CIR0040, CIR0040 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCIR0040
AliasCIR40
CIR040
Genbank IDAJ566989
TypeSSR
SpeciesGossypium hirsutum
GermplasmGuazuncho-2
Source SequenceAJ566989
Source Typegenomic
Repeat Motif(CA)8
PCR ConditionAnnealing temperature: 55
Primer 1CIR040_F: CCCACCAAGAGCATT
Primer 2CIR040_R: TTCTTATATTTGCTACCCAC
Product Length306
PolymorphismP_ CIR0040
Publication[view all]
CommentPrimer data obtained in 2005
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankAJ566989
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D13chromosomeD13:37245769..37246086 -
A13chromosomeA13:68374756..68375061 -
CM018227.1chromosomeCM018227.1:33562926..33563245 -
D5_13chromosomeD5_13:32806965..32807290 -
KI_13chromosomeKI_13:26312795..26313104 -
Chr13_CRI-A2_v1.0.a1chromosomeChr13_CRI-A2_v1.0.a1:84468456..84468761 -
D10_13chromosomeD10_13:34744415..34744726 -
CM016626.1chromosomeCM016626.1:107461093..107461400 -
Dt_chr13chromosomeDt_chr13:32638436..32638753 +
At_chr13chromosomeAt_chr13:32142823..32143128 +
D13chromosomeD13:33149156..33149473 -
A13chromosomeA13:45782997..45783302 -
Ghir_D13chromosomeGhir_D13:36609412..36609729 -
Ghir_A13chromosomeGhir_A13:72637248..72637553 -
D13chromosomeD13:37974836..37975153 -
A13chromosomeA13:75805355..75805660 -
D13chromosomeD13:36723421..36723738 -
A13chromosomeA13:73630923..73631228 -
D13chromosomeD13:33658212..33658529 -
A13chromosomeA13:72330330..72330635 -
scaffold1896supercontigscaffold1896:364268..364587 +
Gbar_D13chromosomeGbar_D13:33313541..33313860 -
D13chromosomeD13:34861931..34862250 -
CM017635.1chromosomeCM017635.1:34830184..34830501 -
CM017622.1chromosomeCM017622.1:75317120..75317425 -
CM017661.1chromosomeCM017661.1:37272854..37273163 -
CM017648.1chromosomeCM017648.1:78720543..78720848 -
CM017713.1chromosomeCM017713.1:34636403..34636722 -
D13chromosomeD13:37684599..37684916 -
A13chromosomeA13:75807387..75807692 -
Chr13chromosomeChr13:79874631..79874936 -
Chr13chromosomeChr13:82804797..82805102 -
Chr13chromosomeChr13:33023899..33024226 -
B_13chromosomeB_13:38679373..38679682 +
Chr13chromosomeChr13:33760498..33760819 -
chr13chromosomechr13:24047541..24047854 -
Chr_13chromosomeChr_13:23110234..23110545 -
Chr13chromosomeChr13:36271568..36271905 -
Chr13chromosomeChr13:23277814..23278143 -
Chr13chromosomeChr13:17708773..17709086 -
Chr13chromosomeChr13:22704624..22704937 -
E13chromosomeE13:73988927..73989242 -
F13chromosomeF13:62011275..62011588 -
Chr13chromosomeChr13:65686750..65687065 +
Germplasm
Stock NameType
Guazuncho-2accession
Relationships

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

Feature NameUnique NameSpeciesType
AJ566989AJ566989Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1CCRI-36 x Hai-7124, F2 (2007)AD_ch13_At.13N/A69.8CIR040View
2Emian-22 x 3-79, BC1 (2011)AD_ch13_At.13N/A78.77CIR040View
3Guazuncho-2 x VH8-4602, consensus (2009)AD_ch18_Dt.13N/A79.38CIR040View
4Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch18_Dt.13N/A99.4CIR040View
5Guazuncho-2 x VH8-4602, RIL (2009)AD_ch18_Dt.13N/A57.67CIR040View
6AD-genome wide Reference Map (2009)AD_ch18_Dt.13N/A98cir0040View
7AD-genome wide Reference Map (2009)AD_ch13_At.13N/A46cir0040View
8TM-1 x Hai-7124, BC1 (2007)AD_ch18_Dt.13N/A75.6CIR040-330View
9TM-1 x Hai-7124, BC1 (2008)AD_ch18_Dt.13N/A58.41CIR040-330View
10TM-1 x Hai-7124, BC1 (2012)AD_ch18_Dt.13N/A62.4CIR040-330View
11PD 94042 x (AD)4-08, F2 (2016)AD_ch18_Dt.13N/A193CIR040View
Sequence
>CIR0040 ID=CIR0040; Name=CIR0040; organism=Gossypium hirsutum; type=genetic_marker; length=306bp
CCCACCAAGAGCATTCAAAATACATGGAAACACTTTAAAAAATTGAATAT
ACCCAAATCAGATTCTTACTCCTTAGTTTATTGAATTGCATAGCATGAAG
AGCAAGTTGGTAAAGGTTTTAGCATAAGGGAAAAGTAGGTTTCCACATGC
CTGAGCATTGCATCTTGAAAAGGAATATCCAAATCTTTACAAAGACCACG
TAAAGTGTCCTGCACATAGATAAGATGAATAAATATGAATCCACACACAC
ACACACATATAGAGCAATTGTATAATTTAATGAACCGTGGGTAGCAAATA
TAAGAA