BNL0390, BNL0390 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL0390
AliasBNL390
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL0390_orig
Source Typegenomic
Repeat Motif(AG)11, (CT)11, (AG)11+T+(GA)5
PCR ConditionAnnealing temperature: 55
Primer 1BNL0390_F: CTTTGGGTTGGAATGTGAGG
Primer 2BNL0390_R: CATTCTGGCCCACACTCAC
PolymorphismP_ BNL0390
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Aligned FeatureFeature TypeAlignment Location
D05chromosomeD05:22786702..22786937 -
A05chromosomeA05:24854930..24855154 -
CM018219.1chromosomeCM018219.1:21606535..21606790 -
Chr05_CRI-A2_v1.0.a1chromosomeChr05_CRI-A2_v1.0.a1:24550323..24550554 -
D10_05chromosomeD10_05:40159947..40160182 +
Dt_chr11chromosomeDt_chr11:47096094..47096329 -
D05chromosomeD05:21843356..21843591 -
Ghir_D05chromosomeGhir_D05:22109979..22110214 -
Ghir_A05chromosomeGhir_A05:24420826..24421050 -
D05chromosomeD05:21578948..21579183 -
D05chromosomeD05:21949131..21949366 -
A05chromosomeA05:24466544..24466768 -
D05chromosomeD05:21830963..21831198 -
A05chromosomeA05:24623582..24623813 -
scaffold4262supercontigscaffold4262:89214..89773 +
Gbar_D05chromosomeGbar_D05:21889213..21889462 -
D05chromosomeD05:21856572..21856817 -
CM017627.1chromosomeCM017627.1:21763520..21763755 -
CM017653.1chromosomeCM017653.1:22156597..22156834 -
CM017640.1chromosomeCM017640.1:24418996..24419227 -
CM017705.1chromosomeCM017705.1:21814956..21815191 -
D05chromosomeD05:22440473..22440708 -
A05chromosomeA05:24854401..24854625 -
Chr05chromosomeChr05:26141671..26141902 -
Chr05chromosomeChr05:24472354..24472585 -
Chr05chromosomeChr05:20374360..20374603 -
Chr09chromosomeChr09:20847507..20847732 -
Chr_09chromosomeChr_09:17248966..17249199 -
Chr09chromosomeChr09:21511561..21512028 -
Chr09chromosomeChr09:17573636..17573861 -
Chr09chromosomeChr09:17960616..17960843 -
F05chromosomeF05:20918311..20918536 -
Chr05chromosomeChr05:104837526..104837754 +
Chr09chromosomeBNL0390:1..288 .
Chr09:20214006..20214301 -
Chr9chromosomeBNL0390:1..288 .
Chr9:28628372..28628667 +
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL0390_origBNL0390_origGossypium hirsutumsequence_feature


Image
File NameLegend
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
1Emian-22 x 3-79, BC1 (2011)AD_ch19_Dt.05N/A102.27BNL390View
2Guazuncho-2 x VH8-4602, BC1 (2005)AD_ch19_Dt.05N/A117.2BNL390View
3Hai-7124 x Junmian-1, BC1 (2008) partAD_ch19_Dt.05N/A34.3BNL390View
4Xinluzao-1 x Hai-7124, F2 (2008)AD_ch19_Dt.05N/A224.6BNL390View
5Handan-208 x Pima-90, F2:3 (2007)AD_ch19_Dt.05N/A398.2BNL390View
6TM-1 x (TX-0256 + TX-1046), CSIL (2016)AD_ch19_Dt.05N/A76.6BNL390View
7CCRI 12-4 x (AD)5-7, F2 (2015)AD_ch19_Dt.05N/A100.5BNL390View
8Guazuncho-2 x VH8-4602, consensus (2009)AD_ch19_Dt.05N/A100.54BNL0390View
9AD-genome wide Reference Map (2009)AD_ch19_Dt.05N/A193BNL0390View
10AD-genome wide Reference Map (2009)AD_ch05_At.05N/A171BNL0390View
11CCRI-35 x Yumian-1, RIL (2015)AD_ch19_Dt.05N/A50.8BNL0390View
12Monsanto SSR Bin Map, (2009)AD_ch19_Dt.05N/A141BNL0390View
13Handan-208 x Pima-90, F2:3 (2007)AD_ch05_At.05N/A232.1BNL390c*View
14Handan-208 x Pima-90, F2:3 (2007)AD_ch05_At.05N/A243.2BNL390aView
15Handan-208 x Pima-90, F2:3 (2007)AD_ch19_Dt.05N/A265BNL390d*View
16Handan-208 x Pima-90, F2:3 (2007)AD_ch25_Dt.06N/A49.3BNL390b*View
17Vsg x (TM-1 x Hai-7124), DH (2005)AD_ch19_Dt.05N/A134.6BNL390-275View
18TM-1 x Hai-7124, BC1 (2007)AD_ch19_Dt.05N/A105.9BNL390-275View
19TM-1 x Hai-7124, BC1 (2008)AD_ch19_Dt.05N/A105.66BNL390-275View
20TM-1 x Hai-7124, BC1 (2012)AD_ch19_Dt.05N/A83.8BNL390-275View
21CCRI-35 x Yumian-1, RIL (2017)AD_ch19_Dt.05N/A92.39BNL0390View
22PD 94042 x (AD)4-08, F2 (2016)AD_ch19_Dt.05N/A150.1BNL390View
Sequence
>BNL0390 ID=BNL0390; Name=BNL0390; organism=Gossypium hirsutum; type=genetic_marker; length=236bp
CTTTGGGTTGGAATGTGAGGGTGATTGGGGTCAAGTGAACTGAGAGAAAG
GATTTAAAGTAGAGAACAAAAAGTGGGGAAACTTGTAGACTAAGAATTGA
TGTTTAGATTTGGTAATACACCAAAAACAAATGCTGCTTTGACACTTGTC
ATAATCTCACCGCACTGTAAGAGAGAGAGAGAGAGAGAGAGTGAGAGAGA
GAATCACTGACAACCACGTGAGTGTGGGCCAGAATG