UCcg10011_47, UCcg10011_47 (genetic_marker) gossypium spp

Marker Overview
NameUCD_cg10011_47
AliasUCcg10011_47
dbSNP IDN/A
TypeSNP
SNP AllelesT/A
5' Flanking SequenceAATCGATGCCAAAAGTATGGACCAAAGCAC
3' Flanking SequenceACAATGGTGGGCGTCCTGTTTTGTCTCCCC
SpeciesGossypium spp.
Source TypeEST 3' end
Primer 1cg10011_F: GAAATTGGCTAAGGATGGCA
Primer 2cg10011_R: CCCAAACAAGTGAGAAAATCG
Primer 3cg10011_F: GAAATTGGCTAAGGATGGCA
Primer 4cg10011_R: CCCAAACAAGTGAGAAAATCG
Publication[view all]
ContactVan Deynze, Allen
CommentPrimer data obtained in 2010
Contact
NameDetails
Van Deynze, Allen
Description:Deployment of moloecular markers in breding and breeding systems. ; Gene Flow and transgenics
First name:Allen
Last name:Van Deynze
Title:Biotechnology Specialist
Institution:University of California
Address:1 Shields Ave, Davis, CA 95616
Country:United States
Email:avandeynze@ucdavis.edu
Phone:530-754-6444
Last update:20-Feb-2007
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
CM018222.1chromosomeCM018222.1:5648379..5648439 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018209.1chromosomeCM018209.1:5962153..5962213 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_08chromosomeD5_08:5508773..5508832 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_08chromosomeKI_08:4409576..4409636 +Gossypioides kirkii genome ISU_v3n/a
Chr08_CRI-A2_v1.0.a1chromosomeChr08_CRI-A2_v1.0.a1:6797125..6797185 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_08chromosomeD10_08:56892486..56892546 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016621.1chromosomeCM016621.1:135635985..135636045 -Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr4chromosomeDt_chr4:30992236..30992296 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr1chromosomeAt_chr1:567252..567312 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D08chromosomeD08:5699189..5699249 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A08chromosomeA08:5563709..5563769 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D08chromosomeGhir_D08:5743511..5743571 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A08chromosomeGhir_A08:6044716..6044776 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D08chromosomeD08:5490717..5490777 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A08chromosomeA08:5992710..5992770 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D08chromosomeD08:5190482..5190542 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A08chromosomeA08:6408499..6408559 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D08chromosomeD08:5808480..5808540 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A08chromosomeA08:5989593..5989653 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D08chromosomeGbar_D08:5775974..5776034 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A08chromosomeGbar_A08:6320093..6320153 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D08chromosomeD08:5889366..5889426 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A08chromosomeA08:6093941..6094001 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017630.1chromosomeCM017630.1:5897870..5897930 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017617.1chromosomeCM017617.1:6263632..6263692 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017656.1chromosomeCM017656.1:6144625..6144685 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017643.1chromosomeCM017643.1:6578101..6578161 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017708.1chromosomeCM017708.1:5740742..5740802 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017695.1chromosomeCM017695.1:6120751..6120811 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D08chromosomeD08:5918459..5918519 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A08chromosomeA08:6507107..6507167 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr08chromosomeChr08:7018436..7018496 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr08chromosomeChr08:7273341..7273401 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr08chromosomeChr08:5510985..5511045 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_08chromosomeB_08:7372291..7372351 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr04chromosomeChr04:5534153..5534213 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr_04chromosomeChr_04:4793508..4793568 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr04chromosomeChr04:5631273..5631333 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr04chromosomeChr04:4994243..4994303 +Gossypium aridum (D4) genome ISU_v1n/a
Chr04_3470591chromosomeChr04_3470591:10079..10139 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr04chromosomeChr04:4783733..4783793 +Gossypium lobatum (D7) genome ISU_v1n/a
E08chromosomeE08:8768354..8768414 -Gossypium stocksii (E1) genome NSF_v1n/a
F08chromosomeF08:5659893..5659953 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr08chromosomeChr08:190262573..190262633 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr04chromosomeUCD_cg10011_47:1..61 .
Chr04:5514314..5514374 +		n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1TM-1 x 3-79, RIL (2012)AD_ch24_Dt.08N/A6.48UCcg10011_47View
2TM-1 x 3-79, RIL (2014)AD_ch24_Dt.08N/A10.4UCcg10011_47View
3TM-1 x 3-79, RIL (2012.v3)AD_ch24_Dt.08N/A10.42UCcg10011_47View
Sequence
>UCD_cg10011_47 ID=UCD_cg10011_47; Name=UCD_cg10011_47; organism=Gossypium spp.; type=genetic_marker; length=65bp
AATCGATGCCAAAAGTATGGACCAAAGCAC[A/T]ACAATGGTGGGCGTC
CTGTTTTGTCTCCCC