BNL3347, BNL3347 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3347
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3347_orig
Source Typegenomic
Repeat Motif(GA)22, (CT)23
PCR ConditionAnnealing temperature: 55
Primer 1BNL3347_F: AGACTGACATGCAGCTTCCA
Primer 2BNL3347_R: ATCTTAATTTTGAGTATAGGATAGGGG
PolymorphismP_ BNL3347
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D05chromosomeD05:57436670..57436808 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018219.1chromosomeCM018219.1:56737573..56737731 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_05chromosomeD5_05:51071327..51071465 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
D5_05chromosomeD5_05:51050059..51050229 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
D10_05chromosomeD10_05:7253295..7253491 +Gossypium turneri (D10) genome NSF_v1_a2n/a
D10_05chromosomeD10_05:7152944..7153099 +Gossypium turneri (D10) genome NSF_v1_a2n/a
D10_05chromosomeD10_05:7279730..7279876 +Gossypium turneri (D10) genome NSF_v1_a2n/a
D10_05chromosomeD10_05:7139183..7139353 +Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr9chromosomeDt_chr9:5719795..5719943 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D05chromosomeD05:55139326..55139486 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D05chromosomeGhir_D05:56342224..56342364 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D05chromosomeD05:57005702..57005844 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
scaffold5607supercontigscaffold5607:102250..102404 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D05chromosomeGbar_D05:56757553..56757721 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D05chromosomeD05:59397600..59397754 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017653.1chromosomeCM017653.1:58634674..58634786 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017705.1chromosomeCM017705.1:57396388..57396532 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017705.1chromosomeCM017705.1:57330318..57330466 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017705.1chromosomeCM017705.1:57375025..57375163 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017705.1chromosomeCM017705.1:57309001..57309121 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D05chromosomeD05:59354011..59354149 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr05chromosomeChr05:51889116..51889274 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr05chromosomeChr05:51910341..51910477 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_05chromosomeB_05:4821294..4821480 -Gossypium anomalum (B1) genome NSF_v1n/a
Chr09chromosomeChr09:51997178..51997328 -Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr09chromosomeChr09:39554546..39554847 -Gossypium lobatum (D7) genome ISU_v1n/a
F05chromosomeF05:70110403..70110552 -Gossypium longicalyx (F1) genome NSF_v1n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3347_origBNL3347_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1(SM3 x SM12) x (X4133 x 8891), 4WC (2008)AD_ch19_Dt.05N/A0BNL3347View
27235 x TM-1, RIL (2007)AD_ch19_Dt.05N/A22.2BNL3347View
3CCRI-36 x Hai-7124, F2 (2007)AD_ch19_Dt.05N/A13.1BNL3347View
4Emian-22 x 3-79, BC1 (2011)AD_ch19_Dt.05N/A41.56BNL3347View
5Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch19_Dt.05N/A219.5BNL3347View
6Guazuncho-2 x VH8-4602, consensus (2009)AD_ch19_Dt.05N/A162.95BNL3347View
7Guazuncho-2 x VH8-4602, consensus (2009)AD_ch02_At.02N/A41.42BNL3347View
8Guazuncho-2 x VH8-4602, RIL (2009)AD_ch02_At.02N/A33.32BNL3347View
9Guazuncho-2 x VH8-4602, RIL (2009)AD_ch19_Dt.05N/A55.54BNL3347View
10AD-genome wide Reference Map (2009)AD_ch19_Dt.05N/A294BNL3347View
11TM-1 x 3-79, RIL (2012)AD_ch19_Dt.05N/A138.35BNL3347View
12Xinluzao-1 x Hai-7124, F2 (2008)AD_ch19_Dt.05N/A109.3BNL3347View
13Handan-208 x Pima-90, F2:3 (2007)AD_ch19_Dt.05N/A251.3BNL3347View
147235 x TM-1, F2:3 (2005)AD_ch19_Dt.05N/A38.7BNL3347View
15TM-1 x 3-79, RIL (2014)AD_ch19_Dt.05N/A48.3BNL3347View
16TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch19_Dt.05N/A140.4BNL3347View
17Emian-22 x 3-79, BC1 (2015)AD_ch19_Dt.05N/A43.2BNL3347View
18CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch19_Dt.05N/A38.5BNL3347View
19Monsanto SSR Bin Map, (2009)AD_ch19_Dt.05N/A81BNL3347View
20Deltapine-61 x Texas-701, F2 (2007)AD_ch19_Dt.05N/A14.1BNL3347-109View
21Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch19_Dt.05N/A16.2BNL3347-140View
22TM-1 x Hai-7124, BC1 (2007)AD_ch19_Dt.05N/A146.5BNL3347-140View
23TM-1 x Hai-7124, BC1 (2008)AD_ch19_Dt.05N/A145.39BNL3347-140View
24TM-1 x Hai-7124, BC1 (2012)AD_ch19_Dt.05N/A46BNL3347-140View
25TM-1 x 3-79, RIL (2011)AD_ch19_Dt.05N/A33.7BNL3347_177/170View
26TM-1 x 3-79, RIL (2012.v3)AD_ch19_Dt.05N/A48.26BNL3347View
27PD 94042 x (AD)4-08, F2 (2016)AD_ch19_Dt.05N/A201.2BNL3347View
28MGG-293-793, MAGIC (2018)AD_ch19_Dt.05N/A43.2BNL3347View
Sequence
>BNL3347 ID=BNL3347; Name=BNL3347; organism=Gossypium hirsutum; type=genetic_marker; length=141bp
AGACTGACATGCAGCTTCCAGTTTTGCTCTCTCTCTCTCTCTCTCTCTCT
CTCTCTCTCTCTCTCTCTCTCTGCCTCTGCATTATATAGGAAAATGGTCA
TTTTTCAAGTTTAGCCCCTATCCTATACTCAAAATTAAGAT