Pcdh17 (protocadherin 17) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Pcdh17 (protocadherin 17) Mus musculus
Analyze
Symbol: Pcdh17
Name: protocadherin 17
RGD ID: 1617378
MGI Page MGI
Description: Involved in synaptic membrane adhesion. Acts upstream of or within several processes, including negative regulation of synaptic transmission; presynaptic active zone assembly; and regulation of synaptic vesicle clustering. Located in GABA-ergic synapse and glutamatergic synapse. Is integral component of presynaptic membrane. Is integral component of postsynaptic membrane. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human PCDH17 (protocadherin 17).
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: C030033F14Rik; Gm78; protocadherin 68; protocadherin-17
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
GRCm391484,680,626 - 84,775,005 (+)NCBIGRCm39mm39
GRCm39 Ensembl1484,681,003 - 84,776,442 (+)Ensembl
GRCm381484,443,563 - 84,537,565 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1484,443,563 - 84,539,002 (+)EnsemblGRCm38mm10GRCm38
MGSCv371484,843,370 - 84,936,867 (+)NCBIGRCm37mm9NCBIm37
MGSCv361483,253,698 - 83,342,225 (+)NCBImm8
Celera1481,944,000 - 82,037,467 (+)NCBICelera
Cytogenetic Map14D3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (EXP)
1-naphthyl isothiocyanate  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
6-propyl-2-thiouracil  (ISO)
acetylsalicylic acid  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldehydo-D-glucose  (EXP)
all-trans-retinoic acid  (ISO)
antirheumatic drug  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
astemizole  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
bisphenol A  (EXP,ISO)
C60 fullerene  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (EXP)
chloroprene  (ISO)
chrysene  (EXP)
clobetasol  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
D-glucose  (EXP)
decabromodiphenyl ether  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
entinostat  (ISO)
ethanol  (EXP)
fucoxanthin  (EXP)
genistein  (EXP)
glucose  (EXP)
medroxyprogesterone acetate  (ISO)
mercury dibromide  (ISO)
methylisothiazolinone  (ISO)
methylmercury chloride  (ISO)
miconazole  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
paracetamol  (EXP)
phenobarbital  (EXP)
pirinixic acid  (EXP)
potassium chromate  (ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (EXP)
sulindac  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
testosterone enanthate  (ISO)
tetraphene  (EXP)
titanium dioxide  (EXP,ISO)
trichostatin A  (ISO)
trimellitic anhydride  (EXP)
triptonide  (EXP)
valproic acid  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10817752   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14681479   PMID:15905963   PMID:16141072  
PMID:16141073   PMID:17953485   PMID:17978184   PMID:18799693   PMID:19449025   PMID:21795542   PMID:21873635   PMID:22415368   PMID:23684785   PMID:23920377   PMID:24642214   PMID:25199687  
PMID:25977363   PMID:27779093   PMID:32436661  


Genomics

Comparative Map Data
Pcdh17
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391484,680,626 - 84,775,005 (+)NCBIGRCm39mm39
GRCm39 Ensembl1484,681,003 - 84,776,442 (+)Ensembl
GRCm381484,443,563 - 84,537,565 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1484,443,563 - 84,539,002 (+)EnsemblGRCm38mm10GRCm38
MGSCv371484,843,370 - 84,936,867 (+)NCBIGRCm37mm9NCBIm37
MGSCv361483,253,698 - 83,342,225 (+)NCBImm8
Celera1481,944,000 - 82,037,467 (+)NCBICelera
Cytogenetic Map14D3NCBI
PCDH17
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1357,631,744 - 57,729,311 (+)EnsemblGRCh38hg38GRCh38
GRCh381357,630,104 - 57,729,311 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371358,205,878 - 58,303,445 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361357,103,790 - 57,201,066 (+)NCBINCBI36hg18NCBI36
Build 341357,103,944 - 57,198,155NCBI
Celera1339,160,322 - 39,257,584 (+)NCBI
Cytogenetic Map13q21.1NCBI
HuRef1338,887,937 - 38,985,207 (+)NCBIHuRef
CHM1_11358,173,338 - 58,270,626 (+)NCBICHM1_1
Pcdh17
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21560,222,088 - 60,316,172 (+)NCBI
Rnor_6.0 Ensembl1567,555,835 - 67,645,088 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01567,555,835 - 67,647,990 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01571,182,073 - 71,273,939 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41566,391,901 - 66,482,530 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11566,405,272 - 66,600,882 (+)NCBI
Celera1559,754,674 - 59,843,809 (+)NCBICelera
Cytogenetic Map15q12NCBI
Pcdh17
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540446,791,148 - 46,886,918 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540446,795,303 - 46,886,918 (-)NCBIChiLan1.0ChiLan1.0
PCDH17
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11357,532,850 - 57,631,725 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1357,532,850 - 57,631,725 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01338,801,514 - 38,900,811 (+)NCBIMhudiblu_PPA_v0panPan3
PCDH17
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12213,865,138 - 13,962,110 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2213,865,900 - 13,958,405 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2213,835,266 - 13,930,999 (+)NCBI
ROS_Cfam_1.02214,087,985 - 14,184,578 (+)NCBI
UMICH_Zoey_3.12213,793,476 - 13,885,812 (+)NCBI
UNSW_CanFamBas_1.02213,818,958 - 13,910,969 (+)NCBI
UU_Cfam_GSD_1.02213,837,878 - 13,933,995 (+)NCBI
Pcdh17
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945147,355,309 - 147,452,093 (-)NCBI
SpeTri2.0NW_004936820764,016 - 860,325 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCDH17
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1130,511,261 - 30,611,727 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11130,510,779 - 30,611,732 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21131,998,284 - 32,036,732 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCDH17
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1335,423,998 - 35,518,776 (+)NCBI
ChlSab1.1 Ensembl335,426,230 - 35,519,023 (+)Ensembl
Vero_WHO_p1.0NW_0236660578,229,314 - 8,327,911 (-)NCBI
Pcdh17
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474818,958,250 - 19,056,278 (+)NCBI

Position Markers
Pcdh17  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381484,534,935 - 84,535,855UniSTSGRCm38
MGSCv371484,934,742 - 84,935,662UniSTSGRCm37
Celera1482,035,349 - 82,036,269UniSTS
Cytogenetic Map14D3UniSTS
cM Map14 UniSTS
LOC144997  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381484,535,403 - 84,535,509UniSTSGRCm38
MGSCv371484,935,210 - 84,935,316UniSTSGRCm37
Celera1482,035,817 - 82,035,923UniSTS
Cytogenetic Map14D3UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357589Kdnw2_mkidney weight 2 (mouse)Not determined1420837405121032392Mouse
27226774Tibl15_mtibia length 15, 10 week (mouse)143060000087700000Mouse
4142364Pbwg18_mpostnatal body weight growth 18 (mouse)Not determined145204453586044676Mouse
1301489Lbm10_mlean body mass 10 (mouse)Not determined145352385687524089Mouse
12880432Fgf23lq3_mFGF23 serum level QTL 3 (mouse)145370000087700000Mouse
10043889Cia52_mcollagen induced arthritis QTL 52 (mouse)Not determined145584494189845069Mouse
1301562Hwq1_mheart weight quantitative locus 1 (mouse)Not determined145630930590309501Mouse
1357565wrmod1_mwobbler modifier 1 (mouse)Not determined1457942183101622037Mouse
1300666Fembm2_mfemoral bone morphometry 2 (mouse)Not determined146216002096160240Mouse
14747006Mancz12_mmandible centroid size 12 (mouse)1469834541103834541Mouse
10054475Ossc3_mosteosarcoma susceptibility 3 (mouse)Not determined1470626332104626490Mouse
1300551Lprm3_mlymphoproliferation modifier 3 (mouse)Not determined1470983788104983908Mouse
1301844Pgia29_mproteoglycan induced arthritis 29 (mouse)Not determined1474114860108114948Mouse
1558819Ossc2_mosteosarcoma susceptibility 2 (mouse)Not determined1474157540108157657Mouse
14928314Manh77_mmandible shape 77 (mouse)1476530354110530354Mouse
1558823Tbbmd6_mtotal body bone mineral density 6 (mouse)Not determined1476836260110836351Mouse
10043997Bw40_mbody weight QTL 40 (mouse)Not determined1482924828116925025Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1013
Count of miRNA genes:512
Interacting mature miRNAs:648
Transcripts:ENSMUST00000071370
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.


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001013753 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006518905 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006518906 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017315983 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001781111 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_003950845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_003950846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_004938388 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AK021116 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK045478 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK046505 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK047338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK048934 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK051160 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK079626 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK133637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK139275 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK142358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK147265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK158668 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC079850 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC089004 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CT009510 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000071370   ⟹   ENSMUSP00000071325
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1484,443,563 - 84,539,002 (+)Ensembl
RefSeq Acc Id: ENSMUST00000226362
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1484,448,507 - 84,479,227 (+)Ensembl
RefSeq Acc Id: NM_001013753   ⟹   NP_001013775
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,681,003 - 84,774,500 (+)NCBI
GRCm381484,443,563 - 84,537,060 (+)NCBI
MGSCv371484,843,370 - 84,936,867 (+)RGD
Celera1481,944,000 - 82,037,467 (+)RGD
cM Map14 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_006518905   ⟹   XP_006518968
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,443,563 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006518906   ⟹   XP_006518969
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,445,876 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017315983   ⟹   XP_017171472
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,445,341 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XR_001781111
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,445,039 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XR_003950845
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,445,039 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XR_003950846
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
GRCm381484,445,039 - 84,537,565 (+)NCBI
Sequence:
RefSeq Acc Id: XR_004938388
RefSeq Status:
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391484,680,626 - 84,775,005 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001013775   ⟸   NM_001013753
- Peptide Label: precursor
- UniProtKB: E9PXF0 (UniProtKB/TrEMBL),   Q3UTP0 (UniProtKB/TrEMBL),   Q5HZI5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006518968   ⟸   XM_006518905
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006518969   ⟸   XM_006518906
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017171472   ⟸   XM_017315983
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: ENSMUSP00000071325   ⟸   ENSMUST00000071370
Protein Domains
Cadherin

Promoters
RGD ID:8683086
Promoter ID:EPDNEW_M19574
Type:multiple initiation site
Name:Pcdh17_1
Description:Mus musculus protocadherin 17 , 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
GRCm381484,443,563 - 84,443,623EPDNEW
RGD ID:6825261
Promoter ID:MM_KWN:17569
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_001013753,   UC007UTO.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361484,843,221 - 84,848,007 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2684924 AgrOrtholog
Ensembl Genes ENSMUSG00000035566 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000071325 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000071370 ENTREZGENE, UniProtKB/TrEMBL
InterPro Cadherin UniProtKB/TrEMBL
  Cadherin-like UniProtKB/TrEMBL
  Cadherin_CS UniProtKB/TrEMBL
  Cadherin_N UniProtKB/TrEMBL
  Protocadherin-17 UniProtKB/TrEMBL
KEGG Report mmu:219228 UniProtKB/TrEMBL
MGD MGI:2684924 ENTREZGENE
NCBI Gene 219228 ENTREZGENE
PANTHER PTHR24028:SF41 UniProtKB/TrEMBL
Pfam Cadherin UniProtKB/TrEMBL
  Cadherin_2 UniProtKB/TrEMBL
PhenoGen Pcdh17 PhenoGen
PRINTS CADHERIN UniProtKB/TrEMBL
PROSITE CADHERIN_1 UniProtKB/TrEMBL
  CADHERIN_2 UniProtKB/TrEMBL
SMART SM00112 UniProtKB/TrEMBL
Superfamily-SCOP Cadherin UniProtKB/TrEMBL
UniProt E9PXF0 ENTREZGENE, UniProtKB/TrEMBL
  Q3UTP0 ENTREZGENE, UniProtKB/TrEMBL
  Q3UZU4_MOUSE UniProtKB/TrEMBL
  Q5HZI5 ENTREZGENE, UniProtKB/TrEMBL