CIR0239, CIR0239 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCIR0239
AliasCIR239
Genbank IDAJ567184
TypeSSR
SpeciesGossypium hirsutum
GermplasmGuazuncho-2
Source SequenceAJ567184
Source Typegenomic
Repeat Motif(TG)8
PCR ConditionAnnealing temperature: 55
Primer 1CIR239_F: CCATTTAACCTTGCTTG
Primer 2CIR239_R: GTTCTGTTGGATAGCATTT
Product Length161
PolymorphismP_ CIR0239
Publication[view all]
CommentPrimer data obtained in 2005
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankAJ567184
Alignments
The following features are aligned
Feature Name Type LocationAnalysis
D02chromosomeD02:60084087..60084248 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1
CM018216.1chromosomeCM018216.1:56553460..56553623 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1
D5_03chromosomeD5_03:10679135..10679296 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1
D10_03chromosomeD10_03:10647684..10647856 -Gossypium turneri (D10) genome NSF_v1_a2
CM016616.1chromosomeCM016616.1:18855066..18855216 -Gossypium australe (G2) genome CRI_v1.1
Dt_chr5chromosomeDt_chr5:20475220..20475381 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1
D02chromosomeD02:57258643..57258804 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1
Ghir_D02chromosomeGhir_D02:59105249..59105410 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1
Ghir_A03chromosomeGhir_A03:98967239..98967389 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1
D02chromosomeD02:59505245..59505406 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1
D02chromosomeD02:60535255..60535416 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1
D02chromosomeD02:57539296..57539457 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1
scaffold3531supercontigscaffold3531:400939..401102 -Gossypium barbadense (AD2) '3-79' genome HAU_v1
scaffold1142supercontigscaffold1142:48710..48860 -Gossypium barbadense (AD2) '3-79' genome HAU_v1
Gbar_D02chromosomeGbar_D02:57097195..57097358 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1
Gbar_A03chromosomeGbar_A03:91687485..91687635 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1
D02chromosomeD02:58421741..58421904 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1
CM017624.1chromosomeCM017624.1:59467481..59467642 +Gossypium tomentosum (AD3) genome HGS_v1.1
CM017650.1chromosomeCM017650.1:60901329..60901490 +Gossypium mustelinum (AD4) genome JGI_v1.1
CM017702.1chromosomeCM017702.1:58015279..58015442 +Gossypium darwinii (AD5) genome HGS_v1.1
D02chromosomeD02:61462812..61462973 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1
Chr03chromosomeChr03:52566760..52566921 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1
Chr05chromosomeChr05:55358461..55358627 +Gossypium thurberi (D1-5) genome CRI_v1
chr05chromosomechr05:41468326..41468494 +Gossypium armourianum (D2-1) genome ISU_v1
Chr_05chromosomeChr_05:36148648..36148903 +Gossypium harknessii (D2-2) genome ISU_v1
Chr05chromosomeChr05:57039206..57039368 +Gossypium davidsonii (D3d-8) genome CRI_v1
Chr05chromosomeChr05:36544448..36544600 +Gossypium aridum (D4) genome ISU_v1
Chr05chromosomeChr05:30976154..30976305 +Gossypium gossypioides (D6) genome ISU_v1
Chr05chromosomeChr05:37903126..37903278 +Gossypium lobatum (D7) genome ISU_v1
Germplasm
Stock NameType
Guazuncho-2accession
Relationships

The following sequence_feature feature(s) derives from this genetic_marker:

Feature NameUnique NameSpeciesType
AJ567184AJ567184Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1CCRI-36 x Hai-7124, F2 (2007)AD_ch14_Dt.02N/A114.5CIR239View
2Guazuncho-2 x VH8-4602, consensus (2009)AD_ch14_Dt.02N/A79.42CIR239View
3Guazuncho-2 x VH8-4602, RIL (2009)AD_ch14_Dt.02N/A68.62CIR239View
4TM-1 x 3-79, RIL (2012)AD_ch14_Dt.02N/A55.68CIR239View
5TM-1 x 3-79, RIL (2014)AD_ch14_Dt.02N/A70.7CIR239View
6Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch14_Dt.02N/A100.5CIR239aView
7AD-genome wide Reference Map (2009)AD_ch14_Dt.02N/A173cir0239View
8TM-1 x 3-79, RIL (2012.v3)AD_ch14_Dt.02N/A70.74CIR239View
Sequence
>CIR0239 ID=CIR0239; Name=CIR0239; organism=Gossypium hirsutum; type=genetic_marker; length=161bp
CCATTTAACCTTGCTTGACGCATCATCATCATTGTCATGTCTTTGAATCT
GAGTAATAAGTATACTTCGGTTTTGTGTGTGTGTGTGTGTTATAATCATT
CGTGACGGTGGCTTAGTACGAATAAAAACAGCAACGAAGCTGAAATGCTA
TCCAACAGAAC