CSIRO_D5chr01_12972998 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCSIRO_D5chr01_12972998
AliasChr01_12972998
dbSNP IDN/A
SNP Array ID
TAMU_CottonSNP63K:i01669Gh
TypeSNP
SNP AllelesA/G
5' Flanking SequenceGGTTTAGCATGCCTTATTCAAATGGATACCCTAAATCCGAGATTTCTAATGGGATTATAT CAAATGACCCATCTTTAGATTTAAGCTCTGTAGGTGCCCC
3' Flanking SequenceTTTTTACCTTCTCTTGGTTTGAATAATTCTAGCACTTATGCTTCATTTTTTAGCACAGAC AAAGAGGGAGATTCTTCATCTCCTTCTGATGACGGTGACT
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 LocationAnalysisReference
Chr01chromosomeChr01:12972998..12972998 .Gossypium raimondii (D5) genome JGI_v2_a2.1n/a
CM018221.1chromosomeCM018221.1:13230258..13230458 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_07chromosomeD5_07:13101306..13101506 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Dt_chr1chromosomeDt_chr1:47461771..47461971 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D07chromosomeD07:13246867..13247067 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D07chromosomeGhir_D07:13670794..13670994 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D07chromosomeD07:13053538..13053738 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D07chromosomeD07:13639039..13639239 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
Gbar_D07chromosomeGbar_D07:13687326..13687526 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D07chromosomeD07:13348086..13348286 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017629.1chromosomeCM017629.1:13633708..13633908 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017655.1chromosomeCM017655.1:13881763..13881963 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017707.1chromosomeCM017707.1:13512071..13512271 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D07chromosomeD07:13844550..13844750 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr07chromosomeChr07:40478186..40478386 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr01chromosomeChr01:13430553..13430753 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr01chromosomechr01:11424932..11425132 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_01chromosomeChr_01:11092925..11093125 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr01chromosomeChr01:13300137..13300337 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr01chromosomeChr01:10900018..10900218 +Gossypium aridum (D4) genome ISU_v1n/a
Chr01chromosomeChr01:8703628..8703828 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr01chromosomeChr01:10716215..10716415 +Gossypium lobatum (D7) genome ISU_v1n/a
E07chromosomeE07:74256697..74256897 -Gossypium stocksii (E1) genome NSF_v1n/a
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_ch07_At.07N/A84.71i01669GhView
Sequence
>CSIRO_D5chr01_12972998 ID=CSIRO_D5chr01_12972998; Name=CSIRO_D5chr01_12972998; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
GGTTTAGCATGCCTTATTCAAATGGATACCCTAAATCCGAGATTTCTAAT
GGGATTATATCAAATGACCCATCTTTAGATTTAAGCTCTGTAGGTGCCCC
[A/G]TTTTTACCTTCTCTTGGTTTGAATAATTCTAGCACTTATGCTTCA
TTTTTTAGCACAGACAAAGAGGGAGATTCTTCATCTCCTTCTGATGACGG
TGACT