CIR0400, CIR0400 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCIR0400
AliasCIR400
Genbank IDAJ567324
TypeSSR
SpeciesGossypium hirsutum
GermplasmGuazuncho-2
Source SequenceAJ567324
Source Typegenomic
Repeat Motif(TG)9
PCR ConditionAnnealing temperature: 51
Primer 1CIR400_F: TTACTGAATATGTGTGTGTG
Primer 2CIR400_R: CAATTTGCTTCAACCT
Product Length154
PolymorphismP_ CIR0400
Publication[view all]
CommentPrimer data obtained in 2005
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankAJ567324
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
CM018211.1chromosomeCM018211.1:33288614..33288769 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
Chr10_CRI-A2_v1.0.a1chromosomeChr10_CRI-A2_v1.0.a1:47660397..47660550 -Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
scaffold4365.1supercontigscaffold4365.1:57945..58098 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr11chromosomeAt_chr11:91660665..91660818 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
A10chromosomeA10:30483337..30483490 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Scaffold3242supercontigScaffold3242:19564..19717 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
A10chromosomeA10:33898768..33898921 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A10chromosomeA10:33438806..33438959 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A10chromosomeA10:32875201..32875354 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
At10chromosomeAt10:32211039..32211194 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold21935supercontigscaffold21935:22851..23006 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_A10chromosomeGbar_A10:33555540..33555695 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
A10chromosomeA10:33662156..33662311 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017619.1chromosomeCM017619.1:33987571..33987724 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017645.1chromosomeCM017645.1:35209017..35209174 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017697.1chromosomeCM017697.1:33955048..33955203 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
A10chromosomeA10:34925479..34925632 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr10chromosomeChr10:75553024..75553183 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr10chromosomeChr10:79792776..79792929 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
F04chromosomeF04:57531565..57531708 -Gossypium longicalyx (F1) genome NSF_v1n/a
F01chromosomeF01:4584094..4584244 -Gossypium longicalyx (F1) genome NSF_v1n/a
Germplasm
Stock NameType
Guazuncho-2accession
Relationships

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

Feature NameUnique NameSpeciesType
AJ567324AJ567324Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Deltapine-61 x Texas-701, F2 (2007)AD_ch10_At.10N/A21.4CIR400-158View
2Emian-22 x 3-79, BC1 (2011)AD_ch10_At.10N/A113.65CIR400View
3Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch10_At.10N/A59.1CIR400View
4Guazuncho-2 x VH8-4602, consensus (2009)AD_ch10_At.10N/A56.07CIR400View
5TM-1 x 3-79, RIL (2012)AD_ch10_At.10N/A76.2CIR400View
6TM-1 x 3-79, RIL (2014)AD_ch10_At.10N/A80.7CIR400View
7HS-46 x MARCABUCAG8US-1-88, RIL (2009)AD_ch10_At.10N/A1CIR400-152View
8AD-genome wide Reference Map (2009)AD_ch10_At.10N/A69cir0400View
9TM-1 x 3-79, RIL (2012.v3)AD_ch10_At.10N/A80.66CIR400View
Sequence
>CIR0400 ID=CIR0400; Name=CIR0400; organism=Gossypium hirsutum; type=genetic_marker; length=154bp
TTACTGAATATGTGTGTGTGTGTGTGTGTAGGTTTGTATTTACTAAATAT
AATACATGTGACTGAAATTGTTCCTTTAGGTACAAATTTACATCAACTAC
TTTTTCAATCATATGTGATAGGATTTTAGTTAGAGATGAGGTTGAAGCAA
ATTG