Cldn9 (claudin 9) - Rat Genome Database

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Gene: Cldn9 (claudin 9) Rattus norvegicus
Analyze
Symbol: Cldn9
Name: claudin 9
RGD ID: 1308999
Description: Predicted to enable virus receptor activity. Predicted to be involved in bicellular tight junction assembly and cell adhesion. Predicted to act upstream of or within tight junction organization. Predicted to be located in cell junction and intracellular membrane-bounded organelle. Predicted to be active in bicellular tight junction and plasma membrane. Human ortholog(s) of this gene implicated in autosomal recessive nonsyndromic deafness 116. Orthologous to human CLDN9 (claudin 9); PARTICIPATES IN hepatitis C pathway; INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: claudin-9; LOC287099
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21012,714,137 - 12,715,568 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1017,457,518 - 17,458,949 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01016,946,311 - 16,947,742 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01012,446,758 - 12,448,189 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11012,947,422 - 12,948,854 (-)NCBI
Celera1012,409,464 - 12,410,895 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:17130295   PMID:18036336   PMID:20375010  


Genomics

Comparative Map Data
Cldn9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21012,714,137 - 12,715,568 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1017,457,518 - 17,458,949 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01016,946,311 - 16,947,742 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01012,446,758 - 12,448,189 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11012,947,422 - 12,948,854 (-)NCBI
Celera1012,409,464 - 12,410,895 (-)NCBICelera
Cytogenetic Map10q12NCBI
CLDN9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38163,012,923 - 3,014,505 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl163,012,923 - 3,014,505 (+)EnsemblGRCh38hg38GRCh38
GRCh37163,062,924 - 3,064,506 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36163,002,207 - 3,004,507 (+)NCBINCBI36Build 36hg18NCBI36
Build 34163,002,206 - 3,004,507NCBI
Celera163,268,017 - 3,270,066 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef163,034,306 - 3,036,355 (+)NCBIHuRef
CHM1_1163,062,331 - 3,064,380 (+)NCBICHM1_1
T2T-CHM13v2.0163,039,495 - 3,041,077 (+)NCBIT2T-CHM13v2.0
Cldn9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391723,901,558 - 23,903,000 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1723,901,558 - 23,903,000 (-)EnsemblGRCm39 Ensembl
GRCm381723,682,584 - 23,684,026 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1723,682,584 - 23,684,026 (-)EnsemblGRCm38mm10GRCm38
MGSCv371723,819,551 - 23,820,985 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361723,410,206 - 23,411,640 (-)NCBIMGSCv36mm8
Celera1724,188,801 - 24,190,235 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
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_v0Mhudiblu_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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0638,482,646 - 38,484,655 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl638,483,161 - 38,483,814 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1638,168,431 - 38,170,439 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0638,140,919 - 38,142,928 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0638,616,706 - 38,618,715 (-)NCBIUU_Cfam_GSD_1.0
Cldn9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344105,552,854 - 105,554,643 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366941,155,259 - 1,155,912 (-)EnsemblSpeTri2.0
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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl52,756,747 - 2,757,400 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606828,074,953 - 28,076,622 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cldn9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624824758,662 - 759,315 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624824757,962 - 759,818 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cldn9
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:75
Count of miRNA genes:68
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000004848
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
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
9590310Scort19Serum corticosterone level QTL 196.30.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9590268Scort13Serum corticosterone level QTL 133.260.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)101147401056474010Rat
9589136Insul27Insulin level QTL 2710.460.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)101147401056474010Rat

Markers in Region
Cldn9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21012,714,551 - 12,715,205 (+)MAPPERmRatBN7.2
Rnor_6.01013,003,425 - 13,004,078NCBIRnor6.0
Rnor_5.01012,826,470 - 12,827,123UniSTSRnor5.0
RGSC_v3.41012,947,838 - 12,948,491UniSTSRGSC3.4
Celera1012,409,879 - 12,410,532UniSTS
Cytogenetic Map10q12UniSTS
Cldn9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21012,714,587 - 12,715,408 (+)MAPPERmRatBN7.2
Rnor_6.01013,003,461 - 13,004,281NCBIRnor6.0
Rnor_5.01012,826,506 - 12,827,326UniSTSRnor5.0
RGSC_v3.41012,947,874 - 12,948,694UniSTSRGSC3.4
Celera1012,409,915 - 12,410,735UniSTS
Cytogenetic Map10q12UniSTS


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 4
Low 10 2 12 2 68 31 25 3
Below cutoff 2 6 22 22 7 22 3 3 6 13 6 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004848   ⟹   ENSRNOP00000004848
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)Ensembl
Rnor_6.0 Ensembl1013,003,011 - 13,004,441 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000111504   ⟹   ENSRNOP00000079837
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1012,709,960 - 12,715,973 (+)Ensembl
RefSeq Acc Id: NM_001011889   ⟹   NP_001011889
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21012,714,137 - 12,715,568 (-)NCBI
Rnor_6.01013,003,010 - 13,004,441 (-)NCBI
Rnor_5.01012,826,055 - 12,827,486 (-)NCBI
RGSC_v3.41012,947,423 - 12,948,854 (-)RGD
Celera1012,409,464 - 12,410,895 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001011889 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87664 (Get FASTA)   NCBI Sequence Viewer  
  EDM03768 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001011889   ⟸   NM_001011889
- UniProtKB: Q5PPJ3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004848   ⟸   ENSRNOT00000004848
RefSeq Acc Id: ENSRNOP00000079837   ⟸   ENSRNOT00000111504

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PPJ3-F1-model_v2 AlphaFold Q5PPJ3 1-217 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:1308999 AgrOrtholog
BioCyc Gene G2FUF-25913 BioCyc
Ensembl Genes ENSRNOG00000003654 Ensembl
IMAGE_CLONE IMAGE:7315462 IMAGE-MGC_LOAD
InterPro Claudin UniProtKB/TrEMBL
  Claudin9 UniProtKB/TrEMBL
  Claudin_CS UniProtKB/TrEMBL
  PMP22/EMP/MP20/Claudin UniProtKB/TrEMBL
KEGG Report rno:287099 UniProtKB/TrEMBL
MGC_CLONE MGC:105509 IMAGE-MGC_LOAD
NCBI Gene 287099 ENTREZGENE
PANTHER Claudin UniProtKB/TrEMBL
  PTHR12002:SF42 UniProtKB/TrEMBL
Pfam PMP22_Claudin UniProtKB/TrEMBL
PhenoGen Cldn9 PhenoGen
PRINTS CLAUDIN9 UniProtKB/TrEMBL
PROSITE CLAUDIN UniProtKB/TrEMBL
UniProt Q5PPJ3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Cldn9  claudin 9  Cldn9_predicted  claudin 9 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Cldn9_predicted  claudin 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED