Cntnap4 (contactin associated protein family member 4) - Rat Genome Database

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Gene: Cntnap4 (contactin associated protein family member 4) Rattus norvegicus
Analyze
Symbol: Cntnap4
Name: contactin associated protein family member 4
RGD ID: 1306459
Description: Predicted to enable PDZ domain binding activity. Predicted to be involved in modulation of chemical synaptic transmission; regulation of grooming behavior; and regulation of synapse organization. Predicted to act upstream of or within neural precursor cell proliferation and neuron differentiation. Predicted to be located in dendrite and plasma membrane. Predicted to be active in GABA-ergic synapse and presynaptic membrane. Orthologous to human CNTNAP4 (contactin associated protein family member 4); INTERACTS WITH 6-propyl-2-thiouracil; atrazine; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: contactin associated protein 4; contactin associated protein-like 4; contactin-associated protein-like 4; LOC307865
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
mRatBN7.21940,568,684 - 40,861,879 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1940,568,684 - 40,854,656 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1947,416,591 - 47,695,446 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01948,069,935 - 48,348,742 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01950,326,557 - 50,605,416 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,817,727 - 45,118,133 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,908,905 - 45,117,309 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01955,658,449 - 55,952,179 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41942,560,079 - 42,850,631 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11942,508,008 - 42,854,853 (+)NCBI
Celera1939,903,489 - 40,188,589 (+)NCBICelera
Cytogenetic Map19q12NCBI
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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12093160   PMID:24870235  


Genomics

Comparative Map Data
Cntnap4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21940,568,684 - 40,861,879 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1940,568,684 - 40,854,656 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1947,416,591 - 47,695,446 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01948,069,935 - 48,348,742 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01950,326,557 - 50,605,416 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01944,817,727 - 45,118,133 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1944,908,905 - 45,117,309 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01955,658,449 - 55,952,179 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41942,560,079 - 42,850,631 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11942,508,008 - 42,854,853 (+)NCBI
Celera1939,903,489 - 40,188,589 (+)NCBICelera
Cytogenetic Map19q12NCBI
CNTNAP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381676,277,401 - 76,560,757 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1676,277,278 - 76,560,757 (+)EnsemblGRCh38hg38GRCh38
GRCh371676,311,299 - 76,594,654 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361674,868,677 - 75,150,636 (+)NCBINCBI36Build 36hg18NCBI36
Celera1660,613,616 - 60,890,640 (+)NCBICelera
Cytogenetic Map16q23.1NCBI
HuRef1662,072,464 - 62,349,684 (+)NCBIHuRef
CHM1_11677,724,035 - 78,004,510 (+)NCBICHM1_1
T2T-CHM13v2.01682,333,540 - 82,616,946 (+)NCBIT2T-CHM13v2.0
Cntnap4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398113,296,523 - 113,609,339 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8113,296,675 - 113,609,349 (+)EnsemblGRCm39 Ensembl
GRCm388112,569,798 - 112,882,707 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8112,570,043 - 112,882,717 (+)EnsemblGRCm38mm10GRCm38
MGSCv378115,093,943 - 115,406,607 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368115,456,020 - 115,768,684 (+)NCBIMGSCv36mm8
Celera8116,793,464 - 117,106,647 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map858.7NCBI
Cntnap4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955484256,328 - 521,073 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955484258,232 - 521,133 (-)NCBIChiLan1.0ChiLan1.0
CNTNAP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11691,583,482 - 92,208,457 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01656,512,541 - 57,138,499 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11676,199,645 - 76,485,958 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1676,199,706 - 76,484,466 (+)Ensemblpanpan1.1panPan2
CNTNAP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1574,507,728 - 74,748,798 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl574,509,885 - 74,748,767 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha574,464,216 - 74,705,564 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0574,820,178 - 75,062,105 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl574,820,183 - 75,061,774 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1574,757,538 - 74,999,913 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0574,593,063 - 74,834,485 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0575,082,944 - 75,324,119 (-)NCBIUU_Cfam_GSD_1.0
Cntnap4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934934,539,730 - 34,779,305 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647524,809,531 - 25,049,854 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647524,809,813 - 25,049,362 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CNTNAP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl611,317,848 - 11,589,300 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1611,316,534 - 11,589,628 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
CNTNAP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1561,706,427 - 61,984,656 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl561,706,444 - 61,982,587 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604714,069,458 - 14,347,466 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cntnap4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474610,378,704 - 10,650,691 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474610,376,304 - 10,649,868 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cntnap4
1645 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:527
Count of miRNA genes:259
Interacting mature miRNAs:306
Transcripts:ENSRNOT00000066057
Prediction methods:Microtar, Miranda, 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
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193383821455283146Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat

Markers in Region
D19Got34  
Rat AssemblyChrPosition (strand)SourceJBrowse
RGSC_v3.41942,605,468 - 42,605,702RGDRGSC3.4
RGSC_v3.41942,605,469 - 42,605,702UniSTSRGSC3.4
RGSC_v3.11942,610,349 - 42,610,583RGD
Celera1939,948,621 - 39,948,854UniSTS
RH 3.4 Map19526.4UniSTS
RH 3.4 Map19526.4RGD
RH 2.0 Map19558.4RGD
Cytogenetic Map19q12UniSTS
D19Got36  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21940,581,542 - 40,581,678 (+)MAPPERmRatBN7.2
Rnor_6.01944,830,550 - 44,830,685NCBIRnor6.0
Rnor_5.01955,671,272 - 55,671,407UniSTSRnor5.0
RGSC_v3.41942,572,903 - 42,573,039RGDRGSC3.4
RGSC_v3.41942,572,904 - 42,573,039UniSTSRGSC3.4
RGSC_v3.11942,577,785 - 42,577,920RGD
Celera1939,916,215 - 39,916,332UniSTS
RH 3.4 Map19521.7UniSTS
RH 3.4 Map19521.7RGD
RH 2.0 Map19558.6RGD
Cytogenetic Map19q12UniSTS
BE121086  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21940,854,193 - 40,854,351 (+)MAPPERmRatBN7.2
Rnor_6.01945,117,671 - 45,117,828NCBIRnor6.0
Rnor_5.01955,951,717 - 55,951,874UniSTSRnor5.0
RGSC_v3.41942,850,169 - 42,850,326UniSTSRGSC3.4
Celera1940,188,127 - 40,188,284UniSTS
RH 3.4 Map19532.6UniSTS
Cytogenetic Map19q12UniSTS
AU048988  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera1940,038,638 - 40,038,826UniSTS
Cytogenetic Map19q12UniSTS


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 54
Low 12 7 14 28 27
Below cutoff 3 14 18 14 10 14 7 10 4 6 13 6 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066057   ⟹   ENSRNOP00000061027
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1940,568,684 - 40,854,656 (+)Ensembl
Rnor_6.0 Ensembl1944,908,905 - 45,117,309 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085072   ⟹   ENSRNOP00000073864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1944,908,905 - 45,117,309 (+)Ensembl
RefSeq Acc Id: NM_001107432   ⟹   NP_001100902
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21940,568,684 - 40,854,656 (+)NCBI
Rnor_6.01944,817,727 - 45,118,133 (+)NCBI
Rnor_5.01955,658,449 - 55,952,179 (+)NCBI
RGSC_v3.41942,560,079 - 42,850,631 (+)RGD
Celera1939,903,489 - 40,188,589 (+)RGD
Sequence:
RefSeq Acc Id: XM_039097771   ⟹   XP_038953699
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21940,770,547 - 40,861,879 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100902 (Get FASTA)   NCBI Sequence Viewer  
  XP_038953699 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92605 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001100902   ⟸   NM_001107432
- Peptide Label: precursor
- UniProtKB: F1M3J7 (UniProtKB/TrEMBL),   A6IZC7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073864   ⟸   ENSRNOT00000085072
RefSeq Acc Id: ENSRNOP00000061027   ⟸   ENSRNOT00000066057
RefSeq Acc Id: XP_038953699   ⟸   XM_039097771
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1M3J7-F1-model_v2 AlphaFold F1M3J7 1-1241 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:1306459 AgrOrtholog
BioCyc Gene G2FUF-5617 BioCyc
Ensembl Genes ENSRNOG00000011231 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061027 ENTREZGENE
  ENSRNOP00000061027.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066057 ENTREZGENE
  ENSRNOT00000066057.4 UniProtKB/TrEMBL
Gene3D-CATH 2.60.120.1000 UniProtKB/TrEMBL
  2.60.120.200 UniProtKB/TrEMBL
  Galactose-binding domain-like UniProtKB/TrEMBL
  Laminin UniProtKB/TrEMBL
InterPro ConA-like_subgrp UniProtKB/TrEMBL
  EG-like_dom UniProtKB/TrEMBL
  FA58C UniProtKB/TrEMBL
  Fibrinogen-like_C UniProtKB/TrEMBL
  Fibrinogen_a/b/g_C_dom UniProtKB/TrEMBL
  Galactose-bd-like UniProtKB/TrEMBL
  Laminin_G UniProtKB/TrEMBL
KEGG Report rno:307865 UniProtKB/TrEMBL
NCBI Gene 307865 ENTREZGENE
PANTHER PIKACHURIN-LIKE PROTEIN UniProtKB/TrEMBL
  PTHR15036:SF40 UniProtKB/TrEMBL
Pfam F5_F8_type_C UniProtKB/TrEMBL
  Laminin_G_2 UniProtKB/TrEMBL
PhenoGen Cntnap4 PhenoGen
PROSITE EGF_3 UniProtKB/TrEMBL
  FA58C_1 UniProtKB/TrEMBL
  FA58C_2 UniProtKB/TrEMBL
  FA58C_3 UniProtKB/TrEMBL
  FIBRINOGEN_C_2 UniProtKB/TrEMBL
  LAM_G_DOMAIN UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  FA58C UniProtKB/TrEMBL
  LamG UniProtKB/TrEMBL
Superfamily-SCOP ConA_like_lec_gl UniProtKB/TrEMBL
  EGF/Laminin UniProtKB/TrEMBL
  SSF49785 UniProtKB/TrEMBL
  SSF56496 UniProtKB/TrEMBL
UniProt A6IZC7 ENTREZGENE, UniProtKB/TrEMBL
  F1M3J7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-11-19 Cntnap4  contactin associated protein family member 4  Cntnap4  contactin associated protein 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2019-11-11 Cntnap4  contactin associated protein 4  Cntnap4  contactin associated protein-like 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Cntnap4  contactin associated protein-like 4  Cntnap4_predicted  contactin associated protein 4 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Cntnap4_predicted  contactin associated protein 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED