UCD_Gh_M_000409, UCD_Gh_M_000409 (genetic_marker) Gossypium hirsutum

Marker Overview
NameUCD_Gh_M_000409
AliasGh_M_000409
Tm1_Mira454_Contig_1758_179
dbSNP IDN/A
TypeSNP
SNP AllelesA/T
5' Flanking SequenceCATTGAATCTATGTTTTGCAGTAGTAAGACAAGAAGGGAAGTAGGAAGATAGTGAACAGA GAGAAAATATGTGGAAAACCAAACGGCTTGATATATATAT
3' Flanking SequenceTTTTTTAATATTATGAAATACTTTTGATATTCTCATTGTAAAACACCAGAACATGATAGC TTTTGTGGAGTTACATTTTTGGTTTTGTTCATACTACATG
SpeciesGossypium hirsutum
GermplasmAcala Maxxa
PD-1
Sealand 542
Fibermax 832
TM-1
Source TypeRNA
Publication[view all]
ContactAshrafi, Hamid
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
CM018215.1chromosomeCM018215.1:45651563..45651763 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_01chromosomeD5_01:40531380..40531580 -Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
D10_01chromosomeD10_01:16865802..16866000 +Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr2chromosomeDt_chr2:5741869..5742069 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D01chromosomeD01:43948759..43948959 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Scaffold679supercontigScaffold679:78792..78992 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D01chromosomeD01:47530699..47530899 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D01chromosomeD01:46991223..46991423 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D01chromosomeD01:44454237..44454437 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D01chromosomeGbar_D01:45867322..45867522 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D01chromosomeD01:46598154..46598354 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017623.1chromosomeCM017623.1:46672844..46673044 -Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017649.1chromosomeCM017649.1:47838950..47839150 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017701.1chromosomeCM017701.1:46086871..46087071 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D01chromosomeD01:47514272..47514472 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr01chromosomeChr01:36055772..36055972 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
chr02chromosomechr02:33763883..33764081 -Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_02chromosomeChr_02:30755137..30755335 -Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr02chromosomeChr02:44763305..44763503 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr02chromosomeChr02:32082612..32082810 -Gossypium lobatum (D7) genome ISU_v1n/a
Germplasm
Stock NameType
Acala Maxxaaccession
PD-1accession
Sealand 542accession
Fibermax 832accession
TM-1accession
Sequence
>UCD_Gh_M_000409 ID=UCD_Gh_M_000409; Name=UCD_Gh_M_000409; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
CATTGAATCTATGTTTTGCAGTAGTAAGACAAGAAGGGAAGTAGGAAGAT
AGTGAACAGAGAGAAAATATGTGGAAAACCAAACGGCTTGATATATATAT
[A/T]TTTTTTAATATTATGAAATACTTTTGATATTCTCATTGTAAAACA
CCAGAACATGATAGCTTTTGTGGAGTTACATTTTTGGTTTTGTTCATACT
ACATG