Ssbp3 (single stranded DNA binding protein 3) - Rat Genome Database

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Gene: Ssbp3 (single stranded DNA binding protein 3) Rattus norvegicus
Analyze
Symbol: Ssbp3
Name: single stranded DNA binding protein 3
RGD ID: 621502
Description: Predicted to have transcription coactivator activity. Predicted to be involved in several processes, including head morphogenesis; nervous system development; and positive regulation of anterior head development. Predicted to localize to nucleus and transcription regulator complex. Orthologous to human SSBP3 (single stranded DNA binding protein 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC102549605; MGC124589; sequence-specific single-stranded-DNA-binding protein; single-stranded DNA-binding protein 3; Ssdp; Ssdp3; uncharacterized LOC102549605
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
mRatBN7.25121,691,370 - 121,828,035 (+)NCBI
Rnor_6.0 Ensembl5126,511,350 - 126,648,661 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05126,511,339 - 126,649,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05130,364,154 - 130,500,627 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45127,987,980 - 128,127,771 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15127,993,205 - 128,132,997 (+)NCBI
Celera5120,438,879 - 120,575,397 (+)NCBICelera
Cytogenetic Map5q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:15857913   PMID:19323994   PMID:24029230   PMID:26494787  


Genomics

Comparative Map Data
Ssbp3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25121,691,370 - 121,828,035 (+)NCBI
Rnor_6.0 Ensembl5126,511,350 - 126,648,661 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.05126,511,339 - 126,649,830 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.05130,364,154 - 130,500,627 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45127,987,980 - 128,127,771 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15127,993,205 - 128,132,997 (+)NCBI
Celera5120,438,879 - 120,575,397 (+)NCBICelera
Cytogenetic Map5q34NCBI
SSBP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl154,225,433 - 54,413,479 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl154,225,432 - 54,413,479 (-)EnsemblGRCh38hg38GRCh38
GRCh38154,225,432 - 54,413,479 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37154,691,105 - 54,872,067 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36154,464,783 - 54,644,680 (-)NCBINCBI36hg18NCBI36
Build 34154,404,615 - 54,583,917NCBI
Celera152,979,826 - 53,159,767 (-)NCBI
Cytogenetic Map1p32.3NCBI
HuRef152,806,513 - 52,987,387 (-)NCBIHuRef
CHM1_1154,807,651 - 54,988,420 (-)NCBICHM1_1
Ssbp3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394106,768,667 - 106,906,891 (+)NCBIGRCm39mm39
GRCm39 Ensembl4106,767,898 - 106,906,891 (+)Ensembl
GRCm384106,911,470 - 107,049,694 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4106,910,701 - 107,049,694 (+)EnsemblGRCm38mm10GRCm38
MGSCv374106,584,075 - 106,722,299 (+)NCBIGRCm37mm9NCBIm37
MGSCv364106,409,402 - 106,547,626 (+)NCBImm8
Celera4105,272,425 - 105,410,615 (+)NCBICelera
Cytogenetic Map4C7NCBI
Ssbp3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554644,901,151 - 5,047,656 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554644,901,150 - 5,049,341 (+)NCBIChiLan1.0ChiLan1.0
SSBP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1155,094,800 - 55,281,039 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl155,094,820 - 55,272,207 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0153,501,656 - 53,680,682 (-)NCBIMhudiblu_PPA_v0panPan3
SSBP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1554,690,632 - 54,826,691 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl554,662,840 - 54,824,960 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha554,729,165 - 54,893,490 (+)NCBI
ROS_Cfam_1.0554,849,788 - 55,013,185 (+)NCBI
UMICH_Zoey_3.1554,844,717 - 55,009,418 (+)NCBI
UNSW_CanFamBas_1.0554,734,421 - 54,898,735 (+)NCBI
UU_Cfam_GSD_1.0555,123,610 - 55,288,431 (+)NCBI
Ssbp3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505868,458,512 - 68,614,243 (-)NCBI
SpeTri2.0NW_0049365226,802,057 - 6,957,640 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SSBP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6157,911,651 - 158,081,420 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16157,911,583 - 158,081,478 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SSBP3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12078,528,630 - 78,708,518 (+)NCBI
Vero_WHO_p1.0NW_02366603338,577,763 - 38,758,509 (-)NCBI
Ssbp3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624934161,323 - 313,621 (+)NCBI

Position Markers
AU046696  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05126,590,714 - 126,590,876NCBIRnor6.0
Rnor_5.05130,442,359 - 130,442,521UniSTSRnor5.0
RGSC_v3.45128,068,368 - 128,068,530UniSTSRGSC3.4
Celera5120,517,973 - 120,518,135UniSTS
Cytogenetic Map5q34UniSTS
RH130317  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.05126,648,624 - 126,648,799NCBIRnor6.0
Rnor_5.05130,499,421 - 130,499,596UniSTSRnor5.0
RGSC_v3.45128,127,711 - 128,127,886UniSTSRGSC3.4
Celera5120,575,337 - 120,575,512UniSTS
RH 3.4 Map5807.3UniSTS
Cytogenetic Map5q34UniSTS
AU047859  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_5.05130,420,058 - 130,420,280NCBIRnor5.0
RGSC_v3.45128,046,344 - 128,046,565UniSTSRGSC3.4
Celera5120,495,899 - 120,496,136UniSTS
Cytogenetic Map5q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531926122136640934Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535788756147487820Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540777918154732375Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)544404276134502294Rat
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)547745646167946134Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)551418671147487820Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)556991667137729065Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)560072951133313852Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)561086525149030144Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)561612600168109659Rat
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)565696672129038896Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)571552569157225114Rat
1298070Scl18Serum cholesterol level QTL 183.7blood LDL cholesterol amount (VT:0000181)calculated plasma low density lipoprotein cholesterol level (CMO:0001245)583424556128424556Rat
1598846Bp293Blood pressure QTL 2933.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)583424556128424556Rat
1598859Cm66Cardiac mass QTL 662heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)583424556128424556Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)584963058173504662Rat
1298086Bp156Blood pressure QTL 156arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)589502294134502294Rat
7411582Foco3Food consumption QTL 37.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)591585539136585539Rat
7411601Foco12Food consumption QTL 1219.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)591585539136585539Rat
7411564Bw135Body weight QTL 1350.001body mass (VT:0001259)body weight gain (CMO:0000420)591585539136585539Rat
6903316Bw113Body weight QTL 11320.0103body mass (VT:0001259)body weight (CMO:0000012)591884213136884213Rat
1358889Bp261Blood pressure QTL 2612.86arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)593037304133313852Rat
1358909Kidm25Kidney mass QTL 251.87kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)593037304133313852Rat
631527Tls1T-lymphoma susceptibility QTL 100.001thymus integrity trait (VT:0010555)post-insult time to onset of T-cell lymphoma (CMO:0001907)593273130138273130Rat
61452Ciaa5CIA Autoantibody QTL 53.5blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)597921932149030144Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)5100723739153577831Rat
2317753Glom24Glomerulus QTL 243.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)5101265591141912026Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)5102945579154732228Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5107119214152119214Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5111278451156278451Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5112279412157279412Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5112279412157279412Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5112279412157279412Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5112279412157279412Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5112279412157279412Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5114140832159140832Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5114140832159140832Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5116767924161767924Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5116767924161767924Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5116767924161767924Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5116767924161767924Rat
7794739Bp372Blood pressure QTL 3720.0058arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5122679716130167412Rat
1582230Bw78Body weight QTL 783.20.0016epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)5123852489133313852Rat
1581510Cm54Cardiac mass QTL 543.40.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)5125455818149568944Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5125455818157225114Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:36
Count of miRNA genes:35
Interacting mature miRNAs:35
Transcripts:ENSRNOT00000011408
Prediction methods:Miranda, Rnahybrid
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 3 35 48 33 19 33 73 29 41 11
Low 8 9 8 8 8 11 1 6 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_053358 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238532 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238533 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238534 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238535 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238537 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238538 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006238539 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593663 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110867 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110869 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110870 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110871 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110872 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039110873 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC122593 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF121893 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY724490 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC107666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ230168 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000011408   ⟹   ENSRNOP00000011408
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl5126,511,350 - 126,648,661 (+)Ensembl
RefSeq Acc Id: NM_053358   ⟹   NP_445810
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,393 - 121,828,015 (+)NCBI
Rnor_6.05126,511,350 - 126,648,684 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
RGSC_v3.45127,987,980 - 128,127,771 (+)RGD
Celera5120,438,879 - 120,575,397 (+)RGD
Sequence:
RefSeq Acc Id: XM_006238532   ⟹   XP_006238594
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,378 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238533   ⟹   XP_006238595
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,380 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238534   ⟹   XP_006238596
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,380 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238535   ⟹   XP_006238597
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,382 - 121,828,031 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238536   ⟹   XP_006238598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,380 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238537   ⟹   XP_006238599
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,382 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238538   ⟹   XP_006238600
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,382 - 121,828,035 (+)NCBI
Rnor_6.05126,511,339 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006238539   ⟹   XP_006238601
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.05126,600,760 - 126,649,830 (+)NCBI
Rnor_5.05130,364,154 - 130,500,627 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017593663   ⟹   XP_017449152
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,765,459 - 121,828,035 (+)NCBI
Rnor_6.05126,585,536 - 126,649,830 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039110866   ⟹   XP_038966794
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,691,370 - 121,825,778 (+)NCBI
RefSeq Acc Id: XM_039110867   ⟹   XP_038966795
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,766,998 - 121,828,035 (+)NCBI
RefSeq Acc Id: XM_039110869   ⟹   XP_038966797
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,728,992 - 121,828,035 (+)NCBI
RefSeq Acc Id: XM_039110870   ⟹   XP_038966798
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,735,114 - 121,828,031 (+)NCBI
RefSeq Acc Id: XM_039110871   ⟹   XP_038966799
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,733,593 - 121,828,035 (+)NCBI
RefSeq Acc Id: XM_039110872   ⟹   XP_038966800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,735,417 - 121,828,031 (+)NCBI
RefSeq Acc Id: XM_039110873   ⟹   XP_038966801
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25121,810,255 - 121,828,035 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_445810   ⟸   NM_053358
- Sequence:
RefSeq Acc Id: XP_006238594   ⟸   XM_006238532
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006238596   ⟸   XM_006238534
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_006238595   ⟸   XM_006238533
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006238598   ⟸   XM_006238536
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006238597   ⟸   XM_006238535
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_006238600   ⟸   XM_006238538
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006238599   ⟸   XM_006238537
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_006238601   ⟸   XM_006238539
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_017449152   ⟸   XM_017593663
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: ENSRNOP00000011408   ⟸   ENSRNOT00000011408
RefSeq Acc Id: XP_038966794   ⟸   XM_039110866
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038966797   ⟸   XM_039110869
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038966799   ⟸   XM_039110871
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038966798   ⟸   XM_039110870
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038966800   ⟸   XM_039110872
- Peptide Label: isoform X14
RefSeq Acc Id: XP_038966795   ⟸   XM_039110867
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038966801   ⟸   XM_039110873
- Peptide Label: isoform X15
Protein Domains
LisH

Transcriptome

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

Promoters
RGD ID:13693886
Promoter ID:EPDNEW_R4411
Type:multiple initiation site
Name:Ssbp3_1
Description:single stranded DNA binding protein 3
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_6.05126,511,336 - 126,511,396EPDNEW

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:621502 AgrOrtholog
Ensembl Genes ENSRNOG00000007920 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000011408 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011408 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7936459 IMAGE-MGC_LOAD
InterPro LisH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSDP_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:84354 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124589 IMAGE-MGC_LOAD
NCBI Gene 84354 ENTREZGENE
PhenoGen Ssbp3 PhenoGen
PRINTS SSDNABINDING UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE LISH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART LisH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Q3B7C9_RAT UniProtKB/TrEMBL
  Q9R050 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Ssbp3  single stranded DNA binding protein 3  LOC102549605  uncharacterized LOC102549605  Data Merged 737654 PROVISIONAL
2013-12-17 LOC102549605  uncharacterized LOC102549605      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-11-17 Ssbp3  single stranded DNA binding protein 3  Ssdp3    Symbol updated 1299863 APPROVED
2004-04-22 Ssdp3  single stranded DNA binding protein 3  Ssdp  sequence-specific single-stranded-DNA-binding protein  Symbol and Name updated to reflect Human and Mouse nomenclature 625702 APPROVED
2002-08-07 Ssdp  sequence-specific single-stranded-DNA-binding protein      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_homology 80% homologous to the chicken gene 634142
gene_protein 361 amino acid protein with a mass of 37.7 kDa 634142