AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060662

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060662.t1 MTR_2g078310 97.959 49 1 0 1 49 170 218 1.80e-28 100
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060662.t1 AT4G22140 76.596 47 11 0 1 47 178 224 1.53e-18 74.7
MS.gene060662.t1 AT4G22140 75.000 40 10 0 1 40 178 217 2.19e-14 63.9
MS.gene060662.t1 AT4G22140 75.000 40 10 0 1 40 178 217 2.19e-14 63.9

Find 11 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TATCGAAGAAGCAAAGAAAT+TGG 0.293372 2.2:+16362065 MS.gene060662:CDS
CTATCAGATCCTGGTGATAC+AGG 0.385003 2.2:-16362150 None:intergenic
AACATTCAGAACAAACAAAA+TGG 0.403224 2.2:-16362089 None:intergenic
GGTCCTCTCTTTCGCCGCTT+CGG 0.470540 2.2:-16363726 None:intergenic
CTCACCTTGCTATCAGATCC+TGG 0.485170 2.2:-16362159 None:intergenic
GAGCCGAAGCGGCGAAAGAG+AGG 0.538999 2.2:+16363723 MS.gene060662:CDS
CGATGATTTGAAGAAACCAC+AGG 0.614767 2.2:+16362119 MS.gene060662:CDS
GCGGCGTTTCCTGTATCACC+AGG 0.621923 2.2:+16362141 MS.gene060662:CDS
ATCACCAGGATCTGATAGCA+AGG 0.624737 2.2:+16362155 MS.gene060662:CDS
GATACAGGAAACGCCGCCTG+TGG 0.630270 2.2:-16362135 None:intergenic
TGATTTGAAGAAACCACAGG+CGG 0.754665 2.2:+16362122 MS.gene060662:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCAAATTTACAAAAATTTA+CGG - chr2.2:16362949-16362968 None:intergenic 10.0%
!! CATATATTCTAATTAAAATT+TGG + chr2.2:16362350-16362369 MS.gene060662:intron 10.0%
!! TGAAAAAAAATAACATATAT+GGG + chr2.2:16362719-16362738 MS.gene060662:intron 10.0%
!! TTGAAAAAAAATAACATATA+TGG + chr2.2:16362718-16362737 MS.gene060662:intron 10.0%
!! TCAAATTTACAAAAATTTAC+GGG - chr2.2:16362948-16362967 None:intergenic 15.0%
!!! AAAGAATTTTGAGAAAAAAA+CGG - chr2.2:16362421-16362440 None:intergenic 15.0%
!!! ACCACATTTAAAATTTATAA+AGG - chr2.2:16362542-16362561 None:intergenic 15.0%
!!! ACCTTTATAAATTTTAAATG+TGG + chr2.2:16362538-16362557 MS.gene060662:intron 15.0%
!!! ATTTAGTTCTAAATATTATG+AGG + chr2.2:16362203-16362222 MS.gene060662:intron 15.0%
!!! ATTTTGTGAGTAATAAATAA+TGG + chr2.2:16363537-16363556 MS.gene060662:intron 15.0%
!!! TCAAATTTTTTATTCCTTTT+TGG + chr2.2:16363572-16363591 MS.gene060662:intron 15.0%
!! TAATCAGTAGTTAATATCTA+GGG + chr2.2:16363026-16363045 MS.gene060662:intron 20.0%
!! TTATATTTAAGCTTATCTGA+TGG + chr2.2:16363065-16363084 MS.gene060662:intron 20.0%
!!! ACATAATCTCTTTTAATCAA+TGG + chr2.2:16363595-16363614 MS.gene060662:intron 20.0%
!!! ATTATTTTGATTGACACTAT+AGG + chr2.2:16363641-16363660 MS.gene060662:intron 20.0%
!!! GTTGTTTTTATAAGCAATAT+TGG - chr2.2:16363182-16363201 None:intergenic 20.0%
!!! TTATTTTGATTGACACTATA+GGG + chr2.2:16363642-16363661 MS.gene060662:intron 20.0%
! AAAAGAGATTATGTCCAAAA+AGG - chr2.2:16363589-16363608 None:intergenic 25.0%
! AACATTCAGAACAAACAAAA+TGG - chr2.2:16362092-16362111 None:intergenic 25.0%
! AATCAGTAGTTAATATCTAG+GGG + chr2.2:16363027-16363046 MS.gene060662:intron 25.0%
! AATGCTGCAATATGATTAAA+AGG + chr2.2:16362488-16362507 MS.gene060662:intron 25.0%
! ATGCTGCAATATGATTAAAA+GGG + chr2.2:16362489-16362508 MS.gene060662:intron 25.0%
! ATTGACATCAGAAATTATCT+AGG + chr2.2:16362643-16362662 MS.gene060662:intron 25.0%
! GTAATCAGTAGTTAATATCT+AGG + chr2.2:16363025-16363044 MS.gene060662:intron 25.0%
! TACCAAGGTAAAAGATAAAA+CGG - chr2.2:16362831-16362850 None:intergenic 25.0%
! TTGTGAGTAATAAATAATGG+AGG + chr2.2:16363540-16363559 MS.gene060662:intron 25.0%
! TTTAATCATATTGCAGCATT+AGG - chr2.2:16362488-16362507 None:intergenic 25.0%
!! ATTCTAACAATTTGAAGCTT+TGG + chr2.2:16363406-16363425 MS.gene060662:intron 25.0%
!! GGATAGAGTTTAAAACAAAA+GGG - chr2.2:16362810-16362829 None:intergenic 25.0%
!! TGGCTTTTACAAGAAAATAA+AGG - chr2.2:16363504-16363523 None:intergenic 25.0%
!! TTGGTGATCTGATAAAATAA+GGG + chr2.2:16363430-16363449 MS.gene060662:intron 25.0%
!! TTTGGTGATCTGATAAAATA+AGG + chr2.2:16363429-16363448 MS.gene060662:intron 25.0%
!!! AAATGTGGTTTTGATATCTA+TGG + chr2.2:16362553-16362572 MS.gene060662:intron 25.0%
AAATATAAGCCAATCCAAAC+AGG - chr2.2:16363053-16363072 None:intergenic 30.0%
ACAAAATGAACACTGCTTAA+TGG - chr2.2:16363524-16363543 None:intergenic 30.0%
ATTGTGTGTTTCTTCATTCT+TGG + chr2.2:16362377-16362396 MS.gene060662:intron 30.0%
CACTACCAAAAGATCATTTA+GGG - chr2.2:16363343-16363362 None:intergenic 30.0%
TATCGAAGAAGCAAAGAAAT+TGG + chr2.2:16362065-16362084 MS.gene060662:CDS 30.0%
TGGTGATCTGATAAAATAAG+GGG + chr2.2:16363431-16363450 MS.gene060662:intron 30.0%
TGTGAAATACAGTTCGAAAA+AGG - chr2.2:16362880-16362899 None:intergenic 30.0%
TTATGTCAAACAACTCAAAC+AGG - chr2.2:16362995-16363014 None:intergenic 30.0%
! AAAGACCCTAAATGATCTTT+TGG + chr2.2:16363335-16363354 MS.gene060662:intron 30.0%
! AACAATTTGAAGCTTTGGTT+TGG + chr2.2:16363411-16363430 MS.gene060662:intron 30.0%
! ATCCGTTTTATCTTTTACCT+TGG + chr2.2:16362826-16362845 MS.gene060662:intron 30.0%
! CGGATAGAGTTTAAAACAAA+AGG - chr2.2:16362811-16362830 None:intergenic 30.0%
! TATCTGATGGCATAAGTTTT+GGG + chr2.2:16363078-16363097 MS.gene060662:intron 30.0%
! TTATCTGATGGCATAAGTTT+TGG + chr2.2:16363077-16363096 MS.gene060662:intron 30.0%
!! AAGATCATTTAGGGTCTTTT+CGG - chr2.2:16363334-16363353 None:intergenic 30.0%
ATCAAGCACAAGAATTACCA+AGG - chr2.2:16362846-16362865 None:intergenic 35.0%
CCACTACCAAAAGATCATTT+AGG - chr2.2:16363344-16363363 None:intergenic 35.0%
CTCAAACAGGTTATCAATAG+CGG - chr2.2:16362982-16363001 None:intergenic 35.0%
GAAATACAGTTCGAAAAAGG+AGG - chr2.2:16362877-16362896 None:intergenic 35.0%
TCAAACAGGTTATCAATAGC+GGG - chr2.2:16362981-16363000 None:intergenic 35.0%
TTTCTTCATTCTTGGTACCA+TGG + chr2.2:16362385-16362404 MS.gene060662:intron 35.0%
! CCTAAATGATCTTTTGGTAG+TGG + chr2.2:16363341-16363360 MS.gene060662:intron 35.0%
! GAACAATGCTTGAATTTTGC+AGG + chr2.2:16363698-16363717 MS.gene060662:intron 35.0%
!! TATGAGGCATTCTTTTGCTT+TGG + chr2.2:16362219-16362238 MS.gene060662:intron 35.0%
!!! ATAAGTTTTGGGAGTCTGTT+TGG + chr2.2:16363089-16363108 MS.gene060662:intron 35.0%
!!! TAAGTTTTGGGAGTCTGTTT+GGG + chr2.2:16363090-16363109 MS.gene060662:intron 35.0%
AATGCTCTACTACTGAGCTA+TGG + chr2.2:16362783-16362802 MS.gene060662:intron 40.0%
ATAACATATATGGGCCCAAC+CGG + chr2.2:16362728-16362747 MS.gene060662:intron 40.0%
CGATGATTTGAAGAAACCAC+AGG + chr2.2:16362119-16362138 MS.gene060662:CDS 40.0%
GCATTTGACTGCAGATCAAA+AGG - chr2.2:16362768-16362787 None:intergenic 40.0%
TGATTTGAAGAAACCACAGG+CGG + chr2.2:16362122-16362141 MS.gene060662:CDS 40.0%
TTAATATCTAGGGGCCTGTT+TGG + chr2.2:16363036-16363055 MS.gene060662:intron 40.0%
TTTGCTTTGGCCCTTTGATA+CGG + chr2.2:16362232-16362251 MS.gene060662:intron 40.0%
! CAATGCTTGAATTTTGCAGG+TGG + chr2.2:16363701-16363720 MS.gene060662:intron 40.0%
!! AAAACGGATTACGCTAACCA+TGG - chr2.2:16362405-16362424 None:intergenic 40.0%
ACTGCAGATCAAAAGGTCAC+CGG - chr2.2:16362761-16362780 None:intergenic 45.0%
ATCACCAGGATCTGATAGCA+AGG + chr2.2:16362155-16362174 MS.gene060662:CDS 45.0%
CTATCAGATCCTGGTGATAC+AGG - chr2.2:16362153-16362172 None:intergenic 45.0%
CTGTGATAGCCCGTATCAAA+GGG - chr2.2:16362245-16362264 None:intergenic 45.0%
TAACATATATGGGCCCAACC+GGG + chr2.2:16362729-16362748 MS.gene060662:intron 45.0%
TCTGTGATAGCCCGTATCAA+AGG - chr2.2:16362246-16362265 None:intergenic 45.0%
TTGCTTTGGCCCTTTGATAC+GGG + chr2.2:16362233-16362252 MS.gene060662:intron 45.0%
ATCTAGGGGCCTGTTTGGAT+TGG + chr2.2:16363041-16363060 MS.gene060662:intron 50.0%
! CTCACCTTGCTATCAGATCC+TGG - chr2.2:16362162-16362181 None:intergenic 50.0%
! TTTTGCAGGTGGAGCCGAAG+CGG + chr2.2:16363712-16363731 MS.gene060662:intron 55.0%
!! AAAGGTCACCGGTTCGAACC+CGG - chr2.2:16362750-16362769 None:intergenic 55.0%
GATACAGGAAACGCCGCCTG+TGG - chr2.2:16362138-16362157 None:intergenic 60.0%
GCGGCGTTTCCTGTATCACC+AGG + chr2.2:16362141-16362160 MS.gene060662:CDS 60.0%
GGTCCTCTCTTTCGCCGCTT+CGG - chr2.2:16363729-16363748 None:intergenic 60.0%
!! TCACCGGTTCGAACCCGGTT+GGG - chr2.2:16362745-16362764 None:intergenic 60.0%
GAGCCGAAGCGGCGAAAGAG+AGG + chr2.2:16363723-16363742 MS.gene060662:CDS 65.0%
!! GTCACCGGTTCGAACCCGGT+TGG - chr2.2:16362746-16362765 None:intergenic 65.0%
GGGCCCAACCGGGTTCGAAC+CGG + chr2.2:16362739-16362758 MS.gene060662:intron 70.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 16362060 16363752 16362060 ID=MS.gene060662
chr2.2 mRNA 16362060 16363752 16362060 ID=MS.gene060662.t1;Parent=MS.gene060662
chr2.2 exon 16362060 16362176 16362060 ID=MS.gene060662.t1.exon1;Parent=MS.gene060662.t1
chr2.2 CDS 16362060 16362176 16362060 ID=cds.MS.gene060662.t1;Parent=MS.gene060662.t1
chr2.2 exon 16363720 16363752 16363720 ID=MS.gene060662.t1.exon2;Parent=MS.gene060662.t1
chr2.2 CDS 16363720 16363752 16363720 ID=cds.MS.gene060662.t1;Parent=MS.gene060662.t1
Gene Sequence

>MS.gene060662

ATGACTATCGAAGAAGCAAAGAAATTGGACCATTTTGTTTGTTCTGAATGTTCATCTGACGATGATTTGAAGAAACCACAGGCGGCGTTTCCTGTATCACCAGGATCTGATAGCAAGGTGAGATAAATCAGATAACTACATGAATTTAGTTCTAAATATTATGAGGCATTCTTTTGCTTTGGCCCTTTGATACGGGCTATCACAGAATGCTGCTTCATGTGTAAAAAATGAATGTTCGAGTTTTGAACTGATTCATGTATTCTAATTAAAATTTGAGTTTTGAAATGATTCATATATTCTAATTAAAATTTGGTTGAATTGTGTGTTTCTTCATTCTTGGTACCATGGTTAGCGTAATCCGTTTTTTTCTCAAAATTCTTTTTCGTTTTTACTGAAATATGCTACAAAGTGTAATTAGTTGAAGACCTAATGCTGCAATATGATTAAAAGGGAATTATACATTTTATTGCTTAGAAACACCTTTATAAATTTTAAATGTGGTTTTGATATCTATGGTTATGTTTGTGTTAGCTCACGTCTCGAGCTTTGATGTACTCTTTTTAAAAAAAGCTTATGCAAATGTATTGACATCAGAAATTATCTAGGCATAAAAAAATATGAAATGATTTTTTTTGTGATTTTCAGAGATTAAAAAGAATTGAAAAAAAATAACATATATGGGCCCAACCGGGTTCGAACCGGTGACCTTTTGATCTGCAGTCAAATGCTCTACTACTGAGCTATGGACCCTTTTGTTTTAAACTCTATCCGTTTTATCTTTTACCTTGGTAATTCTTGTGCTTGATGAACTTATCCTCCTTTTTCGAACTGTATTTCACAAAATATGTGTACTTTATTCTGTCTATTTTCATAAGATTTAATAAGCCCGTAAATTTTTGTAAATTTGATTTTATCGTGCCCGCTATTGATAACCTGTTTGAGTTGTTTGACATAAGTTGTGACTTGTAATCAGTAGTTAATATCTAGGGGCCTGTTTGGATTGGCTTATATTTAAGCTTATCTGATGGCATAAGTTTTGGGAGTCTGTTTGGGAGAACTTATGAAAATAGCTTACAACAATTTTCATAAGCTTTTCTCAACTTATTTTCTTTAAGTTCTCCAATATTGCTTATAAAAACAACTTATAGCGTATACAGAACAATTCAACATTTTTTTTTTATCTTTTTCTATAAAAATAGTTTATGCAAGCTTATACATAAGCGCTTATAATGATAAGTGCTTGTGCTATAAGCTGCAAATAAGTTGTTTATCCGAAAAGACCCTAAATGATCTTTTGGTAGTGGTTTTTCTTTCAAAGTGTTTTTCAAAGCTAATTATGTAATTGAATTCTAACAATTTGAAGCTTTGGTTTGGTGATCTGATAAAATAAGGGGCTGTCTTTGCATACAACATATTGTATTTGTGTTTGTTGAAATTGTTGCCTTTATTTTCTTGTAAAAGCCATTAAGCAGTGTTCATTTTGTGAGTAATAAATAATGGAGGAGATTTTAGTCAAATTTTTTATTCCTTTTTGGACATAATCTCTTTTAATCAATGGTATGTTTGAGTGTTAAGATTTTAATTATTTTGATTGACACTATAGGGTTGTGTGATTGCAAACATGTTTTCATTGATTATGAACAATGCTTGAATTTTGCAGGTGGAGCCGAAGCGGCGAAAGAGAGGACCATGA
Protein sequence

>MS.gene060662.t1

MTIEEAKKLDHFVCSECSSDDDLKKPQAAFPVSPGSDSKVEPKRRKRGP