CIR0005, CIR0005 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCIR0005
AliasCIR5
CIR005
Genbank IDAJ566955
TypeSSR
SpeciesGossypium hirsutum
GermplasmGuazuncho-2
Source SequenceAJ566955
Source Typegenomic
Repeat Motif(TG)8
PCR ConditionAnnealing temperature: 55
Primer 1CIR005_F: AAGCTGAAGATGAGGTTT
Primer 2CIR005_R: GCATGATTTGGTTTGTT
Product Length184
Publication[view all]
CommentPrimer data obtained in 2005
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankAJ566955
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D05chromosomeD05:3937124..3937319 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A05chromosomeA05:4452933..4453118 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018206.1chromosomeCM018206.1:4400473..4400656 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_05chromosomeD5_05:3523916..3524104 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_05chromosomeKI_05:3198628..3198815 +Gossypioides kirkii genome ISU_v3n/a
Chr05_CRI-A2_v1.0.a1chromosomeChr05_CRI-A2_v1.0.a1:4334173..4334356 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
At_chr3chromosomeAt_chr3:33092894..33093077 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Dt_chr9chromosomeDt_chr9:65609013..65609208 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D05chromosomeD05:3777034..3777229 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A05chromosomeA05:3859275..3859460 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D05chromosomeGhir_D05:3910891..3911084 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A05chromosomeGhir_A05:4447663..4447846 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D05chromosomeD05:3710939..3711134 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A05chromosomeA05:4317398..4317583 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D05chromosomeD05:3821959..3822154 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A05chromosomeA05:4418947..4419130 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D05chromosomeD05:3682359..3682554 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A05chromosomeA05:4830060..4830243 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At05chromosomeAt05:2396971..2397154 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold30148supercontigscaffold30148:15117..15300 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_A05chromosomeGbar_A05:4097571..4097754 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
A05chromosomeA05:4572073..4572256 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017627.1chromosomeCM017627.1:3779222..3779417 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017614.1chromosomeCM017614.1:4440384..4440567 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017653.1chromosomeCM017653.1:3967498..3967691 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017640.1chromosomeCM017640.1:4494113..4494296 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017692.1chromosomeCM017692.1:4370780..4370963 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D05chromosomeD05:3846453..3846648 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A05chromosomeA05:4565475..4565660 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr05chromosomeChr05:4727625..4727808 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr05chromosomeChr05:4208352..4208535 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr05chromosomeChr05:3549648..3549834 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_05chromosomeB_05:81898457..81898643 -Gossypium anomalum (B1) genome NSF_v1n/a
Chr09chromosomeChr09:3651522..3651708 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr09chromosomeChr09:3834611..3834801 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr09chromosomeChr09:3444250..3444436 +Gossypium aridum (D4) genome ISU_v1n/a
Chr09chromosomeChr09:2799062..2799258 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr09chromosomeChr09:3380535..3380721 +Gossypium lobatum (D7) genome ISU_v1n/a
E05chromosomeE05:4671066..4671259 +Gossypium stocksii (E1) genome NSF_v1n/a
F05chromosomeF05:3680083..3680269 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr09chromosomeChr09:3512931..3513117 .Gossypium raimondii (D5) genome JGI_v2_a2.1CottonGen marker alignment to genome using marker sequences.
Chr09chromosomeCIR0005:1..337 .
Chr09:3512790..3513129 +		n/a
Chr9chromosomeCIR0005:1..337 .
Chr9:3092371..3092710 -		n/a
Germplasm
Stock NameType
Guazuncho-2accession
Relationships

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

Feature NameUnique NameSpeciesType
AJ566955AJ566955Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1(SM3 x SM12) x (X4133 x 8891), 4WC (2008)AD_ch19_Dt.05N/A24.4CIR005View
27235 x TM-1, RIL (2007)AD_ch10_At.10N/A18.5CIR005View
3TM-1 x 3-79, RIL (2012)AD_ch05_At.05N/A22.36CIR005View
4TM-1 x 3-79, RIL (2014)AD_ch05_At.05N/A180.6CIR005View
5AD-genome wide Reference Map (2009)AD_ch19_Dt.05N/A54cir0005View
6TM-1 x 3-79, RIL (2012.v3)AD_ch05_At.05N/A180.57CIR005View
Sequence
>CIR0005 ID=CIR0005; Name=CIR0005; organism=Gossypium hirsutum; type=genetic_marker; length=184bp
AAGCTGAAGATGAGGTTTTGGTTATGGGGACGTGGCTAATAAAAGTTGGC
CAAAGCAGAGTGAGGTCCCTGTTGCGGTGTTCAATTCCAGCTGTCGACCA
GCACCGGAAACCTTCCCAAAAGTTACAGTATATTATACTATATATGTGTG
TGTGTGTGTGNCCGNCGAACAAACCAAATCATGC