MUSS0123, MUSS0123 (genetic_marker) Gossypium arboreum

Marker Overview
NameMUSS0123
AliasMUSS123
Genbank IDN/A
TypeSSR
SpeciesGossypium arboreum
GermplasmAKA 8401
Source TypeEST
Repeat MotifTCAAA(4)
PCR ConditionAnnealing temperature: 55
Primer 1MUSS123_F: CAATTCCCAAACCTTCTTCTTC
Primer 2MUSS123_R: GAAACCATTCTCCACTTCCTTG
Product Length191
ContactUlloa, Mauricio
CommentPrimer data obtained in 2007-11
Contact
NameDetails
Ulloa, Mauricio
Description:Breeding, genetics, and Genomics
First name:Mauricio
Last name:Ulloa
Title:Research Geneticist
Institution:USDA-ARS, W.I.C.S., Res. Unit
Address:17053 N. Shafter Ave., Shafter, California 93263
Country:United States
Email:mauricio.ulloa@usda.gov
Phone:661-746-8009
Fax:746-746-1619
Keywords:Breeding and Genomics
Last update:27-Apr-2010
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D11chromosomeD11:1537825..1538016 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A11chromosomeA11:1543478..1543674 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018225.1chromosomeCM018225.1:1367261..1367452 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018212.1chromosomeCM018212.1:1574314..1574500 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_11chromosomeD5_11:64386437..64386627 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_11chromosomeKI_11:1284610..1284783 +Gossypioides kirkii genome ISU_v3n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:122977652..122977842 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_11chromosomeD10_11:1596188..1596379 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016624.1chromosomeCM016624.1:1670083..1670274 +Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr9chromosomeDt_chr9:41077949..41078140 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D11chromosomeD11:1429796..1429987 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A11chromosomeA11:1445214..1445410 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D11chromosomeGhir_D11:1453010..1453201 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A11chromosomeGhir_A11:1525769..1525965 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D11chromosomeD11:1397118..1397309 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:1463473..1463669 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D11chromosomeD11:1443436..1443627 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A11chromosomeA11:1401630..1401826 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D11chromosomeD11:1457567..1457758 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A11chromosomeA11:1561680..1561876 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt11chromosomeDt11:1724471..1724662 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold29687supercontigscaffold29687:151176..151367 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold9746supercontigscaffold9746:219334..219520 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D11chromosomeGbar_D11:1415926..1416117 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A11chromosomeGbar_A11:1185014..1185200 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D11chromosomeD11:1438396..1438587 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A11chromosomeA11:1573749..1573935 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017633.1chromosomeCM017633.1:1348033..1348224 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017620.1chromosomeCM017620.1:1586123..1586319 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017659.1chromosomeCM017659.1:1425274..1425465 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017646.1chromosomeCM017646.1:1617946..1618132 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017711.1chromosomeCM017711.1:1391522..1391713 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017698.1chromosomeCM017698.1:1546916..1547112 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D11chromosomeD11:1412213..1412404 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A11chromosomeA11:1548511..1548707 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:1627543..1627754 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:1555888..1556078 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr11chromosomeChr11:61873125..61873315 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_11chromosomeB_11:1556440..1556631 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr07chromosomeChr07:1361761..1361952 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr07chromosomechr07:1281810..1282006 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_07chromosomeChr_07:1176192..1176383 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr07chromosomeChr07:1438234..1438425 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr07chromosomeChr07:1091301..1091497 +Gossypium aridum (D4) genome ISU_v1n/a
Chr07chromosomeChr07:1070516..1070707 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr07chromosomeChr07:1121013..1121204 +Gossypium lobatum (D7) genome ISU_v1n/a
E11chromosomeE11:1515336..1515537 +Gossypium stocksii (E1) genome NSF_v1n/a
F11chromosomeF11:1318864..1319055 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr11chromosomeChr11:185201078..185201269 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Germplasm
Stock NameType
AKA 8401accession
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Emian-22 x 3-79, BC1 (2011)AD_ch11_At.11N/A221.12MUSS123View
2TM-1 x 3-79, RIL (2006)AD_ch11_At.11N/A115.8MUSS123View
3TM-1 x 3-79, RIL (2012)AD_ch11_At.11N/A0MUSS123View
4TM-1 x 3-79, RIL (2014)AD_ch11_At.11N/A0MUSS123View
5TM-1 x 3-79, RIL (2012.v3)AD_ch11_At.11N/A0MUSS123View
6AD-genome wide Reference Map (2009)AD_ch11_At.11N/A284muss0123View
7PD 94042 x (AD)4-08, F2 (2016)AD_ch11_At.11N/A234.7MUSS123bView
8PD 94042 x (AD)4-08, F2 (2016)AD_ch21_Dt.11N/A250.1MUSS123aView
Sequence
>MUSS0123 ID=MUSS0123; Name=MUSS0123; organism=Gossypium arboreum; type=genetic_marker; length=191bp
CAATTCCCAAACCTTCTTCTTCAGTTATACACTCTCAAATCAAATCAAAT
CAAATCGGACACTGAAAAAGCTTAGCGAAAATGGTGCGTATAGAAGAAAA
GCAAGGCACGATGGTGCCTAGTTCGATGCCCGAGCAACAAAACCCTCTGC
AGCAATTGCAAGCTAAGTTCAAGGAAGTGGAGAATGGTTTC