UCD_Gh_M_000398, UCD_Gh_M_000398 (genetic_marker) Gossypium hirsutum

Marker Overview
NameUCD_Gh_M_000398
AliasGh_M_000398
Tm1_Mira454_Contig_1690_117
Gh_M_000398_Class_II
dbSNP IDN/A
TypeSNP
SNP AllelesT/C
5' Flanking SequenceTCATTAGACAATACAAACCAGTGAAACTGCACATAATGCAACTTAAAAGCTACTAAGAGT TTTTTAACTTAAAATTAACCAAAATTTATTGTCCCTTTTT
3' Flanking SequenceCTTTGTCACCCTTAATATTAGTGATATGCAACTAGGATGATGGTTGCAGTAACGATGAGG ACGATGCGAGAGGCTCGTGAACGACAGAATTCGAAGAAAT
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
CM018216.1chromosomeCM018216.1:65798025..65798226 -Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_03chromosomeD5_03:1115592..1115794 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
D10_03chromosomeD10_03:1051044..1051246 +Gossypium turneri (D10) genome NSF_v1_a2n/a
Dt_chr5chromosomeDt_chr5:7519410..7519611 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D02chromosomeD02:66193535..66193736 -Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D02chromosomeGhir_D02:68668197..68668398 -Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D02chromosomeD02:68665551..68665752 -Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D02chromosomeD02:70003549..70003750 -Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D02chromosomeD02:67119686..67119887 -Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D02chromosomeGbar_D02:66542255..66542456 -Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D02chromosomeD02:67745289..67745490 -Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017650.1chromosomeCM017650.1:70421965..70422166 -Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017702.1chromosomeCM017702.1:67338813..67339014 -Gossypium darwinii (AD5) genome HGS_v1.1n/a
D02chromosomeD02:71086395..71086596 -Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr03chromosomeChr03:61960898..61961100 -Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
Chr05_5118312chromosomeChr05_5118312:5423..5625 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr05chromosomeChr05:66494148..66494350 -Gossypium davidsonii (D3d-8) genome CRI_v1n/a
Chr05chromosomeChr05:36750254..36750456 -Gossypium gossypioides (D6) genome ISU_v1n/a
Chr05chromosomeChr05:45427428..45427630 -Gossypium lobatum (D7) genome ISU_v1n/a
F03chromosomeF03:109145579..109145781 -Gossypium longicalyx (F1) genome NSF_v1n/a
Germplasm
Stock NameType
Acala Maxxaaccession
PD-1accession
Sealand 542accession
Fibermax 832accession
TM-1accession
Sequence
>UCD_Gh_M_000398 ID=UCD_Gh_M_000398; Name=UCD_Gh_M_000398; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
TCATTAGACAATACAAACCAGTGAAACTGCACATAATGCAACTTAAAAGC
TACTAAGAGTTTTTTAACTTAAAATTAACCAAAATTTATTGTCCCTTTTT
[C/T]CTTTGTCACCCTTAATATTAGTGATATGCAACTAGGATGATGGTT
GCAGTAACGATGAGGACGATGCGAGAGGCTCGTGAACGACAGAATTCGAA
GAAAT