UCcg10004_824, UCcg10004_824 (genetic_marker) gossypium spp

Marker Overview
NameUCD_cg10004_824
AliasUCcg10004_824
dbSNP IDN/A
TypeSNP
SNP AllelesT/A
5' Flanking SequenceAGAGGTCCAAGAAGCGGAACAAGCCCACCT
3' Flanking SequenceGAAACTGCGTATGCAGAGGCTGATTAGTAA
SpeciesGossypium spp.
Source TypeEST 3' end
Primer 1cg10004_F: AGGTTTCTCTTGGGCTGGTT
Primer 2cg10004_R: TCCCATAACATCAGTTCCGA
Primer 3cg10004_F: AGGTTTCTCTTGGGCTGGTT
Primer 4cg10004_R: TCCCATAACATCAGTTCCGA
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
CM018227.1chromosomeCM018227.1:2355393..2355453 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_13chromosomeD5_13:2097979..2098039 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_13chromosomeKI_13:1471258..1471318 -Gossypioides kirkii genome ISU_v3n/a
Chr13_CRI-A2_v1.0.a1chromosomeChr13_CRI-A2_v1.0.a1:2930167..2930227 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_13chromosomeD10_13:2147082..2147142 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016618.1chromosomeCM016618.1:94156644..94156704 +Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr13chromosomeDt_chr13:54569335..54569395 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D13chromosomeD13:2449400..2449460 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D13chromosomeGhir_D13:2396533..2396593 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D13chromosomeD13:2279816..2279876 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D13chromosomeD13:2404512..2404572 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D13chromosomeD13:2427274..2427334 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D13chromosomeGbar_D13:2154469..2154529 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D13chromosomeD13:2170489..2170549 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017635.1chromosomeCM017635.1:2251480..2251540 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017661.1chromosomeCM017661.1:2466225..2466285 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017713.1chromosomeCM017713.1:2264202..2264262 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D13chromosomeD13:2506620..2506680 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr13chromosomeChr13:2865608..2865668 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr13chromosomeChr13:2762427..2762487 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr13chromosomeChr13:2106892..2106952 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_13chromosomeB_13:92284863..92284923 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr13chromosomeChr13:2208612..2208672 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr13chromosomechr13:2197751..2197811 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_13chromosomeChr_13:2415722..2415782 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr13chromosomeChr13:2408322..2408382 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr13chromosomeChr13:2348637..2348697 -Gossypium aridum (D4) genome ISU_v1n/a
Chr13chromosomeChr13:2357651..2357711 -Gossypium lobatum (D7) genome ISU_v1n/a
F13chromosomeF13:2382294..2382354 -Gossypium longicalyx (F1) genome NSF_v1n/a
Chr05chromosomeChr05:112517366..112517426 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr13chromosomeUCD_cg10004_824:1..61 .
Chr13:2060394..2060454 -		n/a
Sequence
>UCD_cg10004_824 ID=UCD_cg10004_824; Name=UCD_cg10004_824; organism=Gossypium spp.; type=genetic_marker; length=65bp
AGAGGTCCAAGAAGCGGAACAAGCCCACCT[A/T]GAAACTGCGTATGCA
GAGGCTGATTAGTAA