Col25a1 (collagen type XXV alpha 1 chain) - Rat Genome Database
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Gene: Col25a1 (collagen type XXV alpha 1 chain) Rattus norvegicus
Analyze
Symbol: Col25a1
Name: collagen type XXV alpha 1 chain
RGD ID: 1590105
Description: Predicted to have several functions, including amyloid-beta binding activity; heparin binding activity; and identical protein binding activity. Predicted to be involved in axonogenesis involved in innervation and extracellular matrix organization. Predicted to localize to extracellular matrix; extracellular space; and integral component of plasma membrane. Human ortholog(s) of this gene implicated in congenital fibrosis of the extraocular muscles. Orthologous to human COL25A1 (collagen type XXV alpha 1 chain); INTERACTS WITH 17alpha-ethynylestradiol; bisphenol A; valproic acid.
Type: protein-coding
RefSeq Status: MODEL
Also known as: collagen alpha-1(XXV) chain; collagen, type XXV, alpha 1; LOC687064; similar to collagen, type XXV, alpha 1 isoform 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22218,755,152 - 219,154,348 (+)NCBI
Rnor_6.0 Ensembl2235,596,123 - 235,715,057 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02235,515,364 - 235,705,448 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02254,067,074 - 254,256,966 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2211,033,464 - 211,420,527 (+)NCBICelera
Cytogenetic Map2q43NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11927537   PMID:15215182   PMID:15522881   PMID:15615705   PMID:24453327  


Genomics

Comparative Map Data
Col25a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22218,755,152 - 219,154,348 (+)NCBI
Rnor_6.0 Ensembl2235,596,123 - 235,715,057 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02235,515,364 - 235,705,448 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02254,067,074 - 254,256,966 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2211,033,464 - 211,420,527 (+)NCBICelera
Cytogenetic Map2q43NCBI
COL25A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4108,808,725 - 109,302,752 (-)EnsemblGRCh38hg38GRCh38
GRCh384108,808,725 - 109,302,737 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374109,731,877 - 110,223,799 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh374109,729,881 - 110,223,814 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364109,954,421 - 110,443,248 (-)NCBINCBI36hg18NCBI36
Celera4107,029,732 - 107,518,680 (-)NCBI
Cytogenetic Map4q25NCBI
HuRef4105,464,237 - 105,956,593 (-)NCBIHuRef
CHM1_14109,708,453 - 110,200,435 (-)NCBICHM1_1
Col25a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393129,973,992 - 130,393,533 (+)NCBIGRCm39mm39
GRCm383130,180,358 - 130,599,884 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3130,131,501 - 130,599,877 (+)EnsemblGRCm38mm10GRCm38
MGSCv373129,883,796 - 130,299,335 (+)NCBIGRCm37mm9NCBIm37
MGSCv363130,170,033 - 130,585,572 (+)NCBImm8
Celera3136,700,003 - 137,111,818 (+)NCBICelera
Cytogenetic Map3G3NCBI
Col25a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955496839,561 - 1,250,614 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955496839,474 - 1,255,107 (+)NCBIChiLan1.0ChiLan1.0
COL25A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14111,885,022 - 112,378,687 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4111,886,313 - 112,378,062 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04101,311,291 - 101,808,618 (-)NCBIMhudiblu_PPA_v0panPan3
COL25A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl3229,124,996 - 29,567,481 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.13229,119,875 - 29,567,994 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Col25a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936563105,551 - 557,682 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
COL25A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl8112,867,073 - 113,334,115 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.18112,866,597 - 113,335,765 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.28121,286,327 - 121,453,787 (+)NCBISscrofa10.2Sscrofa10.2susScr3
COL25A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1756,730,456 - 57,229,587 (-)NCBI
Col25a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624830440,028 - 842,635 (+)NCBI

Position Markers
D2Rat156  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02235,570,769 - 235,570,970NCBIRnor6.0
Rnor_5.02254,122,117 - 254,122,318UniSTSRnor5.0
RGSC_v3.42227,923,955 - 227,924,156UniSTSRGSC3.4
RGSC_v3.42227,923,954 - 227,924,156RGDRGSC3.4
RGSC_v3.12227,910,694 - 227,910,896RGD
Celera2211,278,782 - 211,278,983UniSTS
SHRSP x BN Map288.6198RGD
SHRSP x BN Map288.6198UniSTS
FHH x ACI Map2101.7199RGD
D2Ulb14  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02234,704,354 - 234,704,524NCBIRnor6.0
Rnor_5.02254,020,469 - 254,020,639UniSTSRnor5.0
RGSC_v3.42227,824,121 - 227,824,291UniSTSRGSC3.4
Celera2211,180,284 - 211,180,454UniSTS
Cytogenetic Map2 RGD
D2Ulb15  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02234,704,354 - 234,704,642NCBIRnor6.0
Rnor_5.02254,020,469 - 254,020,757UniSTSRnor5.0
RGSC_v3.42227,824,121 - 227,824,409UniSTSRGSC3.4
Celera2211,180,284 - 211,180,572UniSTS
Cytogenetic Map2 RGD
AW530842  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02230,542,409 - 230,542,591NCBIRnor6.0
Rnor_5.02249,895,032 - 249,895,214UniSTSRnor5.0
RGSC_v3.42227,710,125 - 227,710,307UniSTSRGSC3.4
Celera2211,087,343 - 211,087,525UniSTS
RH 3.4 Map21547.6UniSTS
AU047490  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera2211,109,025 - 211,109,246UniSTS
D17S802  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.03155,184,712 - 155,185,467UniSTSRnor5.0
RGSC_v3.4204,369,896 - 4,370,394UniSTSRGSC3.4
RGSC_v3.42227,893,021 - 227,893,896UniSTSRGSC3.4
Celera205,968,749 - 5,969,247UniSTS
Celera2211,247,899 - 211,248,773UniSTS
Cytogenetic Map3q41UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631203Gluco14Glucose level QTL 140.0001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)2221880206235570970Rat
1331734Bp204Blood pressure QTL 2043.61192arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2181990297240020001Rat
1331767Hrtrt12Heart rate QTL 123.373heart pumping trait (VT:2000009)heart rate (CMO:0000002)2235289967257110527Rat
1298075Scl17Serum cholesterol level QTL 173.4blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)2228712271266435125Rat
1331794Bp202Blood pressure QTL 2023.66819arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2147122993240020001Rat
1331805Cm29Cardiac mass QTL 293.50746heart mass (VT:0007028)heart wet weight (CMO:0000069)2147122993240020001Rat
1581499Esta2Estrogen-induced thymic atrophy QTL 2thymus mass (VT:0004954)thymus wet weight (CMO:0000855)2204585642243689611Rat
2317885Alcrsp28Alcohol response QTL 282.10.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2229793522266435125Rat
738013Alc15Alcohol consumption QTL 154.10.00022consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)2199380312244380312Rat
631514Scl8Serum cholesterol level QTL84.4blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)2231621666266435125Rat
1300126Bp175Blood pressure QTL 1753.46arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2229606682264899009Rat
1302789Stl26Serum triglyceride level QTL 263.10.0035blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)2218957047240977220Rat
1641891Alcrsp17Alcohol response QTL 17response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557254121739Rat
1641925Alcrsp2Alcohol response QTL 2response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)2155965557237742948Rat
1598813Memor9Memory QTL 92.7exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)2214870793251212353Rat
1598835Anxrr18Anxiety related response QTL 182.98body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)2217743855262743855Rat
2301408Kidm36Kidney mass QTL 360.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)2205583921243562243Rat
2298479Eau5Experimental allergic uveoretinitis QTL 50.0021uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)2217498545254132424Rat
2300189Bmd48Bone mineral density QTL 485.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)2194378622239378622Rat
1358356Srcrt1Stress Responsive Cort QTL13.66blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)2175403337239166203Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)283819608239166203Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266828236243550655Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)283819608243901375Rat
2299161Iddm33Insulin dependent diabetes mellitus QTL 332.98blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)2221488355254121739Rat
1549836Bss2Bone structure and strength QTL 27.5femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)2228712271266435125Rat
2306901Bp337Blood pressure QTL 3370.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2177680772243901375Rat
2313073Bmd75Bone mineral density QTL 754.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)2231224020254132424Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2200453324236318668Rat
1359031Bp275Blood pressure QTL 275arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2200453324236318668Rat
2317752Glom23Glomerulus QTL 233.6urine protein amount (VT:0005160)urine protein level (CMO:0000591)2208594330263179188Rat
61366Iddm3Insulin dependent diabetes mellitus QTL 34.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)2204585642249585642Rat
61398Bp50Blood pressure QTL 504.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2204585642249585642Rat
61417Cia10Collagen induced arthritis QTL 103.4joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)2194998627239998627Rat
8694435Bw166Body weight QTL 16614.080.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)2197253963242253963Rat
9589044Scfw1Subcutaneous fat weight QTL 15.80.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)2197253963242253963Rat
8694383Bw158Body weight QTL 1587.690.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)2197253963242253963Rat
7207490Bss111Bone structure and strength QTL 1116.4femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)2228712271266435125Rat
8662843Vetf9Vascular elastic tissue fragility QTL 92.05thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2169852670243026643Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)283754907237610852Rat
7207482Bss107Bone structure and strength QTL 1077femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)2228712271266435125Rat
7207484Bss108Bone structure and strength QTL 1085.3femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)2228712271266435125Rat
8694194Abfw1Abdominal fat weight QTL 111.70.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)2197253963242253963Rat
8693697Alc36Alcohol consumption QTL 3620.592drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)2233013605253626471Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)216679272245624402Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:221
Count of miRNA genes:148
Interacting mature miRNAs:165
Transcripts:ENSRNOT00000071463, ENSRNOT00000074816, ENSRNOT00000075728
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 6 4 4 42 5
Low 22 34 25 14 25 3 3 32 19 29 2 3
Below cutoff 3 17 17 12 5 12 5 6 6 6 8 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000071463   ⟹   ENSRNOP00000064468
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2235,596,907 - 235,711,272 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000074816   ⟹   ENSRNOP00000067665
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2235,596,123 - 235,715,057 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000075728   ⟹   ENSRNOP00000066571
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2235,596,907 - 235,711,272 (+)Ensembl
RefSeq Acc Id: XM_017591346   ⟹   XP_017446835
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02235,515,364 - 235,705,448 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596908   ⟹   XP_017452397
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,466 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596910   ⟹   XP_017452399
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,465 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596911   ⟹   XP_017452400
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,466 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596917   ⟹   XP_017452406
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,465 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596920   ⟹   XP_017452409
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,465 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596922   ⟹   XP_017452411
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,466 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596923   ⟹   XP_017452412
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,465 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596924   ⟹   XP_017452413
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,467 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596925   ⟹   XP_017452414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,466 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596927   ⟹   XP_017452416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,467 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596933   ⟹   XP_017452422
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,464 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596934   ⟹   XP_017452423
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,467 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596935   ⟹   XP_017452424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,467 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596936   ⟹   XP_017452425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,468 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596937   ⟹   XP_017452426
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,468 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596938   ⟹   XP_017452427
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,469 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596940   ⟹   XP_017452429
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,468 - 211,411,009 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596941   ⟹   XP_017452430
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,468 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596942   ⟹   XP_017452431
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,468 - 211,411,009 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596943   ⟹   XP_017452432
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,467 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017596944   ⟹   XP_017452433
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera2211,033,466 - 211,420,527 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039103837   ⟹   XP_038959765
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,155 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103838   ⟹   XP_038959766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,156 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103839   ⟹   XP_038959767
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,156 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103840   ⟹   XP_038959768
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,156 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103841   ⟹   XP_038959769
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,157 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103842   ⟹   XP_038959770
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,156 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103843   ⟹   XP_038959771
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,157 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103844   ⟹   XP_038959772
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,158 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103845   ⟹   XP_038959773
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,158 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103846   ⟹   XP_038959774
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,154 - 219,154,348 (+)NCBI
RefSeq Acc Id: XM_039103847   ⟹   XP_038959775
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22218,755,152 - 219,154,348 (+)NCBI
Reference Sequences
RefSeq Acc Id: XP_017452422   ⟸   XM_017596933
- Peptide Label: isoform X12
- Sequence:
RefSeq Acc Id: XP_017452399   ⟸   XM_017596910
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017452409   ⟸   XM_017596920
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017452406   ⟸   XM_017596917
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017452412   ⟸   XM_017596923
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_017452433   ⟸   XM_017596944
- Peptide Label: isoform X22
- Sequence:
RefSeq Acc Id: XP_017452397   ⟸   XM_017596908
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_017452414   ⟸   XM_017596925
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_017452411   ⟸   XM_017596922
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017452400   ⟸   XM_017596911
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_017452413   ⟸   XM_017596924
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017452416   ⟸   XM_017596927
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_017452423   ⟸   XM_017596934
- Peptide Label: isoform X13
- Sequence:
RefSeq Acc Id: XP_017452424   ⟸   XM_017596935
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017452432   ⟸   XM_017596943
- Peptide Label: isoform X21
- Sequence:
RefSeq Acc Id: XP_017452425   ⟸   XM_017596936
- Peptide Label: isoform X15
- Sequence:
RefSeq Acc Id: XP_017452426   ⟸   XM_017596937
- Peptide Label: isoform X16
- Sequence:
RefSeq Acc Id: XP_017452430   ⟸   XM_017596941
- Peptide Label: isoform X19
- Sequence:
RefSeq Acc Id: XP_017452429   ⟸   XM_017596940
- Peptide Label: isoform X18
- Sequence:
RefSeq Acc Id: XP_017452431   ⟸   XM_017596942
- Peptide Label: isoform X20
- Sequence:
RefSeq Acc Id: XP_017452427   ⟸   XM_017596938
- Peptide Label: isoform X17
- Sequence:
RefSeq Acc Id: XP_017446835   ⟸   XM_017591346
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000066571   ⟸   ENSRNOT00000075728
RefSeq Acc Id: ENSRNOP00000064468   ⟸   ENSRNOT00000071463
RefSeq Acc Id: ENSRNOP00000067665   ⟸   ENSRNOT00000074816
RefSeq Acc Id: XP_038959775   ⟸   XM_039103847
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038959774   ⟸   XM_039103846
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038959765   ⟸   XM_039103837
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038959768   ⟸   XM_039103840
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038959766   ⟸   XM_039103838
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038959770   ⟸   XM_039103842
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038959767   ⟸   XM_039103839
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038959769   ⟸   XM_039103841
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038959771   ⟸   XM_039103843
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038959772   ⟸   XM_039103844
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038959773   ⟸   XM_039103845
- Peptide Label: isoform X9

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1590105 AgrOrtholog
Ensembl Genes ENSRNOG00000050706 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064468 UniProtKB/TrEMBL
  ENSRNOP00000066571 UniProtKB/TrEMBL
  ENSRNOP00000067665 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000071463 UniProtKB/TrEMBL
  ENSRNOT00000074816 UniProtKB/TrEMBL
  ENSRNOT00000075728 UniProtKB/TrEMBL
InterPro Collagen UniProtKB/TrEMBL
NCBI Gene 687064 ENTREZGENE
Pfam Collagen UniProtKB/TrEMBL
PhenoGen Col25a1 PhenoGen
UniProt M0R513_RAT UniProtKB/TrEMBL
  M0RAM0_RAT UniProtKB/TrEMBL
  M0RDG5_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-07-27 Col25a1  collagen type XXV alpha 1 chain  Col25a1  collagen, type XXV, alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-16 Col25a1  collagen, type XXV, alpha 1  LOC687064  similar to collagen, type XXV, alpha 1 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC687064  similar to collagen, type XXV, alpha 1 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL