NAU3409, NAU3409 (genetic_marker) Gossypium raimondii

Marker Overview
NameNAU3409
Genbank IDCO105317
TypeSSR
SpeciesGossypium raimondii
Source TypeEST
Repeat Motif(taa)5
PCR ConditionAnnealing temperature: 57
Primer 1NAU3409_F: GTTGGCACCCATTAAGTACC
Primer 2NAU3409_R: TTCCCACTGGTATTTGGTTT
Restriction EnzymeNotI; EcoRV
Publication[view all]
ContactZhang, Tian-Zhen
CommentPrimer data obtained in 2007-05
Contact
NameDetails
Zhang, Tian-Zhen
First name:Tian-Zhen
Last name:Zhang
Title:Professor
Institution:Zhejiang University
Address:College of Agriculture and Biotechnology, Zhejiang University, Hangzhou , 310058 , Zhejiang , China
Country:China
Email:cotton@zju.edu.cn
Phone:+86 571 88982971
Fax:+86 571 88982971
Keywords:cotton genetics and genomics, and breeding
Last update:18-Mar-2022
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankCO105317
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D11chromosomeD11:7761266..7761446 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A11chromosomeA11:7996436..7996620 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018225.1chromosomeCM018225.1:7229307..7229493 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018212.1chromosomeCM018212.1:7975718..7975899 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_11chromosomeD5_11:58688336..58688521 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:116344251..116344437 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_11chromosomeD10_11:7195467..7195653 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016624.1chromosomeCM016624.1:10153124..10153310 +Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr7chromosomeDt_chr7:5758716..5758896 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr9chromosomeAt_chr9:22455155..22455339 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D11chromosomeD11:7787139..7787319 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A11chromosomeA11:7609429..7609613 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D11chromosomeGhir_D11:7578426..7578606 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A11chromosomeGhir_A11:8185551..8185735 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D11chromosomeD11:7460535..7460715 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:7825947..7826131 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D11chromosomeD11:7638955..7639135 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A11chromosomeA11:8053593..8053777 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D11chromosomeD11:7576006..7576186 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:8227844..8228028 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At11chromosomeAt11:8827071..8827252 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold15549supercontigscaffold15549:108532..108713 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold25700supercontigscaffold25700:95442..95628 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D11chromosomeGbar_D11:7413344..7413530 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A11chromosomeGbar_A11:7811792..7811973 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D11chromosomeD11:7474854..7475040 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A11chromosomeA11:8009807..8009988 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017633.1chromosomeCM017633.1:7378368..7378548 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017620.1chromosomeCM017620.1:8153793..8153977 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017659.1chromosomeCM017659.1:7749660..7749846 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017646.1chromosomeCM017646.1:8245269..8245453 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017711.1chromosomeCM017711.1:7481231..7481417 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017698.1chromosomeCM017698.1:8149174..8149355 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D11chromosomeD11:7789480..7789660 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A11chromosomeA11:8353086..8353270 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:8360182..8360366 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:7971771..7971957 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr11chromosomeChr11:56179682..56179868 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_11chromosomeB_11:7916465..7916648 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr07chromosomeChr07:7205094..7205249 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr07chromosomechr07:6423141..6423327 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_07chromosomeChr_07:6943029..6943215 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr07chromosomeChr07:7434298..7434474 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr07chromosomeChr07:6073209..6073395 +Gossypium aridum (D4) genome ISU_v1n/a
Chr07chromosomeChr07:5453556..5453717 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr07chromosomeChr07:6158597..6158783 +Gossypium lobatum (D7) genome ISU_v1n/a
E11chromosomeE11:8905565..8905754 +Gossypium stocksii (E1) genome NSF_v1n/a
F11chromosomeF11:7031562..7031748 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr11chromosomeChr11:176399884..176400063 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr07chromosomeNAU3409:1..642 .
Chr07:7020407..7021048 -		n/a
Chr7chromosomeNAU3409:1..642 .
Chr7:47329601..47330242 +		n/a
Chr7chromosomeNAU3409:1..642 .
Chr7:47321581..47322222 +		n/a
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1AD-genome wide Reference Map (2009)AD_ch11_At.11N/A276nau3409View
2SG 747 x Giza 75, BIL (2013)AD_ch11_At.11N/A66.1nau3409View
3TM-1 x Hai-7124, BC1 (2008)AD_ch11_At.11N/A127.33NAU3409-290View
4TM-1 x Hai-7124, BC1 (2007)AD_ch11_At.11N/A126.9NAU3409-290View
5TM-1 x Hai-7124, BC1 (2012)AD_ch11_At.11N/A37.4NAU3409-290View
Sequence
>NAU3409 ID=NAU3409; Name=NAU3409; organism=Gossypium raimondii; type=genetic_marker; length=187bp
GTTGGCACCCATTAAGTACCTTTTAGCCCCCAAAACCCAGATTTTGATTC
GGAATCTGGGTTTTCCCAAAGACACAGAAATGATTCCAAAATAATAATAA
TAATAAATCTGAACAGAGGAGTCTAATCAAACAATGAATATATAGAACCT
GCAGTTGAAGTCAAGTGAAACCAAATACCAGTGGGAA