CSIRO_D5chr02_61552574 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCSIRO_D5chr02_61552574
AliasChr02_61552574
dbSNP IDN/A
SNP Array ID
TAMU_CottonSNP63K:i14779Gh
TypeSNP
SNP AllelesC/T
5' Flanking SequenceAACTGTGAAGAATGCACATCTCTTCCAGCTGGTAAAGTTTTTTTCCCCCTTTTGTCCCAT ACTTTATTCTTAGGAGCTGTTATGCCATATTAATGGCCAA
3' Flanking SequenceGGGCTTGTTTAAGGCATTGCTTGATTCAGTTCCTTTTTATGGATGTTAGTTATTCCATTT TGTATACCAGCTCTTCTCTTGTCCTCAATAGTTAGGTGCT
SpeciesGossypium hirsutum
GermplasmNamcala
Sicala 40
Sicot 81
Sicala V-2
Sicot 71
Sicala 3-2
Lu Mian 14
Deltapine 90
Coker 315
Tamcot SP37
Delta Opal
Sicot 70
Sicot 189
Siokra 1-4
Riverina Paplar
Deltapine 16
MCU-5 (PI 694627)
Source TypeRNA-seq
Publication[view all]
ContactZhu, Qian-Hao
Wilson, Iain
Stelly, David M.
CommentData obtained 2014. SNP location is based on D5 JGI 221 position
Contact
NameDetails
Zhu, Qian-Hao
First name:Qian-Hao
Last name:Zhu
Title:Research Scientist
Institution:CSIRO
Address:CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601,
Country:Australia
Email:Qianhao.Zhu@csiro.au
Phone:61 2 62464903
Last update:24-Aug-2014
Wilson, Iain
Description:SNPs; Disease resistance
First name:Iain
Last name:Wilson
Title:Senior Scientist
Institution:CSIRO
Address:Black Mountain Laboratories Clunies Ross Street, Black Mountain, ACT 2601
Country:Australia
Email:iain.wilson@csiro.au
Phone:+61 (0)2 62465211
Last update:28-Feb-2010
Stelly, David M.
Description:Integrative structural genomics; Cytogenetics; Genetics; Cytogenomics; Radiation hybrid mapping; Chromosome manipulations. ; Wide-cross introgression.; QTL definition. ; Reproductive cytology, genetics and manipulations. ; Fiber cell initiation.
First name:David
Last name:Stelly
Title:Professor
Institution:Texas A&M University
Address:370 Olsen Blvd. , Dept. Soil & Crop Sci., TAMU, College Station, TX 77843-2474
Country:United States
Email:stelly@tamu.edu
Phone:+1 979 845 2745
Fax:+1 979 845 0456
Last update:19-Feb-2007
Libraries
Library NameType
TAMU_CottonSNP63KSNP_chip
Alignments
The following features are aligned
Feature Name Type LocationAnalysis
Chr02chromosomeChr02:61552574..61552574 .Gossypium raimondii (D5) genome JGI_v2_a2.1
D5_01chromosomeD5_01:55420357..55420557 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1
D10_01chromosomeD10_01:1174787..1174987 -Gossypium turneri (D10) genome NSF_v1_a2
At_chr9chromosomeAt_chr9:41070762..41070956 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1
Dt_chr9chromosomeDt_chr9:50437194..50437388 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1
D01chromosomeD01:60240551..60240745 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1
Ghir_D01chromosomeGhir_D01:61941184..61941378 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1
D01chromosomeD01:63392736..63392930 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1
D01chromosomeD01:63373010..63373204 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1
CM017623.1chromosomeCM017623.1:62725462..62725656 +Gossypium tomentosum (AD3) genome HGS_v1.1
CM017649.1chromosomeCM017649.1:64193215..64193409 +Gossypium mustelinum (AD4) genome JGI_v1.1
CM017701.1chromosomeCM017701.1:62182578..62182772 +Gossypium darwinii (AD5) genome HGS_v1.1
D01chromosomeD01:63849665..63849859 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1
Chr01chromosomeChr01:51207659..51207859 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1
Chr02chromosomeChr02:60121680..60121880 +Gossypium thurberi (D1-5) genome CRI_v1
chr02chromosomechr02:46261498..46261698 +Gossypium armourianum (D2-1) genome ISU_v1
Chr02chromosomeChr02:44717777..44717972 +Gossypium aridum (D4) genome ISU_v1
Germplasm
Stock NameType
Namcalaaccession
Sicala 40accession
Sicot 81accession
Sicala V-2accession
Sicot 71accession
Sicala 3-2accession
Lu Mian 14accession
Deltapine 90accession
Coker 315accession
Tamcot SP37accession
Delta Opalaccession
Sicot 70accession
Sicot 189accession
Siokra 1-4accession
Riverina Paplaraccession
Deltapine 16accession
MCU-5 (PI 694627)accession
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
13-79 x TM-1, F2 (2015 SNP)AD_ch01_At.01N/A8.16i14779GhView
2Phytogen 72 x Stoneville 474, F2 (2015 SNP)AD_ch01_At.01N/A0i14779GhView
Sequence
>CSIRO_D5chr02_61552574 ID=CSIRO_D5chr02_61552574; Name=CSIRO_D5chr02_61552574; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
AACTGTGAAGAATGCACATCTCTTCCAGCTGGTAAAGTTTTTTTCCCCCT
TTTGTCCCATACTTTATTCTTAGGAGCTGTTATGCCATATTAATGGCCAA
[C/T]GGGCTTGTTTAAGGCATTGCTTGATTCAGTTCCTTTTTATGGATG
TTAGTTATTCCATTTTGTATACCAGCTCTTCTCTTGTCCTCAATAGTTAG
GTGCT