Col27a1 (collagen type XXVII alpha 1 chain) - Rat Genome Database

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Gene: Col27a1 (collagen type XXVII alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col27a1
Name: collagen type XXVII alpha 1 chain
RGD ID: 735115
Description: Predicted to be an extracellular matrix structural constituent. Predicted to be involved in extracellular matrix organization. Predicted to act upstream of or within growth plate cartilage chondrocyte development. Predicted to be part of fibrillar collagen trimer. Predicted to be active in extracellular matrix and extracellular space. Orthologous to human COL27A1 (collagen type XXVII alpha 1 chain); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: collagen alpha-1(XXVII) chain; collagen type XXVII proalpha 1 chain; collagen, type XXVII, alpha 1; procollagen, type XXVII, alpha 1
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
mRatBN7.2576,647,302 - 76,765,987 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl576,647,429 - 76,765,174 (+)Ensembl
Rnor_6.0579,054,004 - 79,172,442 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,055,521 - 79,170,765 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,168,893 - 83,286,676 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4580,198,078 - 80,316,354 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1580,203,190 - 80,321,467 (+)NCBI
Celera575,584,269 - 75,698,202 (+)NCBICelera
Cytogenetic Map5q24NCBI
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
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
3-chloropropane-1,2-diol  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aldrin  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
choline  (ISO)
copper(II) sulfate  (ISO)
Cuprizon  (EXP)
curcumin  (EXP)
cyclosporin A  (ISO)
dibutyl phthalate  (EXP)
dichloroacetic acid  (ISO)
dicrotophos  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
glycidol  (ISO)
L-methionine  (ISO)
leflunomide  (EXP)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
Nor-9-carboxy-delta9-THC  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium dichromate  (EXP)
sunitinib  (ISO)
tetrachloroethene  (ISO)
tetraphene  (ISO)
thioacetamide  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:17331945   PMID:22206015  


Genomics

Comparative Map Data
Col27a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2576,647,302 - 76,765,987 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl576,647,429 - 76,765,174 (+)Ensembl
Rnor_6.0579,054,004 - 79,172,442 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl579,055,521 - 79,170,765 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0583,168,893 - 83,286,676 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4580,198,078 - 80,316,354 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1580,203,190 - 80,321,467 (+)NCBI
Celera575,584,269 - 75,698,202 (+)NCBICelera
Cytogenetic Map5q24NCBI
COL27A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389114,154,098 - 114,312,511 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9114,155,537 - 114,312,511 (+)EnsemblGRCh38hg38GRCh38
GRCh379116,917,817 - 117,074,791 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369115,958,052 - 116,112,796 (+)NCBINCBI36hg18NCBI36
Build 349113,997,784 - 114,152,529NCBI
Celera987,566,107 - 87,720,603 (+)NCBI
Cytogenetic Map9q32NCBI
HuRef986,524,630 - 86,679,150 (+)NCBIHuRef
CHM1_19117,064,706 - 117,219,685 (+)NCBICHM1_1
T2T-CHM13v2.09126,354,203 - 126,511,655 (+)NCBI
Col27a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39463,132,246 - 63,253,228 (+)NCBIGRCm39mm39
GRCm39 Ensembl463,132,241 - 63,253,228 (+)Ensembl
GRCm38463,214,009 - 63,334,991 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl463,214,004 - 63,334,991 (+)EnsemblGRCm38mm10GRCm38
MGSCv37462,876,446 - 62,996,025 (+)NCBIGRCm37mm9NCBIm37
MGSCv36462,702,187 - 62,819,669 (+)NCBImm8
Celera461,872,330 - 61,991,872 (+)NCBICelera
Cytogenetic Map4B3NCBI
Col27a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495541913,289,006 - 13,411,118 (-)NCBIChiLan1.0ChiLan1.0
COL27A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19113,619,322 - 113,777,099 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9113,627,633 - 113,775,284 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0985,252,277 - 85,410,714 (+)NCBIMhudiblu_PPA_v0panPan3
COL27A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11168,413,101 - 68,548,408 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1168,420,263 - 68,546,947 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1166,815,437 - 66,950,500 (+)NCBI
ROS_Cfam_1.01169,536,838 - 69,671,970 (+)NCBI
UMICH_Zoey_3.11168,052,533 - 68,187,417 (+)NCBI
UNSW_CanFamBas_1.01168,083,568 - 68,228,679 (+)NCBI
UU_Cfam_GSD_1.01168,822,715 - 68,957,841 (+)NCBI
Col27a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947183,711,795 - 183,833,263 (+)NCBI
SpeTri2.0NW_0049364873,487,776 - 3,601,779 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL27A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1254,769,519 - 254,923,823 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11254,768,576 - 254,924,893 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21285,841,755 - 285,901,568 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL27A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11225,272,617 - 25,431,308 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1225,272,609 - 25,429,086 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603517,388,410 - 17,548,127 (+)NCBIVero_WHO_p1.0
Col27a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476020,861,505 - 20,979,826 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
BE116809  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2576,670,772 - 76,670,924 (+)MAPPERmRatBN7.2
Rnor_6.0579,078,669 - 79,078,820NCBIRnor6.0
Rnor_5.0583,192,917 - 83,193,068UniSTSRnor5.0
RGSC_v3.4580,220,946 - 80,221,097UniSTSRGSC3.4
Celera575,604,679 - 75,604,830UniSTS
RH 3.4 Map5578.5UniSTS
Cytogenetic Map5q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1598845Mcs14Mammary carcinoma susceptibility QTL 140.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)57636977680813390Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:92
Count of miRNA genes:71
Interacting mature miRNAs:74
Transcripts:ENSRNOT00000010333
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.


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 20 4 4 4 18 27 28 1
Low 3 23 53 37 19 37 5 7 56 8 6 10 5
Below cutoff 3 4 7 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010333   ⟹   ENSRNOP00000010333
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl576,647,429 - 76,765,174 (+)Ensembl
Rnor_6.0 Ensembl579,055,521 - 79,170,765 (+)Ensembl
RefSeq Acc Id: NM_198747   ⟹   NP_942042
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,647,594 - 76,764,308 (+)NCBI
Rnor_6.0579,055,521 - 79,170,765 (+)NCBI
Rnor_5.0583,168,893 - 83,286,676 (+)NCBI
RGSC_v3.4580,198,078 - 80,316,354 (+)RGD
Celera575,584,269 - 75,698,202 (+)RGD
Sequence:
RefSeq Acc Id: XM_006238245   ⟹   XP_006238307
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,647,304 - 76,765,987 (+)NCBI
Rnor_6.0579,054,725 - 79,172,442 (+)NCBI
Rnor_5.0583,168,893 - 83,286,676 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039109470   ⟹   XP_038965398
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,647,302 - 76,741,172 (+)NCBI
RefSeq Acc Id: XM_039109471   ⟹   XP_038965399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,686,821 - 76,765,159 (+)NCBI
RefSeq Acc Id: XM_039109472   ⟹   XP_038965400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,686,817 - 76,765,159 (+)NCBI
RefSeq Acc Id: XM_039109473   ⟹   XP_038965401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,704,824 - 76,765,159 (+)NCBI
RefSeq Acc Id: XR_005504388
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,647,302 - 76,750,810 (+)NCBI
RefSeq Acc Id: XR_005504389
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2576,647,302 - 76,733,174 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_942042   ⟸   NM_198747
- Peptide Label: precursor
- UniProtKB: Q80ZF0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006238307   ⟸   XM_006238245
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000010333   ⟸   ENSRNOT00000010333
RefSeq Acc Id: XP_038965398   ⟸   XM_039109470
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038965400   ⟸   XM_039109472
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965399   ⟸   XM_039109471
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965401   ⟸   XM_039109473
- Peptide Label: isoform X4
Protein Domains
Collagen-like   Fibrillar collagen NC1   Laminin G-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80ZF0-F1-model_v2 AlphaFold Q80ZF0 1-1855 view protein structure

Transcriptome

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


Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 79169137 79169138 A G snv SHR/NHsd (RGD)


Assembly: Rnor_5.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 83283371 83283372 A G snv SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 80314726 80314727 A G snv SR/JrHsd (MCW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:735115 AgrOrtholog
BioCyc Gene G2FUF-41074 BioCyc
Ensembl Genes ENSRNOG00000007657 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010333 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010333 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Collagen UniProtKB/Swiss-Prot
  ConA-like_dom_sf UniProtKB/Swiss-Prot
  Fib_collagen_C UniProtKB/Swiss-Prot
  Laminin_G UniProtKB/Swiss-Prot
KEGG Report rno:298101 UniProtKB/Swiss-Prot
NCBI Gene 298101 ENTREZGENE
Pfam COLFI UniProtKB/Swiss-Prot
  Collagen UniProtKB/Swiss-Prot
PhenoGen Col27a1 PhenoGen
PROSITE NC1_FIB UniProtKB/Swiss-Prot
SMART COLFI UniProtKB/Swiss-Prot
  TSPN UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49899 UniProtKB/Swiss-Prot
UniProt CORA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col27a1  collagen type XXVII alpha 1 chain  Col27a1  collagen, type XXVII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-10 Col27a1  collagen, type XXVII, alpha 1  Col27a1  procollagen, type XXVII, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Col27a1  procollagen, type XXVII, alpha 1    collagen, type XXVII, alpha 1  Name updated 1299863 APPROVED