeligmosomoides bakeri nematode resistance 2 (mouse)Not determined1166699745667145Mouse
14747010Mancz14_mmandible centroid size 14 (mouse)171177921045779210Mouse
4142507Obrq13_mobesity resistance QTL 13 (mouse)Not determined1197944224857795Mouse
4142150Stheal11_msoft tissue heal 11 (mouse)Not determined171206732483054339Mouse
12904946Tammq8_mtibialis anterior muscle mass QTL 8 (mouse)171223281346232813Mouse
1558807Ceat1_mchronic experimental autoimmune thyroiditis 1 (mouse)Not determined171241779526182159Mouse
13524847Asrq8a_macoustic startle response 8a (mouse)171242798746427987Mouse
11081168Tir7_mtrypanosome infection response 7 (mouse)171390439847904522Mouse
1300914Pcir4_mperiosteal circumference 4 (mouse)Not determined171484267848842786Mouse
1558886Lgth9_mbody length 9 (mouse)Not determined171484267848842786Mouse
1302070Tbbmd7_mtotal body bone mineral density 7 (mouse)Not determined171484267848842786Mouse
1300995Fembrs4_mfemur breaking strength 4 (mouse)Not determined171484267848842786Mouse
1302140Wta4_mweight adult 4 (mouse)Not determined171660074750600869Mouse
1302152Skull25_mskull morphology 25 (mouse)Not determined171660074750600869Mouse
1301505Tir1_mtrypanosome infection response 1 (mouse)Not determined171660074750600869Mouse
1302038Radpf1_mradiation pulmonary fibrosis 1 (mouse)Not determined171661519333600869Mouse
10412083Sm2_msusceptibility to Schistosoma mansoni infection 2 (mouse)Not determined171681096950811104Mouse
1302042Acsns3_mAngiostrongylus costaricensis nematode susceptibility 3 (mouse)Not determined171724323451243371Mouse
1300535Char3_mP. chabaudi malaria resistance QTL 3 (mouse)Not determined171724323451243371Mouse
10412214Sxbq3_mSGC/Knj cross B6 QTL 3 (mouse)Not determined171724323451243371Mouse
13452396Leusq3_mleucocytosis susceptibility QTL 3 (mouse)171724323451243371Mouse
13452399Leusq6_mleucocytosis susceptibility QTL 6 (mouse)171724323451243371Mouse
1301840Ssial4_msusceptibility to sialadenitiss 4 (mouse)Not determined171795643651959238Mouse
1301331Lbw1_mlupus NZB x NZW 1 (mouse)Not determined171819938152202007Mouse
1301056Pas2_mpulmonary adenoma susceptibility 2 (mouse)Not determined171820316552205351Mouse
15039354Nmrs36_mNAFLD-associated magnetic resonance shift 36 (mouse)171883413352834133Mouse
12910769Rtmq1_mrenal tumor modifier QTL 1 (mouse)172268105525502498Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:150
Interacting mature miRNAs:151
Transcripts:ENSMUST00000085989
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000085989   ⟹   ENSMUSP00000093236
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1723,901,558 - 23,903,000 (-)Ensembl
GRCm38.p6 Ensembl1723,682,584 - 23,684,026 (-)Ensembl
RefSeq Acc Id: NM_020293   ⟹   NP_064689
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391723,901,558 - 23,903,000 (-)NCBI
GRCm381723,682,584 - 23,684,026 (-)ENTREZGENE
MGSCv371723,819,551 - 23,820,985 (-)RGD
Celera1724,188,801 - 24,190,243 (-)ENTREZGENE
cM Map17 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_064689 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD17319 (Get FASTA)   NCBI Sequence Viewer  
  AAH58186 (Get FASTA)   NCBI Sequence Viewer  
  EDL22263 (Get FASTA)   NCBI Sequence Viewer  
  Q9Z0S7 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_064689   ⟸   NM_020293
- UniProtKB: Q9Z0S7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000093236   ⟸   ENSMUST00000085989

Promoters
RGD ID:13674942
Promoter ID:EPDNEW_M21621
Type:single initiation site
Name:Cldn9_1
Description:Mus musculus claudin 9 , 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
GRCm381723,684,026 - 23,684,086EPDNEW
RGD ID:6827941
Promoter ID:MM_KWN:22442
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:ES_Cell
Transcripts:NM_020293
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361723,820,706 - 23,821,206 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1913100 AgrOrtholog
Ensembl Genes ENSMUSG00000066720 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000093236 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000085989 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Claudin UniProtKB/Swiss-Prot
  Claudin9 UniProtKB/Swiss-Prot
  Claudin_CS UniProtKB/Swiss-Prot
  PMP22/EMP/MP20/Claudin UniProtKB/Swiss-Prot
KEGG Report mmu:56863 UniProtKB/Swiss-Prot
MGD MGI:1913100 ENTREZGENE
NCBI Gene 56863 ENTREZGENE
PANTHER PTHR12002 UniProtKB/Swiss-Prot
  PTHR12002:SF42 UniProtKB/Swiss-Prot
Pfam PMP22_Claudin UniProtKB/Swiss-Prot
PhenoGen Cldn9 PhenoGen
PRINTS CLAUDIN9 UniProtKB/Swiss-Prot
PROSITE CLAUDIN UniProtKB/Swiss-Prot
UniProt CLD9_MOUSE UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q6PEA4 UniProtKB/Swiss-Prot