Cntnap5c (contactin associated protein-like 5C) - Rat Genome Database

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Gene: Cntnap5c (contactin associated protein-like 5C) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cntnap5c (Ensembl: LOC304725)
Name: contactin associated protein-like 5C (Ensembl:similar to contactin associated protein-like 5 isoform 1)
RGD ID: 1566343
Description: Predicted to enable calcium ion binding activity. Predicted to be involved in cell adhesion. Predicted to be located in basement membrane and membrane. Orthologous to human CNTNAP5 (contactin associated protein family member 5).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Caspr5-4; cell recognition molecule Caspr5-3; cell recognition molecule Caspr5-4; cell recognition molecule Caspr5c; cell recognition molecule Caspr5d; Cntnap5; Cntnap5d; contactin associated protein-like 5; contactin associated protein-like 5-4; contactin-associated protein like 5-4; contactin-associated protein-like 5d; LOC297846; RGD1566343; similar to contactin associated protein-like 5 isoform 1
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8133,521,265 - 4,553,884 (+)NCBIGRCr8
mRatBN7.2133,513,615 - 4,546,285 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl133,514,198 - 4,542,745 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx133,539,615 - 4,587,031 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0134,848,877 - 5,896,314 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0133,519,073 - 4,566,500 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0136,312,302 - 7,538,647 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl136,679,368 - 7,537,275 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01311,594,156 - 12,421,307 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.01312,597,108 - 12,804,561 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41322,856,230 - 23,913,512 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera134,468,107 - 5,491,533 (+)NCBICelera
Cytogenetic Map13p13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. GOA pipeline RGD automated data pipeline
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16845472  


Genomics

Variants

.
Variants in Cntnap5c
7876 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:175
Count of miRNA genes:132
Interacting mature miRNAs:141
Transcripts:ENSRNOT00000067198
Prediction methods:Miranda
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
2317027Aia22Adjuvant induced arthritis QTL 222.29joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)13134266636Rat
738036Lnnr4Liver neoplastic nodule remodeling QTL 43.64liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)13142356786Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat

Markers in Region
D13Rat9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,611,007 - 3,611,148 (+)MAPPERmRatBN7.2
Rnor_6.0136,411,215 - 6,411,355NCBIRnor6.0
Rnor_5.01311,693,801 - 11,693,941UniSTSRnor5.0
RGSC_v3.41322,952,154 - 22,952,295RGDRGSC3.4
RGSC_v3.41322,952,155 - 22,952,295UniSTSRGSC3.4
RGSC_v3.11322,954,895 - 22,955,036RGD
Celera134,564,861 - 4,565,001UniSTS
SHRSP x BN Map131.1799UniSTS
SHRSP x BN Map131.1799RGD
Cytogenetic Map13p12-p11UniSTS
D13Rat169  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,885,124 - 3,885,302 (+)MAPPERmRatBN7.2
Rnor_6.0136,836,597 - 6,836,774NCBIRnor6.0
Rnor_5.01312,114,539 - 12,114,716UniSTSRnor5.0
RGSC_v3.41323,227,922 - 23,228,100RGDRGSC3.4
RGSC_v3.41323,227,923 - 23,228,100UniSTSRGSC3.4
RGSC_v3.11323,230,663 - 23,230,841RGD
Celera134,834,975 - 4,835,152UniSTS
SHRSP x BN Map131.0999UniSTS
SHRSP x BN Map131.0999RGD
FHH x ACI Map131.4701RGD
Cytogenetic Map13p12-p11UniSTS
D13Rat168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,885,090 - 3,885,298 (+)MAPPERmRatBN7.2
Rnor_6.0136,836,563 - 6,836,770NCBIRnor6.0
Rnor_5.01312,114,505 - 12,114,712UniSTSRnor5.0
RGSC_v3.41323,227,888 - 23,228,096RGDRGSC3.4
RGSC_v3.41323,227,889 - 23,228,096UniSTSRGSC3.4
RGSC_v3.11323,230,629 - 23,230,837RGD
Celera134,834,941 - 4,835,148UniSTS
SHRSP x BN Map131.1799UniSTS
SHRSP x BN Map131.1799RGD
Cytogenetic Map13p12-p11UniSTS
D6Got154  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,573,658 - 3,573,830 (+)MAPPERmRatBN7.2
Rnor_6.0136,373,876 - 6,374,047NCBIRnor6.0
Rnor_5.01311,656,462 - 11,656,633UniSTSRnor5.0
RGSC_v3.41322,914,852 - 22,915,024RGDRGSC3.4
RGSC_v3.41322,914,853 - 22,915,024UniSTSRGSC3.4
RGSC_v3.11322,917,594 - 22,917,765RGD
Celera134,527,108 - 4,527,279UniSTS
RH 3.4 Map6776.09UniSTS
RH 3.4 Map6776.09RGD
Cytogenetic Map13p12-p11UniSTS
D13Got264  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,269,328 - 4,269,614 (+)MAPPERmRatBN7.2
Rnor_6.0137,267,590 - 7,267,875NCBIRnor6.0
Rnor_5.01312,534,460 - 12,534,745UniSTSRnor5.0
RGSC_v3.41323,617,250 - 23,617,535UniSTSRGSC3.4
Celera135,218,546 - 5,218,831UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got234  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2133,956,109 - 3,956,248 (+)MAPPERmRatBN7.2
Rnor_6.0136,908,135 - 6,908,273NCBIRnor6.0
Rnor_5.01312,186,077 - 12,186,215UniSTSRnor5.0
RGSC_v3.41323,298,909 - 23,299,047UniSTSRGSC3.4
Celera134,905,852 - 4,905,989UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got203  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,363,875 - 4,364,022 (+)MAPPERmRatBN7.2
Rnor_6.0137,361,000 - 7,361,145NCBIRnor6.0
Rnor_5.01312,628,290 - 12,628,431NCBIRnor5.0
RGSC_v3.41323,714,026 - 23,714,171UniSTSRGSC3.4
Cytogenetic Map13p12-p11UniSTS
D13Got255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,269,393 - 4,269,612 (+)MAPPERmRatBN7.2
Rnor_6.0137,267,655 - 7,267,873NCBIRnor6.0
Rnor_5.01312,534,525 - 12,534,743UniSTSRnor5.0
RGSC_v3.41323,617,315 - 23,617,533UniSTSRGSC3.4
Celera135,218,611 - 5,218,829UniSTS
Cytogenetic Map13p12-p11UniSTS
D13Got236  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0137,041,710 - 7,041,875NCBIRnor6.0
Rnor_5.01312,320,126 - 12,320,291UniSTSRnor5.0
RGSC_v3.41323,434,122 - 23,434,327UniSTSRGSC3.4
Celera135,040,381 - 5,040,586UniSTS
Cytogenetic Map13p12-p11UniSTS
AU048969  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,126,461 - 4,126,661 (+)MAPPERmRatBN7.2
Rnor_6.0137,092,403 - 7,092,602NCBIRnor6.0
Rnor_5.01312,362,625 - 12,362,824UniSTSRnor5.0
RGSC_v3.41323,470,008 - 23,470,207UniSTSRGSC3.4
Celera135,076,433 - 5,076,632UniSTS
Cytogenetic Map13p12-p11UniSTS
AU049039  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2134,346,072 - 4,346,220 (+)MAPPERmRatBN7.2
Rnor_6.0137,343,579 - 7,343,726NCBIRnor6.0
Rnor_5.01312,610,449 - 12,610,596UniSTSRnor5.0
RGSC_v3.41323,696,246 - 23,696,393UniSTSRGSC3.4
Celera135,294,973 - 5,295,120UniSTS
Cytogenetic Map13p12-p11UniSTS


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

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 8
Low 4 58 12 2
Below cutoff 13 11 6 1 6 2 2 8 2 24 6 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000046060   ⟹   ENSRNOP00000044394
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl133,514,198 - 4,542,745 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000067198   ⟹   ENSRNOP00000062287
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl133,727,163 - 4,542,745 (+)Ensembl
Rnor_6.0 Ensembl136,679,368 - 7,537,275 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000092965   ⟹   ENSRNOP00000076029
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl136,679,369 - 7,382,961 (+)Ensembl
RefSeq Acc Id: NM_001047866   ⟹   NP_001041331
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,521,544 - 4,553,884 (+)NCBI
mRatBN7.2133,513,908 - 4,546,285 (+)NCBI
Rnor_6.0136,312,877 - 7,537,275 (+)NCBI
Rnor_5.01311,594,156 - 12,421,307 (+)NCBI
Rnor_5.01312,597,108 - 12,804,561 (+)NCBI
RGSC_v3.41322,856,230 - 23,913,512 (+)RGD
Celera134,468,107 - 5,491,533 (+)RGD
Sequence:
RefSeq Acc Id: NM_001415869   ⟹   NP_001402798
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,521,427 - 4,553,884 (+)NCBI
mRatBN7.2133,513,791 - 4,546,285 (+)NCBI
RefSeq Acc Id: XM_039090654   ⟹   XP_038946582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,521,265 - 4,370,667 (+)NCBI
mRatBN7.2133,513,615 - 4,372,179 (+)NCBI
RefSeq Acc Id: XM_063272211   ⟹   XP_063128281
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8133,735,760 - 4,553,547 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001041331   ⟸   NM_001047866
- Peptide Label: isoform 1 precursor
- UniProtKB: Q0V8T3 (UniProtKB/Swiss-Prot),   F1LMS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000062287   ⟸   ENSRNOT00000067198
RefSeq Acc Id: ENSRNOP00000076029   ⟸   ENSRNOT00000092965
RefSeq Acc Id: XP_038946582   ⟸   XM_039090654
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000044394   ⟸   ENSRNOT00000046060
RefSeq Acc Id: NP_001402798   ⟸   NM_001415869
- Peptide Label: isoform 2 precursor
- UniProtKB: A0A8L2QLT5 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063128281   ⟸   XM_063272211
- Peptide Label: isoform X1
Protein Domains
EGF-like   F5/8 type C   Fibrinogen C-terminal   Laminin G   Laminin G-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LMS4-F1-model_v2 AlphaFold F1LMS4 1-1279 view protein structure
AF-Q0V8T3-F1-model_v2 AlphaFold Q0V8T3 1-1305 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:1566343 AgrOrtholog
BioCyc Gene G2FUF-18732 BioCyc
Ensembl Genes ENSRNOG00000029556 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOG00000043185 Ensembl
Ensembl Transcript ENSRNOT00000046060 ENTREZGENE
  ENSRNOT00000046060.5 UniProtKB/TrEMBL
  ENSRNOT00000067198 ENTREZGENE
  ENSRNOT00000067198.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-binding domain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro ConA-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EGF-like_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Galactose-bd-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:297846 UniProtKB/Swiss-Prot
NCBI Gene 297846 ENTREZGENE
PANTHER CONTACTIN-ASSOCIATED PROTEIN-LIKE 5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PIKACHURIN-LIKE PROTEIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam F5_F8_type_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cntnap5c PhenoGen
PROSITE EGF_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029556 RatGTEx
  ENSRNOG00000043185 RatGTEx
SMART EGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FA58C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LamG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP EGF/Laminin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49785 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF49899 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF56496 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QLT5 ENTREZGENE, UniProtKB/TrEMBL
  CTP5D_RAT UniProtKB/Swiss-Prot
  F1LMS4 ENTREZGENE, UniProtKB/TrEMBL
  Q0V8T3 ENTREZGENE
  Q0V8T4 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-16 Cntnap5c  contactin associated protein-like 5C  Cntnap5  contactin associated protein-like 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 Cntnap5  contactin associated protein-like 5  RGD1566343  similar to contactin associated protein-like 5 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-30 RGD1566343  similar to contactin associated protein-like 5 isoform 1  Cntnap5b  contactin associated protein-like 5B  Symbol and Name updated 1299863 APPROVED
2008-09-30 Cntnap5b  contactin associated protein-like 5B  RGD1566343  similar to contactin associated protein-like 5 isoform 1   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1566343  similar to contactin associated protein-like 5 isoform 1   RGD1566343_predicted  similar to contactin associated protein-like 5 isoform 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1566343_predicted  similar to contactin associated protein-like 5 isoform 1 (predicted)  LOC297846  similar to contactin associated protein-like 5 isoform 1  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC297846  similar to contactin associated protein-like 5 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL