BNL2939, BNL2939 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL2939
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL2939_orig
Source Typegenomic
Repeat Motif(AG)11
PCR ConditionAnnealing temperature: 55
Primer 1BNL2939_F: GCAACTGCCACAAGGTATGA
Primer 2BNL2939_R: ATTAATGCTCCCCCCAAAAG
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D04chromosomeD04:40109321..40109554 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
A04chromosomeA04:60719414..60719659 -Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018218.1chromosomeCM018218.1:38464835..38465068 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018205.1chromosomeCM018205.1:59928742..59928983 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_04chromosomeD5_04:15551006..15551241 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Chr04_CRI-A2_v1.0.a1chromosomeChr04_CRI-A2_v1.0.a1:23358736..23358982 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_04chromosomeD10_04:37441796..37442029 -Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016617.1chromosomeCM016617.1:98417528..98417765 -Gossypium australe (G2) genome CRI_v1.1n/a
Dt_chr12chromosomeDt_chr12:25244255..25244488 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D04chromosomeD04:35346787..35347020 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
A04chromosomeA04:42049902..42050147 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D04chromosomeGhir_D04:40159202..40159435 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_A04chromosomeGhir_A04:63262959..63263204 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D04chromosomeD04:41299204..41299437 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A04chromosomeA04:66098217..66098462 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D04chromosomeD04:40345151..40345384 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A04chromosomeA04:63037135..63037380 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D04chromosomeD04:37983170..37983403 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A04chromosomeA04:58618664..58618909 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt04chromosomeDt04:35801352..35801585 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Dt04chromosomeDt04:35797121..35797354 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold7450supercontigscaffold7450:169819..170060 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold2674supercontigscaffold2674:171568..171801 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold2674supercontigscaffold2674:167337..167570 -Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D04chromosomeGbar_D04:36542425..36542658 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A04chromosomeGbar_A04:60350026..60350267 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D04chromosomeD04:41734730..41734963 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A04chromosomeA04:60971997..60972238 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017626.1chromosomeCM017626.1:38971365..38971598 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017613.1chromosomeCM017613.1:61957570..61957813 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017652.1chromosomeCM017652.1:41585965..41586198 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017639.1chromosomeCM017639.1:69861202..69861453 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017704.1chromosomeCM017704.1:38771977..38772210 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017691.1chromosomeCM017691.1:60446090..60446333 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D04chromosomeD04:41825596..41825829 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A04chromosomeA04:66573147..66573392 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr04chromosomeChr04:79034416..79034657 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr04chromosomeChr04:88071962..88072209 -Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
B_02chromosomeB_02:21117420..21117657 +Gossypium anomalum (B1) genome NSF_v1n/a
Chr12chromosomeChr12:38603627..38603860 -Gossypium thurberi (D1-5) genome CRI_v1n/a
chr09chromosomechr09:49347161..49347394 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_09chromosomeChr_09:47933131..47933364 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr12chromosomeChr12:38063784..38064015 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr09chromosomeChr09:45589169..45589402 -Gossypium aridum (D4) genome ISU_v1n/a
Chr09chromosomeChr09:38622453..38622690 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr09chromosomeChr09:47725687..47725920 -Gossypium lobatum (D7) genome ISU_v1n/a
E04chromosomeE04:65867477..65867711 +Gossypium stocksii (E1) genome NSF_v1n/a
Chr04chromosomeChr04:121854844..121855079 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL2939_origBNL2939_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Handan-208 x Pima-90, F2:3 (2007)AD_ch04_At.04N/A41.1BNL2939View
2AD-genome wide Reference Map (2009)AD_ch04_At.04N/A100BNL2939View
3Emian-22 x 3-79, BC1 (2011)AD_ch04_At.04N/A84.78BNL2939View
4TM-1 x Hai-7124, BC1 (2008)AD_ch04_At.04N/A53.63BNL2939-330View
5TM-1 x Hai-7124, BC1 (2012)AD_ch04_At.04N/A70.9BNL2939-330View
Sequence
>BNL2939 ID=BNL2939; Name=BNL2939; organism=Gossypium hirsutum; type=genetic_marker; length=246bp
GCAACTGCCACAAGGTATGACTCTATTCCCCATCTTCCTCCATTTGGTAA
TGCATGCCTTTAGAAATTTCCCCTTCATTGTCTAGCAATATGCCAACATA
GACAGAGAGTAGATGGGGGAAAGGAACTTGCACATGTAATCTGAAATGGA
GATTTGGGTAGTGAAACAGATGGAACTGAAAGAAAGGATTATATAGCAGT
AGAAAGAGAGAGAGAGAGAGAGAGAGCTTTTGGGGGGAGCATTAAT