Col17a1 (collagen type XVII alpha 1 chain) - Rat Genome Database

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Gene: Col17a1 (collagen type XVII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col17a1
Name: collagen type XVII alpha 1 chain
RGD ID: 1311130
Description: Predicted to be an extracellular matrix structural constituent conferring tensile strength. Predicted to be involved in hemidesmosome assembly. Predicted to be located in several cellular components, including anchoring junction; basement membrane; and extracellular region. Predicted to be part of collagen trimer. Predicted to be active in extracellular matrix and hemidesmosome. Human ortholog(s) of this gene implicated in epithelial recurrent erosion dystrophy and junctional epidermolysis bullosa. Orthologous to human COL17A1 (collagen type XVII alpha 1 chain); PARTICIPATES IN syndecan signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: collagen alpha-1(XVII) chain; collagen, type XVII, alpha 1; LOC294027; procollagen, type XVII, alpha 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Is Marker For: Strains:   WAG.OXYS-(D1Rat219-D1Rat81)/Nov
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81256,472,648 - 256,518,857 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1256,472,648 - 256,518,851 (-)EnsemblGRCr8
mRatBN7.21246,530,589 - 246,577,559 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1246,531,367 - 246,577,632 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1254,658,448 - 254,704,506 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01261,351,957 - 261,398,095 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01254,001,093 - 254,047,233 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01267,416,681 - 267,465,049 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1267,417,459 - 267,463,705 (-)Ensemblrn6Rnor6.0
Rnor_5.01274,849,878 - 274,896,696 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41253,012,167 - 253,059,385 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1242,298,011 - 242,344,027 (-)NCBICelera
RGSC_v3.11253,276,739 - 253,365,907 (-)NCBI
Cytogenetic Map1q54NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
basement membrane  (IEA)
hemidesmosome  (IEA,ISO)
membrane  (IEA)
plasma membrane  (IEA,ISO)

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. Mutations in the 180-kD bullous pemphigoid antigen (BPAG2), a hemidesmosomal transmembrane collagen (COL17A1), in generalized atrophic benign epidermolysis bullosa. McGrath JA, etal., Nat Genet. 1995 Sep;11(1):83-6.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. PID Annotation Import Pipeline Pipeline to import Pathway Interaction Database annotations from NCI into RGD
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8707838   PMID:12482924   PMID:39265891  


Genomics

Comparative Map Data
Col17a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81256,472,648 - 256,518,857 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1256,472,648 - 256,518,851 (-)EnsemblGRCr8
mRatBN7.21246,530,589 - 246,577,559 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1246,531,367 - 246,577,632 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1254,658,448 - 254,704,506 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01261,351,957 - 261,398,095 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01254,001,093 - 254,047,233 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01267,416,681 - 267,465,049 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1267,417,459 - 267,463,705 (-)Ensemblrn6Rnor6.0
Rnor_5.01274,849,878 - 274,896,696 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41253,012,167 - 253,059,385 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1242,298,011 - 242,344,027 (-)NCBICelera
RGSC_v3.11253,276,739 - 253,365,907 (-)NCBI
Cytogenetic Map1q54NCBI
COL17A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3810104,031,286 - 104,085,880 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl10104,030,753 - 104,086,225 (-)Ensemblhg38GRCh38
GRCh3710105,791,044 - 105,845,638 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3610105,781,036 - 105,835,628 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3410105,781,035 - 105,835,628NCBI
Celera1099,531,633 - 99,586,511 (-)NCBICelera
Cytogenetic Map10q25.1NCBI
HuRef1099,422,100 - 99,477,424 (-)NCBIHuRef
CHM1_110106,074,725 - 106,129,542 (-)NCBICHM1_1
T2T-CHM13v2.010104,918,673 - 104,973,997 (-)NCBIT2T-CHM13v2.0
Col17a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391947,634,783 - 47,680,460 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1947,634,783 - 47,680,533 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381947,646,341 - 47,692,042 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1947,646,344 - 47,692,094 (-)Ensemblmm10GRCm38
MGSCv371947,720,831 - 47,766,532 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361947,699,673 - 47,745,405 (-)NCBIMGSCv36mm8
Celera1948,408,158 - 48,454,017 (-)NCBICelera
Cytogenetic Map19D1NCBI
cM Map1940.07NCBI
Col17a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554856,568,178 - 6,616,972 (+)NCBIChiLan1.0ChiLan1.0
COL17A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v28115,912,488 - 115,972,924 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan110115,923,022 - 115,977,708 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v010100,630,959 - 100,685,715 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.110104,090,730 - 104,145,169 (-)NCBIPanPan1.1PanPan1.1panPan2
COL17A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12816,349,926 - 16,402,213 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2816,350,564 - 16,402,056 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2816,522,798 - 16,574,963 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02816,828,097 - 16,880,517 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2816,828,097 - 16,880,431 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12816,376,759 - 16,428,925 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02816,404,948 - 16,457,119 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02816,543,707 - 16,595,892 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Col17a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721330,481,695 - 30,529,815 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366002,091,150 - 2,132,173 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366002,084,854 - 2,133,028 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL17A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14114,959,411 - 115,064,783 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.114114,959,404 - 115,007,734 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214124,874,698 - 124,925,355 (-)NCBISscrofa10.2Sscrofa10.2susScr3
COL17A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1997,079,444 - 97,136,878 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl997,080,191 - 97,135,545 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604858,196,574 - 58,253,351 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Col17a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248313,146,527 - 3,185,396 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248313,145,445 - 3,190,498 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Col17a1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1247,170,555 - 47,216,963 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Col17a1
563 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:524
Count of miRNA genes:259
Interacting mature miRNAs:319
Transcripts:ENSRNOT00000016645
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1208479811269633915Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1224633915269633915Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1232312773270518180Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1186658830266453731Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1226175591270518180Rat
1578775Iddm21Insulin dependent diabetes mellitus QTL 214.13blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1245782829270518180Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1212738576257738576Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1205233991267096252Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1218829748263829748Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1186658830266453731Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1248619887269633915Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1176288899270518180Rat
631836Stl31Serum triglyceride level QTL 314.645e-06blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1247133834270518180Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1194786607262083703Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1237995023269633915Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1233480549270108840Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1234540191270518180Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1233204160270518180Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1233480549270108840Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1207163993269633915Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1255849111270518180Rat
1581544Rf52Renal function QTL 520.05urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1241569529269633915Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1223134011262090599Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1243953669270518180Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1225108840270108840Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1185857683270518180Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1226175591270518180Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233349180270518180Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1228174566270518180Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1228180370266453608Rat

Markers in Region
RH133997  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,531,473 - 246,531,668 (+)MAPPERmRatBN7.2
Rnor_6.01267,417,566 - 267,417,760NCBIRnor6.0
Rnor_5.01274,850,763 - 274,850,957UniSTSRnor5.0
RGSC_v3.41253,012,274 - 253,012,468UniSTSRGSC3.4
Celera1242,298,118 - 242,298,312UniSTS
RH 3.4 Map11625.9UniSTS
Cytogenetic Map1q54UniSTS
RH143451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21246,531,445 - 246,531,586 (+)MAPPERmRatBN7.2
Rnor_6.01267,417,538 - 267,417,678NCBIRnor6.0
Rnor_5.01274,850,735 - 274,850,875UniSTSRnor5.0
RGSC_v3.41253,012,246 - 253,012,386UniSTSRGSC3.4
Celera1242,298,090 - 242,298,230UniSTS
RH 3.4 Map11626.7UniSTS
Cytogenetic Map1q54UniSTS


Related Rat Strains
The following Strains have been annotated to Col17a1
WAG.OXYS-(D1Rat219-D1Rat81)/Nov    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 64 148 86 85 54 91 54 6 347 188 11 127 81 89 31 13 13

Sequence


Ensembl Acc Id: ENSRNOT00000016645   ⟹   ENSRNOP00000016645
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1256,472,648 - 256,518,851 (-)Ensembl
mRatBN7.2 Ensembl1246,531,367 - 246,577,632 (-)Ensembl
Rnor_6.0 Ensembl1267,417,459 - 267,463,705 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000084851   ⟹   ENSRNOP00000072907
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1256,472,648 - 256,518,851 (-)Ensembl
mRatBN7.2 Ensembl1246,531,367 - 246,577,632 (-)Ensembl
Rnor_6.0 Ensembl1267,417,459 - 267,463,694 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000110696   ⟹   ENSRNOP00000084162
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1246,531,367 - 246,569,823 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116489   ⟹   ENSRNOP00000086285
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1246,531,367 - 246,577,632 (-)Ensembl
RefSeq Acc Id: NM_001415840   ⟹   NP_001402769
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81256,472,648 - 256,518,857 (-)NCBI
mRatBN7.21246,531,349 - 246,577,559 (-)NCBI
RefSeq Acc Id: NM_001415841   ⟹   NP_001402770
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81256,472,648 - 256,518,857 (-)NCBI
mRatBN7.21246,531,349 - 246,577,559 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001402769 (Get FASTA)   NCBI Sequence Viewer  
  NP_001402770 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94384 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000016645
  ENSRNOP00000016645.6
  ENSRNOP00000072907
  ENSRNOP00000072907.1
Ensembl Acc Id: ENSRNOP00000072907   ⟸   ENSRNOT00000084851
Ensembl Acc Id: ENSRNOP00000016645   ⟸   ENSRNOT00000016645
Ensembl Acc Id: ENSRNOP00000084162   ⟸   ENSRNOT00000110696
Ensembl Acc Id: ENSRNOP00000086285   ⟸   ENSRNOT00000116489
RefSeq Acc Id: NP_001402770   ⟸   NM_001415841
- Peptide Label: isoform 2
- UniProtKB: A6JHR0 (UniProtKB/TrEMBL),   D3ZSH7 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001402769   ⟸   NM_001415840
- Peptide Label: isoform 1
- UniProtKB: A0A8I6GBI7 (UniProtKB/TrEMBL),   A0A0G2K449 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K449-F1-model_v2 AlphaFold A0A0G2K449 1-1465 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13690984
Promoter ID:EPDNEW_R1504
Type:multiple initiation site
Name:Col17a1_1
Description:collagen type XVII alpha 1 chain
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01267,463,632 - 267,463,692EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311130 AgrOrtholog
BioCyc Gene G2FUF-55469 BioCyc
Ensembl Genes ENSRNOG00000012110 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016645 ENTREZGENE
  ENSRNOT00000016645.8 UniProtKB/TrEMBL
  ENSRNOT00000084851 ENTREZGENE
  ENSRNOT00000084851.3 UniProtKB/TrEMBL
Gene3D-CATH 6-Phosphogluconate Dehydrogenase, domain 3 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
  Collagen_superfamily UniProtKB/TrEMBL
NCBI Gene 294027 ENTREZGENE
PANTHER COLLAGEN ALPHA UniProtKB/TrEMBL
  COLLAGEN ALPHA-1(X) CHAIN UniProtKB/TrEMBL
Pfam Collagen UniProtKB/TrEMBL
PhenoGen Col17a1 PhenoGen
RatGTEx ENSRNOG00000012110 RatGTEx
UniProt A0A0G2K449 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GBI7 ENTREZGENE
  A6JHR0 ENTREZGENE, UniProtKB/TrEMBL
  D3ZSH7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col17a1  collagen type XVII alpha 1 chain  Col17a1  collagen, type XVII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Col17a1  collagen, type XVII, alpha 1  Col17a1_predicted  procollagen, type XVII, alpha 1 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-12 Col17a1_predicted  procollagen, type XVII, alpha 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED