USDA_CFB0042, USDA_CFB0042 (genetic_marker) Gossypium hirsutum

Marker Overview
NameUSDA_CFB0042
AliasCFB0042
dbSNP IDN/A
TypeSNP
SNP AllelesT/A
5' Flanking SequenceCTACTTTTACC
3' Flanking SequenceTGCTAAATGAATAATTAGGTAAATCTCAAATTGATTATTTTTATTTTCATCCATCAGGAA TGAGTCCGAGA
SpeciesGossypium hirsutum
Publication[view all]
ContactFang, David D.
CommentSNP generated in Data2Bio, LLC, Ames, IA
Contact
NameDetails
Fang, David D.
Description:Molecular markers, fiber development
First name:David
Last name:Fang
Title:Supervisory Research Geneticist
Institution:USDA-ARS-SRRC-CFBRU
Address:1100 Robert E. Lee Blvd, New Orleans, LA 70124
Country:United States
Email:david.fang@usda.gov
Phone:504 286 4527
Fax:001662686-5218
Keywords:Structural Genomics
Last update:2-Jul-2009
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
CM018215.1chromosomeCM018215.1:5231778..5231860 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018202.1chromosomeCM018202.1:5991775..5991856 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_01chromosomeD5_01:4962121..4962203 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
KI_01chromosomeKI_01:4022366..4022446 +Gossypioides kirkii genome ISU_v3n/a
Chr01_CRI-A2_v1.0.a1chromosomeChr01_CRI-A2_v1.0.a1:6690371..6690453 +Gossypium arboreum (A2) 'SXY1' genome CRI-updated_v1n/a
D10_01chromosomeD10_01:55616612..55616694 -Gossypium turneri (D10) genome NSF_v1_a2n/a
D10_01chromosomeD10_01:55347608..55347690 -Gossypium turneri (D10) genome NSF_v1_a2n/a
At_chr2chromosomeAt_chr2:6062590..6062672 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
At_chr2chromosomeAt_chr2:5927022..5927104 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
A01chromosomeA01:5636191..5636273 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
scaffold3716_D01supercontigscaffold3716_D01:17237..17319 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_A01chromosomeGhir_A01:6190466..6190548 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Scaffold781supercontigScaffold781:62210..62292 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D01chromosomeD01:5246662..5246744 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
A01chromosomeA01:5870721..5870803 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D01chromosomeD01:5276268..5276350 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
A01chromosomeA01:6170653..6170735 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D01chromosomeD01:5366943..5367025 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
A01chromosomeA01:6118072..6118154 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D01chromosomeGbar_D01:5717713..5717795 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_A01chromosomeGbar_A01:5941692..5941773 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D01chromosomeD01:5507677..5507759 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
A01chromosomeA01:5880044..5880126 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017623.1chromosomeCM017623.1:5353420..5353502 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017610.1chromosomeCM017610.1:6715869..6715951 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017649.1chromosomeCM017649.1:5809068..5809150 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017636.1chromosomeCM017636.1:6035058..6035140 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017701.1chromosomeCM017701.1:5468827..5468909 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017688.1chromosomeCM017688.1:6134604..6134686 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D01chromosomeD01:5665974..5666056 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
A01chromosomeA01:6161155..6161237 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr01chromosomeChr01:5948889..5948971 +Gossypium herbaceum (A1) 'Mutema' genome WHU_v1n/a
Chr01chromosomeChr01:6487989..6488071 +Gossypium arboreum (A2) 'SXY1' genome WHU-updated v1n/a
Chr01chromosomeChr01:4953739..4953821 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr02chromosomeChr02:5371901..5371983 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr_02chromosomeChr_02:4159481..4159563 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr02chromosomeChr02:5560482..5560564 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr02chromosomeChr02:3541237..3541319 +Gossypium gossypioides (D6) genome ISU_v1n/a
Chr02chromosomeChr02:4857575..4857657 +Gossypium lobatum (D7) genome ISU_v1n/a
F01chromosomeF01:5194679..5194761 +Gossypium longicalyx (F1) genome NSF_v1n/a
Chr01chromosomeChr01:191952757..191952839 -Gossypium rotundifolium (K2) 'Grot K201' genome HAU_v1n/a
Chr02chromosomeChr02:4867920..4867921 .Gossypium raimondii (D5) genome JGI_v2_a2.1Islam MS, Thyssen GN, Jenkins JN, and Fang DD. Detection, Validation, and Application of Genotyping-by-Sequencing Based Single Nucleotide Polymorphisms in Upland Cotton. The Plant Genome. 2015 March; 8(1):1-10.
Sequence
>USDA_CFB0042 ID=USDA_CFB0042; Name=USDA_CFB0042; organism=Gossypium hirsutum; type=genetic_marker; length=87bp
CTACTTTTACC[A/T]TGCTAAATGAATAATTAGGTAAATCTCAAATTGA
TTATTTTTATTTTCATCCATCAGGAATGAGTCCGAGA