Stab1 (stabilin 1) - Rat Genome Database
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Gene: Stab1 (stabilin 1) Rattus norvegicus
Analyze
Symbol: Stab1
Name: stabilin 1
RGD ID: 2324745
Description: Predicted to have low-density lipoprotein particle binding activity; low-density lipoprotein particle receptor activity; and scavenger receptor activity. Predicted to be involved in cell-cell signaling; defense response to bacterium; and negative regulation of angiogenesis. Predicted to localize to integral component of plasma membrane. Orthologous to human STAB1 (stabilin 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,3',4,4',5-pentachlorobiphenyl.
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOC100363145; LOC290559; stabilin-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
mRatBN7.2166,330,435 - 6,360,934 (-)NCBI
Rnor_6.0 Ensembl167,222,067 - 7,250,924 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0167,220,434 - 7,250,934 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0167,149,003 - 7,179,503 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,567,583 - 6,597,972 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1166,567,700 - 6,598,257 (-)NCBI
Celera168,827,983 - 8,858,792 (+)NCBICelera
Cytogenetic Map16p16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:12077138   PMID:15572036  


Genomics

Comparative Map Data
Stab1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2166,330,435 - 6,360,934 (-)NCBI
Rnor_6.0 Ensembl167,222,067 - 7,250,924 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0167,220,434 - 7,250,934 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0167,149,003 - 7,179,503 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4166,567,583 - 6,597,972 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1166,567,700 - 6,598,257 (-)NCBI
Celera168,827,983 - 8,858,792 (+)NCBICelera
Cytogenetic Map16p16NCBI
STAB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl352,495,338 - 52,524,495 (+)EnsemblGRCh38hg38GRCh38
GRCh38352,495,338 - 52,524,496 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37352,529,354 - 52,558,511 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36352,504,396 - 52,533,551 (+)NCBINCBI36hg18NCBI36
Build 34352,504,439 - 52,533,540NCBI
Celera352,508,595 - 52,537,970 (+)NCBI
Cytogenetic Map3p21.1NCBI
HuRef352,591,899 - 52,621,386 (+)NCBIHuRef
CHM1_1352,481,711 - 52,510,878 (+)NCBICHM1_1
Stab1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391430,860,974 - 30,890,616 (-)NCBIGRCm39mm39
GRCm39 Ensembl1430,860,970 - 30,890,598 (-)Ensembl
GRCm381431,139,017 - 31,168,651 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1431,139,013 - 31,168,641 (-)EnsemblGRCm38mm10GRCm38
MGSCv371431,952,203 - 31,981,827 (-)NCBIGRCm37mm9NCBIm37
MGSCv361429,968,026 - 29,997,581 (-)NCBImm8
Celera1427,397,577 - 27,427,203 (-)NCBICelera
Cytogenetic Map14BNCBI
Stab1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554302,491,974 - 2,518,063 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554302,491,960 - 2,518,063 (+)NCBIChiLan1.0ChiLan1.0
STAB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1353,665,387 - 53,694,138 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl353,665,386 - 53,694,139 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0352,437,378 - 52,466,143 (+)NCBIMhudiblu_PPA_v0panPan3
STAB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2037,249,746 - 37,276,535 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12037,249,744 - 37,276,642 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Stab1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364733,333,988 - 3,363,256 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
STAB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1334,631,693 - 34,664,420 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11334,630,448 - 34,659,371 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21337,845,303 - 37,872,110 (+)NCBISscrofa10.2Sscrofa10.2susScr3
STAB1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12213,862,105 - 13,892,199 (+)NCBI
ChlSab1.1 Ensembl2213,870,551 - 13,896,970 (+)Ensembl
Stab1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248224,683,955 - 4,711,161 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16110660736Rat
1600369Hcas8Hepatocarcinoma susceptibility QTL 8liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)16124228366Rat
631830Alc7Alcohol consumption QTL 72.9consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16127556253Rat
634355Rends4Renal damage susceptibility QTL 40.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)16127556253Rat
1582235Insul8Insulin level QTL 83.30.0063blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)16127556253Rat
9590151Scort8Serum corticosterone level QTL 88.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)16131816439Rat
2302380Slep6Serum leptin concentration QTL 63.36blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16133160624Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16134465490Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16141240937Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16141240937Rat
631561Hcuc2Hepatic copper content QTL 22.8hepatic copper amount (VT:0003065)liver total copper weight (CMO:0001507)16141240957Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)1624459345244593Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)16109005486162972Rat
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16134074146340741Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)16155018749247447Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)16155018763210301Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)16155018763210301Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)16155018763210301Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)16155018763210301Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16172829746728297Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)16329668817464293Rat
1300133Rf24Renal function QTL 243.64blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)16413635523105837Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16413635545905331Rat
737825Alc13Alcohol consumption QTL 134.5consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380218360147Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380245905331Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16501380245905331Rat
61338Bp23Blood pressure QTL 234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16501380250013802Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16501380250169318Rat
61405Niddm6Non-insulin dependent diabetes mellitus QTL 63.660.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)16501380252144919Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16501380264012784Rat
61372Bp40Blood pressure QTL 402.2blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)16509870419398181Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:142
Count of miRNA genes:116
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000025394
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 23 5 4 12 4 8 16 29 1
Low 3 20 52 37 7 37 8 11 66 19 12 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025394   ⟹   ENSRNOP00000025394
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl167,222,067 - 7,250,924 (-)Ensembl
RefSeq Acc Id: XM_006222122   ⟹   XP_006222184
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera168,827,984 - 8,858,792 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222123   ⟹   XP_006222185
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera168,827,983 - 8,858,792 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006222125   ⟹   XP_006222187
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Celera168,827,984 - 8,858,792 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008771053   ⟹   XP_008769275
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,330,435 - 6,360,933 (-)NCBI
Rnor_6.0167,220,434 - 7,250,934 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771054   ⟹   XP_008769276
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,330,435 - 6,360,934 (-)NCBI
Rnor_6.0167,220,434 - 7,250,934 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771055   ⟹   XP_008769277
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,330,435 - 6,360,933 (-)NCBI
Rnor_6.0167,220,434 - 7,250,934 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039095096   ⟹   XP_038951024
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,330,435 - 6,360,934 (-)NCBI
RefSeq Acc Id: XM_039095097   ⟹   XP_038951025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,330,435 - 6,360,933 (-)NCBI
RefSeq Acc Id: XM_039095098   ⟹   XP_038951026
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,331,569 - 6,360,934 (-)NCBI
RefSeq Acc Id: XM_039095100   ⟹   XP_038951028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,338,470 - 6,360,934 (-)NCBI
RefSeq Acc Id: XR_005494942
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,331,785 - 6,360,934 (-)NCBI
RefSeq Acc Id: XR_005494943
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2166,333,256 - 6,360,934 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_006222184   ⟸   XM_006222122
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006222185   ⟸   XM_006222123
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006222187   ⟸   XM_006222125
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008769277   ⟸   XM_008771055
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008769276   ⟸   XM_008771054
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008769275   ⟸   XM_008771053
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000025394   ⟸   ENSRNOT00000025394
RefSeq Acc Id: XP_038951024   ⟸   XM_039095096
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038951025   ⟸   XM_039095097
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038951026   ⟸   XM_039095098
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038951028   ⟸   XM_039095100
- Peptide Label: isoform X7
Protein Domains
EGF-like   FAS1   Link

Transcriptome

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

Promoters
RGD ID:13699925
Promoter ID:EPDNEW_R10448
Type:single initiation site
Name:Stab1_1
Description:stabilin 1
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_6.0167,250,922 - 7,250,982EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
16 7222463 7222464 G A snv SR/JrHsd (MCW), F344/NRrrc (MCW), F344/NCrl (RGD), WAG/Rij (RGD), LN/MavRrrc (RGD), SHRSP/Gcrc (RGD), SR/JrHsd (RGD), LH/MavRrrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2324745 AgrOrtholog
Ensembl Genes ENSRNOG00000018434 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000025394 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000025394 UniProtKB/TrEMBL
Gene3D-CATH 2.30.180.10 UniProtKB/TrEMBL
  3.10.100.10 UniProtKB/TrEMBL
InterPro C-type_lectin-like UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
  EGF-like_Ca-bd_dom UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  EGF_dom_MSP1-like UniProtKB/TrEMBL
  EGF_laminin UniProtKB/TrEMBL
  FAS1_dom_sf UniProtKB/TrEMBL
  FAS1_domain UniProtKB/TrEMBL
  Link UniProtKB/TrEMBL
NCBI Gene 100363145 ENTREZGENE
Pfam EGF_3 UniProtKB/TrEMBL
  Fasciclin UniProtKB/TrEMBL
PhenoGen Stab1 PhenoGen
PROSITE EGF_1 UniProtKB/TrEMBL
  EGF_2 UniProtKB/TrEMBL
  EGF_3 UniProtKB/TrEMBL
  FAS1 UniProtKB/TrEMBL
  LINK_2 UniProtKB/TrEMBL
SMART EGF UniProtKB/TrEMBL
  EGF_CA UniProtKB/TrEMBL
  EGF_Lam UniProtKB/TrEMBL
  FAS1 UniProtKB/TrEMBL
Superfamily-SCOP BIgH3_FAS1 UniProtKB/TrEMBL
  C-type_lectin_fold UniProtKB/TrEMBL
UniProt D3ZWH1_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-08-30 LOC100363145  stabilin 1  Stab1  stabilin 1  Data Merged 737654 APPROVED
2012-08-30 Stab1  stabilin 1  LOC100363145  stabilin 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-12 LOC100363145  stabilin 1      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Stab1  stabilin 1   Stab1_predicted  stabilin 1 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Stab1_predicted  stabilin 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED