BNL3442, BNL3442 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL3442
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL3442_orig
Source Typegenomic
Repeat Motif(CA)14(TA)5
PCR ConditionAnnealing temperature: 55
Primer 1BNL3442_F: CATTAGCGGATTTGTCGTGA
Primer 2BNL3442_R: AACGAACAAAGCAAAGCGAT
PolymorphismP_ BNL3442
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
A11chromosomeA11:3749727..3749856 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018212.1chromosomeCM018212.1:3888850..3888991 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
Chr11_CRI-A2_v1.0.a1chromosomeChr11_CRI-A2_v1.0.a1:120505976..120506105 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
At_chr7chromosomeAt_chr7:5539208..5539337 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
A11chromosomeA11:3511622..3511751 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_A11chromosomeGhir_A11:3977035..3977162 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
A11chromosomeA11:3821520..3821649 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A11chromosomeA11:3857799..3857928 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A11chromosomeA11:4006989..4007118 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
scaffold16955supercontigscaffold16955:165412..165551 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_A11chromosomeGbar_A11:3559337..3559474 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
A11chromosomeA11:3922080..3922221 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017620.1chromosomeCM017620.1:3996266..3996401 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017646.1chromosomeCM017646.1:4062361..4062510 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017698.1chromosomeCM017698.1:3933699..3933840 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
A11chromosomeA11:4065811..4065940 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr11chromosomeChr11:4017545..4017682 -Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr11chromosomeChr11:3932806..3932937 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL3442_origBNL3442_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1CCRI-36 x Hai-7124, F2 (2007)AD_ch11_At.11N/A15.4BNL3442View
2Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch11_At.11N/A217BNL3442View
3Guazuncho-2 x VH8-4602, BC2 (2005)AD_ch11_At.11N/A145.7BNL3442View
4Guazuncho-2 x VH8-4602, consensus (2009)AD_ch11_At.11N/A209.99BNL3442View
5Handan-208 x Pima-90, F2:3 (2007)AD_ch11_At.11N/A274.7BNL3442View
6AD-genome wide Reference Map (2009)AD_ch11_At.11N/A217BNL3442View
7TM-1 x 3-79, RIL (2012)AD_ch11_At.11N/A21.43BNL3442View
8Emian-22 x 3-79, BC1 (2011)AD_ch11_At.11N/A205.56BNL3442View
9Palmeri x K-101, F2 (2007)AD_ch11_At.11N/A179.1BNL3442View
10AD-genome wide Reference Map (2009)AD_ch21_Dt.11N/A249BNL3442View
11Yumian-1 x T586, F2:7 (2008)AD_ch21_Dt.11N/A76.7BNL3442View
12Yumian-1 x T586, RIL (2006)AD_ch21_Dt.11N/A134BNL3442View
13(YM1 x CCRI35) x (YM1 x 7235), 4WC (2012)AD_ch11_At.11N/A71.7BNL3442View
14Yumian-1 x T586, RIL (2015)AD_ch21_Dt.11N/A37.2BNL3442View
15TM-1 x 3-79, RIL (2014)AD_ch11_At.11N/A22.3BNL3442View
16GX1135 x GX100-2, F2 (2013)AD_ch11_At.11N/A137.1BNL3442View
17CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch21_Dt.11N/A105.3BNL3442View
18SG 747 x Giza 75, BIL (2013)AD_ch11_At.11N/A85.2BNL3442View
19CCRI-35 x Yumian-1, RIL (2015)AD_ch21_Dt.11N/A55.3BNL3442View
20GX1135 x GX100-2, RIL (2015)AD_ch21_Dt.11N/A262.9BNL3442aView
21GX1135 x GX100-2, RIL (2016)AD_ch21_Dt.11N/A262.5BNL3442aView
22Monsanto SSR Bin Map, (2009)AD_ch11_At.11N/A21BNL3442aView
23TM-1 x Hai-7124, BC1 (2007)AD_ch11_At.11N/A146BNL3442-125View
24TM-1 x Hai-7124, BC1 (2008)AD_ch11_At.11N/A146.99BNL3442-125View
25Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch11_At.11N/A148.9BNL3442-125View
26TM-1 x Hai-7124, BC1 (2012)AD_ch11_At.11N/A20.7BNL3442-125View
27Xinluzao-1 x Hai-7124, F2 (2008)AD_chUN/A51.9BNL3442-2View
28Xinluzao-1 x Hai-7124, F2 (2008)AD_chUN/A27.5BNL3442-1View
29Yumian-1 x T586, RIL (2009)AD_ch21_Dt.11N/A152.4BNL3442/120y(C11)View
30Yumian-1 x T586, F2:3 (2005.v0)AD_ch18_Dt.13N/A10.6BNL3442(C18)View
31Yumian-1 x T586, F2:3 (2005.v0)AD_ch21_Dt.11N/A10.6BNL3442(C18)View
32GX1135 x GX100-2, RIL (2016)AD_ch11_At.11N/A97.9BNL3442bView
33CCRI-35 x Yumian-1, RIL (2017)AD_ch21_Dt.11N/A13.83BNL3442View
34TM-1 x 3-79, RIL (2012.v3)AD_ch11_At.11N/A22.29BNL3442View
35PD 94042 x (AD)4-08, F2 (2016)AD_ch11_At.11N/A219.2BNL3442View
36MGG-293-793, MAGIC (2018)AD_ch11_At.11N/A31.5BNL3442View
Sequence
>BNL3442 ID=BNL3442; Name=BNL3442; organism=Gossypium hirsutum; type=genetic_marker; length=130bp
CATTAGCGGATTTGTCGTGACCTATATATATATGTGTGTGTGTGTGTGTG
TGTGTGTGTGGAGCCCATGAATGCCCGTATTCATTTGCTGGCTATGCCCA
TCATTCAGCCATCGCTTTGCTTTGTTCGTT