CIR0342, CIR0342 (genetic_marker) Gossypium hirsutum

Marker Overview
NameCIR0342
AliasCIR342
Genbank IDAJ567279
TypeSSR
SpeciesGossypium hirsutum
GermplasmGuazuncho-2
Source SequenceAJ567279
Source Typegenomic
Repeat Motif(AC)8(AT)5
PCR ConditionAnnealing temperature: 51
Primer 1CIR342_F: CTGGGTTTCTTTGGTG
Primer 2CIR342_R: TGCTGGGAAGATGTAAG
Product Length173
PolymorphismP_ CIR0342
Publication[view all]
CommentPrimer data obtained in 2005
Cross References
External references for this genetic_marker
DatabaseAccession
DB:genbankAJ567279
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D13chromosomeD13:11819586..11819758 +
A10chromosomeA10:45829316..45829482 -
CM018227.1chromosomeCM018227.1:11060887..11061059 +
CM018214.1chromosomeCM018214.1:9691560..9691728 +
D5_13chromosomeD5_13:10961862..10962046 +
KI_13chromosomeKI_13:5346677..5346843 -
Chr13_CRI-A2_v1.0.a1chromosomeChr13_CRI-A2_v1.0.a1:14026207..14026375 -
D10_13chromosomeD10_13:11076653..11076827 +
CM016626.1chromosomeCM016626.1:47783955..47784119 -
scaffold684.1supercontigscaffold684.1:62995..63161 +
Dt_chr2chromosomeDt_chr2:22424537..22424703 +
Dt_chr13chromosomeDt_chr13:47436622..47436794 +
scaffold3432_A13supercontigscaffold3432_A13:636731..636897 +
D13chromosomeD13:11403476..11403648 +
Ghir_D13chromosomeGhir_D13:11379797..11379969 +
Ghir_A13chromosomeGhir_A13:9643708..9643874 +
D13chromosomeD13:11120792..11120964 +
A13chromosomeA13:9898653..9898819 +
D13chromosomeD13:11602076..11602248 +
A13chromosomeA13:9614366..9614532 +
D13chromosomeD13:11277966..11278138 +
A13chromosomeA13:9801278..9801444 +
Gbar_D13chromosomeGbar_D13:11261311..11261483 +
Gbar_A13chromosomeGbar_A13:9617255..9617423 +
D13chromosomeD13:10658490..10658662 +
A13chromosomeA13:9771430..9771598 +
CM017635.1chromosomeCM017635.1:11127541..11127713 +
CM017622.1chromosomeCM017622.1:9718720..9718888 +
CM017661.1chromosomeCM017661.1:11681619..11681791 +
CM017648.1chromosomeCM017648.1:10331469..10331635 +
CM017713.1chromosomeCM017713.1:11264747..11264919 +
CM017700.1chromosomeCM017700.1:9681490..9681658 +
D13chromosomeD13:11772565..11772737 +
A13chromosomeA13:10354286..10354452 +
Chr13chromosomeChr13:14450019..14450187 -
Chr13chromosomeChr13:10873041..10873225 +
B_13chromosomeB_13:81790769..81790939 +
Chr13chromosomeChr13:11402621..11402791 +
chr13chromosomechr13:9239203..9239373 +
Chr_13chromosomeChr_13:9383935..9384109 +
Chr13chromosomeChr13:11602248..11602424 +
Chr13chromosomeChr13:9643415..9643587 +
Chr13_3411776chromosomeChr13_3411776:18341..18527 +
Chr13chromosomeChr13:9407164..9407338 +
E13chromosomeE13:15163359..15163541 -
F13chromosomeF13:12270642..12270807 -
Chr13chromosomeChr13:144306770..144306944 -
Chr13chromosomeCIR0342:1..194 .
Chr13:10940401..10940606 +
Chr13chromosomeCIR0342:1..194 .
Chr13:22669436..22669641 +
Germplasm
Stock NameType
Guazuncho-2accession
Relationships

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

Feature NameUnique NameSpeciesType
AJ567279AJ567279Gossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1CCRI-36 x Hai-7124, F2 (2007)AD_ch13_At.13N/A92.4CIR342View
2Guazuncho-2 x VH8-4602, consensus (2009)AD_ch13_At.13N/A101CIR342View
3Guazuncho-2 x VH8-4602, RIL (2009)AD_ch13_At.13N/A46.15CIR342View
4TM-1 x 3-79, RIL (2012)AD_ch13_At.13N/A58.96CIR342View
5Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch13_At.13N/A162.1CIR342View
6H18 x TM-1, F2 (2005)AD_ch13_At.13N/A56.3CIR342View
7TM-1 x 3-79, RIL (2014)AD_ch13_At.13N/A55.2CIR342View
8TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch13_At.13N/A59.2CIR342View
9CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch13_At.13N/A107.9CIR342View
10Deltapine-61 x Texas-701, F2 (2007)AD_ch13_At.13N/A0CIR342-163View
11AD-genome wide Reference Map (2009)AD_ch13_At.13N/A154cir0342View
12TM-1 x Hai-7124, BC1 (2007)AD_ch13_At.13N/A66.6CIR342-250View
13TM-1 x Hai-7124, BC1 (2008)AD_ch13_At.13N/A66.65CIR342-250View
14TM-1 x Hai-7124, BC1 (2012)AD_ch13_At.13N/A71.2CIR342-250View
15TM-1 x 3-79, RIL (2012.v3)AD_ch13_At.13N/A55.17CIR342View
Sequence
>CIR0342 ID=CIR0342; Name=CIR0342; organism=Gossypium hirsutum; type=genetic_marker; length=173bp
CTGGGTTTCTTTGGTGGATTTGGCTTTGTTCCCACTTCATATTTTGTAAG
CAACACACACACACACACATATATATATAAACATATATGACTGATTTCAA
TTCAGTATTGCTATCTGCAACTCACTTAAATCTATATCTGTCATCAAAAT
TTTTGGCTTACATCTTCCCAGCA