Cntn5 (contactin 5) - Rat Genome Database

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Gene: Cntn5 (contactin 5) Rattus norvegicus
Analyze
Symbol: Cntn5
Name: contactin 5
RGD ID: 621302
Description: Predicted to enable cell-cell adhesion mediator activity. Predicted to be involved in cell-cell adhesion and nervous system development. Predicted to act upstream of or within sensory perception of sound. Predicted to be located in side of membrane. Predicted to be active in GABA-ergic synapse; axon; and presynaptic membrane. Orthologous to human CNTN5 (contactin 5); INTERACTS WITH 1,3,5-trinitro-1,3,5-triazinane; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: contactin-5; Nb-2; neural recognition molecule NB-2
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
GRCr8815,017,424 - 16,249,418 (-)NCBIGRCr8
mRatBN7.286,735,715 - 7,967,727 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl86,738,239 - 7,967,957 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx810,662,191 - 11,387,303 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.088,959,815 - 9,684,932 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.086,995,473 - 7,722,132 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.087,812,371 - 9,033,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl87,814,895 - 8,524,643 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.087,791,458 - 9,011,097 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.486,530,878 - 7,190,594 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.186,530,883 - 7,190,594 (-)NCBI
Celera88,261,993 - 8,970,431 (-)NCBICelera
Cytogenetic Map8q11NCBI
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
axon  (IBA,IEA)
GABA-ergic synapse  (IEA,ISO)
plasma membrane  (IBA,IEA)
presynaptic membrane  (IEA,ISO)
side of membrane  (IEA)

Molecular Function

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. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
3. Novel neural adhesion molecules in the Contactin/F3 subgroup of the immunoglobulin superfamily: isolation and characterization of cDNAs from rat brain. Ogawa J, etal., Neurosci Lett 1996 Nov 8;218(3):173-6.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11438979   PMID:12653969   PMID:19177518   PMID:22285261   PMID:24411736  


Genomics

Comparative Map Data
Cntn5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8815,017,424 - 16,249,418 (-)NCBIGRCr8
mRatBN7.286,735,715 - 7,967,727 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl86,738,239 - 7,967,957 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx810,662,191 - 11,387,303 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.088,959,815 - 9,684,932 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.086,995,473 - 7,722,132 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.087,812,371 - 9,033,962 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl87,814,895 - 8,524,643 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.087,791,458 - 9,011,097 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.486,530,878 - 7,190,594 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.186,530,883 - 7,190,594 (-)NCBI
Celera88,261,993 - 8,970,431 (-)NCBICelera
Cytogenetic Map8q11NCBI
CNTN5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381199,020,949 - 100,358,885 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1199,020,949 - 100,358,885 (+)EnsemblGRCh38hg38GRCh38
GRCh371198,891,679 - 100,229,616 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361198,397,081 - 99,732,683 (+)NCBINCBI36Build 36hg18NCBI36
Build 341198,397,080 - 99,732,683NCBI
Celera1196,061,589 - 97,396,830 (+)NCBICelera
Cytogenetic Map11q22.1NCBI
HuRef1194,824,853 - 96,165,763 (+)NCBIHuRef
CHM1_11198,775,013 - 100,112,923 (+)NCBICHM1_1
T2T-CHM13v2.01199,027,636 - 100,368,160 (+)NCBIT2T-CHM13v2.0
Cntn5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3999,627,928 - 10,904,992 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl99,660,896 - 10,904,780 (-)EnsemblGRCm39 Ensembl
GRCm3899,634,223 - 10,904,775 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl99,660,891 - 10,904,775 (-)EnsemblGRCm38mm10GRCm38
MGSCv3799,660,891 - 10,904,775 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3699,622,723 - 10,145,039 (-)NCBIMGSCv36mm8
Celera97,036,870 - 8,280,842 (-)NCBICelera
Cytogenetic Map9A1NCBI
cM Map92.46NCBI
Cntn5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554123,436,462 - 4,123,202 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554123,105,095 - 4,122,484 (+)NCBIChiLan1.0ChiLan1.0
CNTN5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2999,853,422 - 101,182,095 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan111100,949,024 - 102,277,334 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01194,012,914 - 95,340,930 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11197,528,796 - 98,851,566 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1198,062,341 - 98,848,900 (+)Ensemblpanpan1.1panPan2
CNTN5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1211,127,965 - 2,408,282 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl211,130,393 - 1,865,309 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha211,140,922 - 2,419,677 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0211,289,066 - 2,569,970 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1211,072,303 - 2,352,365 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0211,158,463 - 2,442,659 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0211,212,566 - 2,489,898 (-)NCBIUU_Cfam_GSD_1.0
Cntn5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494783,260,849 - 84,440,282 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365517,098,632 - 7,804,064 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365517,097,064 - 7,571,894 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNTN5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl930,572,372 - 31,469,858 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1930,259,603 - 31,469,860 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2934,328,486 - 35,529,593 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CNTN5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1190,912,614 - 91,742,510 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl191,195,724 - 91,739,825 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604334,119,947 - 35,447,665 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cntn5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248782,372,472 - 3,092,507 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248782,369,865 - 3,348,339 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cntn5
7055 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:30
Count of miRNA genes:28
Interacting mature miRNAs:30
Transcripts:ENSRNOT00000009418
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat

Markers in Region
AU048094  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.287,131,168 - 7,131,382 (+)MAPPERmRatBN7.2
Rnor_6.088,206,877 - 8,207,090NCBIRnor6.0
Rnor_5.088,185,857 - 8,186,070UniSTSRnor5.0
RGSC_v3.486,868,552 - 6,868,765UniSTSRGSC3.4
Cytogenetic Map8q11UniSTS


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 33
Low 35 2 13
Below cutoff 3 10 15 6 16 6 3 3 6 13 23 6 3

Sequence


RefSeq Acc Id: ENSRNOT00000009418   ⟹   ENSRNOP00000009418
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl86,738,239 - 7,967,957 (-)Ensembl
Rnor_6.0 Ensembl87,814,895 - 8,524,643 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103707   ⟹   ENSRNOP00000093216
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl86,738,239 - 7,450,228 (-)Ensembl
RefSeq Acc Id: NM_053746   ⟹   NP_446198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8815,019,948 - 15,731,957 (-)NCBI
mRatBN7.286,738,239 - 7,450,249 (-)NCBI
Rnor_6.087,814,895 - 8,524,643 (-)NCBI
Rnor_5.087,791,458 - 9,011,097 (-)NCBI
RGSC_v3.486,530,878 - 7,190,594 (-)RGD
Celera88,261,993 - 8,970,431 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595408   ⟹   XP_017450897
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8815,017,424 - 16,249,318 (-)NCBI
mRatBN7.286,735,715 - 7,967,614 (-)NCBI
Rnor_6.087,812,371 - 9,033,826 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595409   ⟹   XP_017450898
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8815,017,424 - 16,249,418 (-)NCBI
mRatBN7.286,735,715 - 7,967,727 (-)NCBI
Rnor_6.087,812,371 - 9,033,962 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017595411   ⟹   XP_017450900
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8815,017,424 - 16,249,318 (-)NCBI
mRatBN7.286,735,715 - 7,967,614 (-)NCBI
Rnor_6.087,812,371 - 9,033,826 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080701   ⟹   XP_038936629
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8815,085,224 - 16,249,318 (-)NCBI
mRatBN7.286,803,525 - 7,967,614 (-)NCBI
RefSeq Acc Id: NP_446198   ⟸   NM_053746
- Peptide Label: precursor
- UniProtKB: P97527 (UniProtKB/Swiss-Prot),   A6JN62 (UniProtKB/TrEMBL),   F1M173 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450898   ⟸   XM_017595409
- Peptide Label: isoform X1
- UniProtKB: P97527 (UniProtKB/Swiss-Prot),   A6JN62 (UniProtKB/TrEMBL),   F1M173 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450900   ⟸   XM_017595411
- Peptide Label: isoform X2
- UniProtKB: F1M173 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450897   ⟸   XM_017595408
- Peptide Label: isoform X1
- UniProtKB: P97527 (UniProtKB/Swiss-Prot),   A6JN62 (UniProtKB/TrEMBL),   F1M173 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009418   ⟸   ENSRNOT00000009418
RefSeq Acc Id: XP_038936629   ⟸   XM_039080701
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000093216   ⟸   ENSRNOT00000103707
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P97527-F1-model_v2 AlphaFold P97527 1-1099 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:621302 AgrOrtholog
BioCyc Gene G2FUF-31745 BioCyc
Ensembl Genes ENSRNOG00000007038 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009418 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000009418.8 UniProtKB/Swiss-Prot
  ENSRNOT00000103707 ENTREZGENE
  ENSRNOT00000103707.1 UniProtKB/TrEMBL
Gene3D-CATH 2.60.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro FN3_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FN3_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_sub2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114589 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 114589 ENTREZGENE
PANTHER PROTEIN SIDEKICK UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR44170:SF17 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam fn3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  I-set UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ig_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cntn5 PhenoGen
PROSITE FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IG_LIKE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000007038 RatGTEx
SMART FN3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IGc2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SM00409 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48726 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49265 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AFE0_RAT UniProtKB/TrEMBL
  A6JN62 ENTREZGENE, UniProtKB/TrEMBL
  CNTN5_RAT UniProtKB/Swiss-Prot
  F1M173 ENTREZGENE, UniProtKB/TrEMBL
  P97527 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Cntn5  contactin 5      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Cntn5  contactin 5      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expression restricted to cerebrum and the cerebellum 61556
gene_product member of the immunoglobulin superfamily 61556
gene_protein 1099 amino acids 61556