BNL3627, BNL3627 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3627
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3627_orig
Source Typegenomic
Repeat Motif(TC)17
PCR ConditionAnnealing temperature: 55
Primer 1BNL3627_F: TATGGGCCTGTCCACCTAAG
Primer 2BNL3627_R: CAAAGCAACATGCACACACA
PolymorphismP_ BNL3627
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D08chromosomeD08:4877498..4877663 +
A08chromosomeA08:4201049..4201231 +
CM018222.1chromosomeCM018222.1:3970933..3971097 +
CM018209.1chromosomeCM018209.1:4225969..4226143 +
D5_08chromosomeD5_08:4056882..4057047 +
KI_08chromosomeKI_08:3440021..3440191 +
Chr08_CRI-A2_v1.0.a1chromosomeChr08_CRI-A2_v1.0.a1:4471818..4472008 +
D10_08chromosomeD10_08:58311604..58311771 -
CM016621.1chromosomeCM016621.1:138530769..138530939 -
scaffold417.1supercontigscaffold417.1:1130605..1130787 +
Dt_chr4chromosomeDt_chr4:31394680..31394845 +
D08chromosomeD08:4253462..4253627 +
A08chromosomeA08:3731681..3731863 +
Ghir_D08chromosomeGhir_D08:4221789..4221954 +
Ghir_A08chromosomeGhir_A08:4186904..4187086 +
D08chromosomeD08:4006356..4006521 +
A08chromosomeA08:4276807..4276989 +
D08chromosomeD08:4217810..4217975 +
A08chromosomeA08:4580569..4580750 +
D08chromosomeD08:4291407..4291572 +
A08chromosomeA08:4162173..4162355 +
At08chromosomeAt08:3790338..3790502 +
scaffold11030supercontigscaffold11030:137402..137566 +
scaffold1102supercontigscaffold1102:261611..261775 -
Gbar_D08chromosomeGbar_D08:4161359..4161523 +
Gbar_A08chromosomeGbar_A08:4553087..4553259 +
D08chromosomeD08:4117579..4117743 +
A08chromosomeA08:4396556..4396730 +
CM017630.1chromosomeCM017630.1:4305198..4305363 +
CM017617.1chromosomeCM017617.1:4446841..4447011 +
CM017656.1chromosomeCM017656.1:4309799..4309963 +
CM017643.1chromosomeCM017643.1:4596272..4596456 +
CM017708.1chromosomeCM017708.1:4293763..4293927 +
CM017695.1chromosomeCM017695.1:4370270..4370450 +
D08chromosomeD08:4318359..4318524 +
A08chromosomeA08:4630039..4630221 +
Chr08chromosomeChr08:4535656..4535842 +
Chr08chromosomeChr08:4812747..4812937 +
Chr08chromosomeChr08:4055873..4056038 +
B_08chromosomeB_08:4816516..4816694 +
Chr04chromosomeChr04:4062536..4062701 +
chr04chromosomechr04:3783392..3783557 +
Chr_04chromosomeChr_04:3423897..3424064 +
Chr04chromosomeChr04:4187089..4187254 +
Chr04chromosomeChr04:3974284..3974465 +
Chr04chromosomeChr04:3024165..3024336 +
Chr04chromosomeChr04:3506433..3506598 +
E08chromosomeE08:5882931..5883103 +
F08chromosomeF08:3814086..3814270 +
Chr08chromosomeChr08:193014230..193014414 -
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3627_origBNL3627_origGossypium hirsutumsequence_feature


Image
File NameLegend
45_FISH_GEN-178-1117_fig2.jpgBAC clones and their corresponding genetic markers of the 22 probes according to FISH signal patterns in Figure 1. [Image from Wang et al., 2008, GEN-178-1117]
48_FISH_TAG-115-675.jpgTwenty-six individual cotton mitotic chromosomes with FISH signals derived from the chromosome-speciWc BACs, and comparisons of linkage and FISH maps. [Image from Wang 2007, TAG-115-675]
Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
13-79 x NM24016, RIL (2008)AD_ch03_At.03N/A0BNL3627View
2Guazuncho-2 x VH8-4602, BC2 (2005)AD_ch24_Dt.08N/A66.7BNL3627View
3Guazuncho-2 x VH8-4602, consensus (2009)AD_ch24_Dt.08N/A99.34BNL3627View
4Guazuncho-2 x VH8-4602, consensus (2009)AD_ch03_At.03N/A37.25BNL3627View
5Guazuncho-2 x VH8-4602, consensus (2009)AD_ch08_At.08N/A109.66BNL3627View
6Guazuncho-2 x VH8-4602, RIL (2009)AD_ch08_At.08N/A36.06BNL3627View
7Guazuncho-2 x VH8-4602, RIL (2009)AD_ch24_Dt.08N/A82.32BNL3627View
8Handan-208 x Pima-90, F2:3 (2007)AD_ch08_At.08N/A164.9BNL3627View
9Palmeri x K-101, F2 (2007)AD_ch08_At.08N/A128.3BNL3627View
10AD-genome wide Reference Map (2009)AD_ch08_At.08N/A200BNL3627View
11TM-1 x 3-79, RIL (2006)AD_ch08_At.08N/A27.9BNL3627View
12TM-1 x 3-79, RIL (2012)AD_ch08_At.08N/A36.72BNL3627View
13Xinluzao-1 x Hai-7124, F2 (2008)AD_ch08_At.08N/A16BNL3627View
14Emian-22 x 3-79, BC1 (2011)AD_ch08_At.08N/A126.71BNL3627View
15AD-genome wide Reference Map (2009)AD_ch24_Dt.08N/A43BNL3627View
16AD-genome wide Reference Map (2009)AD_ch03_At.03N/A109BNL3627View
17TM-1 x 3-79, RIL (2014)AD_ch08_At.08N/A46.3BNL3627View
18TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch08_At.08N/A96.9BNL3627View
19CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch08_At.08N/A75.4BNL3627View
20SG 747 x Giza 75, BIL (2013)AD_ch08_At.08N/A45BNL3627View
21CCRI-36 x Hai-7124, F2 (2007)AD_ch08_At.08N/A148.9BNL3627aView
22Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch24_Dt.08N/A136.5BNL3627aView
23Monsanto SSR Bin Map, (2009)AD_ch08_At.08N/A141BNL3627aView
24CCRI-36 x Hai-7124, F2 (2007)AD_ch24_Dt.08N/A68.6BNL3627bView
25Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch03_At.03N/A41BNL3627bView
26Handan-208 x Pima-90, F2:3 (2007)AD_ch26_Dt.12N/A22.5BNL3627bView
27Monsanto SSR Bin Map, (2009)AD_ch24_Dt.08N/A101BNL3627bView
28TM-1 x Hai-7124, BC1 (2007)AD_ch08_At.08N/A45.3BNL3627-180View
29TM-1 x Hai-7124, BC1 (2008)AD_ch08_At.08N/A83.72BNL3627-180View
30Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch08_At.08N/A11BNL3627-180View
31TM-1 x Hai-7124, BC1 (2012)AD_ch08_At.08N/A49.6BNL3627-180View
32TM-1 x Hai-7124, BC1S1 (2007)AD_ch08_At.08N/A14.6BNL3627_180View
33TM-1 x 3-79, RIL (2012.v3)AD_ch08_At.08N/A46.34BNL3627View
34PD 94042 x (AD)4-08, F2 (2016)AD_ch08_At.08N/A101.3BNL3627bView
35PD 94042 x (AD)4-08, F2 (2016)AD_ch24_Dt.08N/A5.8BNL3627aView
Sequence
>BNL3627 ID=BNL3627; Name=BNL3627; organism=Gossypium hirsutum; type=genetic_marker; length=183bp
TATGGGCCTGTCCACCTAAGAAAGGAGAAGATTATATCTTCTATTTCCAC
CCAGAGATTCAGAAAATACCGAAGTCTGATAAGCTGAGGCAGTGGTCTCT
CTCTCTCTCTCTCTCTCTCTCTCTCTCTCCCTGTCACATATCTCTTATAC
ATGCATGTCTTTATGTGTGTGCATGTTGCTTTG