UCD_Gh_M_000283, UCD_Gh_M_000283 (genetic_marker) Gossypium hirsutum

Marker Overview
NameUCD_Gh_M_000283
AliasGh_M_000283_Class_II
Gh_M_000283
Tm1_Mira454_Contig_1019_998
dbSNP IDN/A
TypeSNP
SNP AllelesC/T
5' Flanking SequenceAACGTGGTTGCCACAGGTAACCACAGTGGAACCAAGAGGGACATCAGGTGGCGTCGTACT CAAAACGTCAGAGATTTCACCTCTTTCCAGATCCAAAAAG
3' Flanking SequenceGCAAATCAGTCCTGCGTTTACCTTCGGTATCCCGCTGTGTCTTATCGAGGAAAAACAAGC CCTTGATCTCTCCATCTCGTTGTCGCGCATCAAAGTAACT
SpeciesGossypium hirsutum
GermplasmAcala Maxxa
PD-1
Sealand 542
Fibermax 832
TM-1
Source TypeRNA
Publication[view all]
ContactAshrafi, Hamid
Commentclass_II: Only SNPs with one homeo-SNP in a position on the contig outside of 100 bases window on each side of the putative SNP position
Contact
NameDetails
Ashrafi, Hamid
First name:Hamid
Last name:Ashrafi
Title:Bioinformatics Specialist
Institution:University of California
Address:1 Shields Ave, Davis, CA 95616
Country:United States
Email:ashrafi@ucdavis.edu
Last update:24-Aug-2014
Alignments
The following features are aligned
Feature Name Type LocationAnalysisReference
CM018220.1chromosomeCM018220.1:2700988..2701188 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
CM018220.1chromosomeCM018220.1:2730931..2731131 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
Dt_chr9chromosomeDt_chr9:68118439..68118639 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
Dt_chr9chromosomeDt_chr9:68088915..68089115 -Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D06chromosomeD06:2457416..2457616 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
D06chromosomeD06:2426640..2426840 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D06chromosomeGhir_D06:2874231..2874431 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
Ghir_D06chromosomeGhir_D06:2844402..2844602 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D06chromosomeD06:2729702..2729902 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D06chromosomeD06:2700519..2700719 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D06chromosomeD06:2875477..2875677 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D06chromosomeD06:2845603..2845803 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
Gbar_D06chromosomeGbar_D06:2786917..2787117 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
Gbar_D06chromosomeGbar_D06:2816859..2817059 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D06chromosomeD06:2815846..2816046 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
D06chromosomeD06:2786308..2786508 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017654.1chromosomeCM017654.1:2946614..2946814 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017706.1chromosomeCM017706.1:2833947..2834147 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
CM017706.1chromosomeCM017706.1:2804031..2804231 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D06chromosomeD06:2941717..2941917 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
D06chromosomeD06:2911842..2912042 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr10chromosomeChr10:2866188..2866388 +Gossypium thurberi (D1-5) genome CRI_v1n/a
Chr10chromosomeChr10:2901324..2901524 +Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr10chromosomeChr10:2536204..2536404 +Gossypium lobatum (D7) genome ISU_v1n/a
Germplasm
Stock NameType
Acala Maxxaaccession
PD-1accession
Sealand 542accession
Fibermax 832accession
TM-1accession
Sequence
>UCD_Gh_M_000283 ID=UCD_Gh_M_000283; Name=UCD_Gh_M_000283; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
AACGTGGTTGCCACAGGTAACCACAGTGGAACCAAGAGGGACATCAGGTG
GCGTCGTACTCAAAACGTCAGAGATTTCACCTCTTTCCAGATCCAAAAAG
[C/T]GCAAATCAGTCCTGCGTTTACCTTCGGTATCCCGCTGTGTCTTAT
CGAGGAAAAACAAGCCCTTGATCTCTCCATCTCGTTGTCGCGCATCAAAG
TAACT