NAU3478, NAU3478 (genetic_marker) Gossypium raimondii

Marker Overview
NameNAU3478
Genbank IDCO107844
TypeSSR
SpeciesGossypium raimondii
Source TypeEST
Repeat Motif(atc)5
PCR ConditionAnnealing temperature: 57
Primer 1NAU3478_F: ATGGCACTTCCTCATCATCT
Primer 2NAU3478_R: TGTTGGTTGACTGGAATGAC
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:genbankCO107844
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D11chromosomeD11:22680427..22680614 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A11chromosomeA11:27226518..27226705 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018225.1chromosomeCM018225.1:21539299..21539486 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018212.1chromosomeCM018212.1:26174334..26174551 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_11chromosomeD5_11:44618394..44618581 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_11chromosomeKI_11:14765797..14765993 +Gossypioides kirkii genome ISU_v3n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:96424095..96424306 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_11chromosomeD10_11:20954934..20955121 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016624.1chromosomeCM016624.1:36985062..36985246 +Gossypium australe (G2) genome CRI_v1.1n/a
At_chr1chromosomeAt_chr1:55428578..55428765 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Dt_chr7chromosomeDt_chr7:22596896..22597083 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D11chromosomeD11:21657659..21657846 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A11chromosomeA11:26528972..26529159 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D11chromosomeGhir_D11:22177020..22177207 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A11chromosomeGhir_A11:27082534..27082721 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D11chromosomeD11:21597361..21597548 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:26095063..26095250 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D11chromosomeD11:22199271..22199458 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A11chromosomeA11:26630343..26630530 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D11chromosomeD11:21986927..21987114 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:27219941..27220128 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt11chromosomeDt11:23655438..23655625 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
At11chromosomeAt11:28867220..28867437 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold7270supercontigscaffold7270:377333..377550 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold6126supercontigscaffold6126:720410..720597 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D11chromosomeGbar_D11:21839744..21839931 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A11chromosomeGbar_A11:25960562..25960779 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D11chromosomeD11:21718538..21718725 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A11chromosomeA11:26126085..26126302 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017633.1chromosomeCM017633.1:21644315..21644502 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017620.1chromosomeCM017620.1:26773550..26773746 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017659.1chromosomeCM017659.1:22111690..22111877 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017646.1chromosomeCM017646.1:27056340..27056551 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017711.1chromosomeCM017711.1:21719010..21719197 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017698.1chromosomeCM017698.1:26579824..26580029 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D11chromosomeD11:22565533..22565720 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A11chromosomeA11:27437499..27437686 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:27621019..27621221 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:42533509..42533696 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_11chromosomeB_11:25329089..25329297 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr07chromosomeChr07:21789546..21789733 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr07chromosomechr07:18151478..18151665 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_07chromosomeChr_07:18100237..18100424 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr07chromosomeChr07:21726492..21726682 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr07chromosomeChr07:16409028..16409322 +Gossypium aridum (D4) genome ISU_v1n/a
Chr07chromosomeChr07:14424521..14424708 +Gossypium gossypioides (D6) genome ISU_v1n/a
E11chromosomeE11:29174327..29174550 +Gossypium stocksii (E1) genome NSF_v1n/a
F11chromosomeF11:21533836..21534059 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr11chromosomeChr11:139638537..139638730 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr07chromosomeNAU3478:1..769 .
Chr07:21049241..21050009 -
n/a
scaffold261supercontigNAU3478:1..769 .
scaffold261:565110..565878 +
n/a
Image
File NameLegend
45_FISH_GEN-178-1117_fig2.jpgBAC clones and their corresponding genetic markers of the 22 probes according to FISH signal patterns in Figure 1. [Image from Wang et al., 2008, GEN-178-1117]
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Emian-22 x 3-79, BC1 (2011)AD_ch11_At.11N/A113.31NAU3478View
2JLZM x ZJXSLS, F2 (2008)A_JZ_A11N/A115.7NAU3478View
3AD-genome wide Reference Map (2009)AD_ch11_At.11N/A61NAU3478View
4TM-1 x Hai-7124, BC1 (2008)AD_ch11_At.11N/A78.5NAU3478-225View
5TM-1 x Hai-7124, BC1 (2007)AD_ch11_At.11N/A79.7NAU3478-225View
6TM-1 x Hai-7124, BC1 (2012)AD_ch11_At.11N/A84.6NAU3478-225View
Sequence
>NAU3478 ID=NAU3478; Name=NAU3478; organism=Gossypium raimondii; type=genetic_marker; length=188bp
ATGGCACTTCCTCATCATCTTCAACTTCTTCCTCCTCTTCTACATCATCA
TCATCATCGCCATCTTCTTCTTCTTCATTCCCTGGGTCCATATCACTACC
TTCAGCATCATGTTCTTCAGCTTGGGCCACTGGTTGAACCAGGTAGCCTT
CACCATAGTCTTCATCCTGTCATTCCAGTCAACCAACA