UCD_Gh_M_000414, UCD_Gh_M_000414 (genetic_marker) Gossypium hirsutum

Marker Overview
NameUCD_Gh_M_000414
AliasGh_M_000414
Tm1_Mira454_Contig_1798_132
Gh_M_000414_Class_I
dbSNP IDN/A
TypeSNP
SNP AllelesC/T
5' Flanking SequenceGGTAGCAACAAATTATTATTACATCTTTAAATATCCACAGGCTGGCTTTTACAGCCCATA CAAGTGCAAAACACAGGTGCTAAAAGCCATTCATCCTTTC
3' Flanking SequenceACACACTCTTCTCATCTCCCAACCAAAATACACACCCATCAACTCCTCGTATTTAACACT ACAATAGGCCTGTGCTTCCACCAAATGGATTATTCGCATG
SpeciesGossypium hirsutum
GermplasmAcala Maxxa
PD-1
Sealand 542
Fibermax 832
TM-1
Source TypeRNA
Publication[view all]
ContactAshrafi, Hamid
Commentclass_I: no only SNPs derived from contigs with no known homeo-SNP positions in the contig within our data set
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
CM018219.1chromosomeCM018219.1:36247047..36247247 +Gossypium barbadense (AD2) '3-79' genome HGS_v1.1n/a
D5_05chromosomeD5_05:34332136..34332336 +Gossypium raimondii (D5) 'D5-4' genome NSF_v1n/a
Dt_chr9chromosomeDt_chr9:26150070..26150270 +Gossypium hirsutum (AD1) 'TM-1' genome CGP-BGI_v1n/a
D05chromosomeD05:36720006..36720206 +Gossypium hirsutum (AD1) 'TM-1' genome NAU-NBI_v1.1n/a
Ghir_D05chromosomeGhir_D05:36991122..36991322 +Gossypium hirsutum (AD1) 'TM-1' genome HAU_v1 / v1.1n/a
D05chromosomeD05:36138012..36138212 +Gossypium hirsutum (AD1) 'TM-1' genome ZJU-improved_v2.1_a1n/a
D05chromosomeD05:36742882..36743082 +Gossypium hirsutum (AD1) 'TM-1' genome CRI_v1n/a
D05chromosomeD05:36365375..36365575 +Gossypium hirsutum (AD1) 'ZM24' genome CRI_v1n/a
Gbar_D05chromosomeGbar_D05:37126593..37126793 +Gossypium barbadense (AD2) '3-79' genome HAU_v2_a1n/a
D05chromosomeD05:36594400..36594600 +Gossypium barbadense (AD2) 'H7124' genome ZJU_v1.1_a1n/a
CM017627.1chromosomeCM017627.1:36506832..36507032 +Gossypium tomentosum (AD3) genome HGS_v1.1n/a
CM017653.1chromosomeCM017653.1:37122768..37122968 +Gossypium mustelinum (AD4) genome JGI_v1.1n/a
CM017705.1chromosomeCM017705.1:36631169..36631369 +Gossypium darwinii (AD5) genome HGS_v1.1n/a
D05chromosomeD05:37553794..37553994 +Gossypium hirsutum (AD1) 'TM-1' genome UTX_v2.1n/a
Chr05chromosomeChr05:34474345..34474545 +Gossypium raimondii (D5) 'Grai D502' genome HAU_v1n/a
B_05chromosomeB_05:38659956..38660156 -Gossypium anomalum (B1) genome NSF_v1n/a
Chr09chromosomeChr09:35334025..35334225 +Gossypium thurberi (D1-5) genome CRI_v1n/a
chr09chromosomechr09:30268371..30268571 +Gossypium armourianum (D2-1) genome ISU_v1n/a
Chr_09chromosomeChr_09:28909480..28909680 +Gossypium harknessii (D2-2) genome ISU_v1n/a
Chr09chromosomeChr09:27222437..27222637 +Gossypium aridum (D4) genome ISU_v1n/a
Chr09chromosomeChr09:27914891..27915091 +Gossypium lobatum (D7) genome ISU_v1n/a
E05chromosomeE05:60277434..60277634 -Gossypium stocksii (E1) genome NSF_v1n/a
F05chromosomeF05:41606188..41606388 +Gossypium longicalyx (F1) genome NSF_v1n/a
Germplasm
Stock NameType
Acala Maxxaaccession
PD-1accession
Sealand 542accession
Fibermax 832accession
TM-1accession
Sequence
>UCD_Gh_M_000414 ID=UCD_Gh_M_000414; Name=UCD_Gh_M_000414; organism=Gossypium hirsutum; type=genetic_marker; length=205bp
GGTAGCAACAAATTATTATTACATCTTTAAATATCCACAGGCTGGCTTTT
ACAGCCCATACAAGTGCAAAACACAGGTGCTAAAAGCCATTCATCCTTTC
[C/T]ACACACTCTTCTCATCTCCCAACCAAAATACACACCCATCAACTC
CTCGTATTTAACACTACAATAGGCCTGTGCTTCCACCAAATGGATTATTC
GCATG