BNL1038, BNL1038 (genetic_marker) Gossypium hirsutum

Marker Overview
NameBNL1038
Genbank IDN/A
TypeSSR
SpeciesGossypium hirsutum
GermplasmDeltapine 90
Source SequenceBNL1038_orig
Source Typegenomic
Repeat Motif(CA)10, (GT)10
PCR ConditionAnnealing temperature: 55
Primer 1BNL1038_F: GCGTATGTGGGGAACAGAAC
Primer 2BNL1038_R: TGCTTGAGAATCAATTGCCA
CommentPrimer data obtained in 2000
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
D04chromosomeD04:6208258..6208449 +Gossypium hirsutum (AD1) 'TM-1' genome UTX-JGI-Interim-release_v1.1n/a
CM018218.1chromosomeCM018218.1:5679088..5679279 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
KI_06chromosomeKI_06:47030989..47031179 +Gossypioides kirkii genome ISU_v3n/a
D10_04chromosomeD10_04:5599694..5599893 +Gossypium turneri (D10) genome NSF_v1_a2n/a
CM016617.1chromosomeCM016617.1:9499884..9500076 +Gossypium australe (G2) genome CRI_v1.1n/a
At_chr9chromosomeAt_chr9:61823144..61823335 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D04chromosomeD04:5439265..5439456 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D04chromosomeGhir_D04:6111359..6111550 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D04chromosomeD04:6023126..6023317 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D04chromosomeD04:5983826..5984017 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D04chromosomeD04:5720385..5720576 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Dt04chromosomeDt04:5754814..5755005 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
scaffold13974supercontigscaffold13974:501035..501226 +Gossypium barbadense (AD2) '3-79' genome HAU_v1n/a
Gbar_D04chromosomeGbar_D04:5669403..5669594 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D04chromosomeD04:5627184..5627375 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017626.1chromosomeCM017626.1:5772588..5772779 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017652.1chromosomeCM017652.1:5978260..5978451 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017704.1chromosomeCM017704.1:5935153..5935346 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D04chromosomeD04:6477493..6477684 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr04chromosomeChr04:45004349..45004542 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_02chromosomeB_02:77594424..77594616 -Gossypium anomalum (B1) genome NSF_v1n/a
Chr12chromosomeChr12:5985638..5985832 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr12chromosomechr12:5505118..5505312 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr12chromosomeChr12:5734913..5735119 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr12chromosomeChr12:5718223..5718415 +Gossypium aridum (D4) genome ISU_v1n/a
Chr12chromosomeChr12:3863707..3863897 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr12chromosomeChr12:5457734..5457924 +Gossypium lobatum (D7) genome ISU_v1n/a
F04chromosomeF04:6134365..6134559 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr04chromosomeChr04:9148043..9148237 +Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr12chromosomeBNL1038:1..230 .
Chr12:5578056..5578287 +		n/a
Chr12chromosomeBNL1038:1..230 .
Chr12:20186080..20186311 +		n/a
Germplasm
Stock NameType
Deltapine 90accession
Relationships

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

Feature NameUnique NameSpeciesType
BNL1038_origBNL1038_origGossypium hirsutumsequence_feature


Map Positions
#Map NameLinkage GroupBinPositionLocusMapViewer
1Emian-22 x 3-79, BC1 (2011)AD_ch05_At.05N/A175.74BNL1038View
2JLZM x ZJXSLS, F2 (2008)A_JZ_A05N/A116.8BNL1038View
3AD-genome wide Reference Map (2009)AD_ch17_Dt.03N/A100BNL1038View
4AD-genome wide Reference Map (2009)AD_ch05_At.05N/A287BNL1038View
5Xinluzao-1 x Hai-7124, F2 (2008)AD_chUN/A5.2BNL1038View
6SG 747 x Giza 75, BIL (2013)AD_ch05_At.05N/A100.3BNL1038View
7Monsanto SSR Bin Map, (2009)AD_ch05_At.05N/A21BNL1038View
8Handan-208 x Pima-90, F2:3 (2007)AD_ch17_Dt.03N/A203.6BNL1038bView
9Handan-208 x Pima-90, F2:3 (2007)AD_ch17_Dt.03N/A205.4BNL1038aView
10TM-1 x Hai-7124, BC1 (2008)AD_ch05_At.05N/A158.85BNL1038-160View
11TM-1 x Hai-7124, BC1 (2012)AD_ch05_At.05N/A45.6BNL1038-160View
Sequence
>BNL1038 ID=BNL1038; Name=BNL1038; organism=Gossypium hirsutum; type=genetic_marker; length=192bp
GCGTATGTGGGGAACAGAACTTGAGTATAAGTTTATTCACGAACTCTCCA
TCCTGCAACATTGTAAAACCTGTTACACACACACACACACACACATATTC
AAAAAAAGTTACCAAATTGTAAACCTTAGTTCCATTGCTATCTACAGCAA
CCAAGCTGAAGAGAACAGGAATTGGCAATTGATTCTCAAGCA