AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene71851

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71851.t1 MTR_1g111150 94.286 105 5 1 3 106 20 124 2.07e-54 166
MS.gene71851.t1 MTR_5g055200 67.961 103 31 1 2 104 19 119 2.73e-42 135
MS.gene71851.t1 MTR_5g055200 78.846 52 11 0 2 53 19 70 2.47e-22 84.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene71851.t1 AT1G68585 49.451 91 38 3 8 92 24 112 4.09e-19 76.3

Find 20 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTTTGATAATGGCAAATTT+AGG 0.131684 1.3:-75794102 None:intergenic
TGGGACTAGTCTTGCATCTT+TGG 0.189720 1.3:+75793181 MS.gene71851:CDS
GGGGAAGGAGTCTTGTTTAA+TGG 0.240314 1.3:-75794081 None:intergenic
AGAAGGTGATACTTACATTT+AGG 0.262994 1.3:+75794013 MS.gene71851:CDS
GTTTGATAATGGCAAATTTA+GGG 0.296856 1.3:-75794101 None:intergenic
TAATGTCAGCAACTCTCTTC+TGG 0.333777 1.3:-75793366 None:intergenic
GCGGAATATCCGTTTGATAA+TGG 0.404318 1.3:-75794112 None:intergenic
GGAGTCTTTGTCACTGCCAC+TGG 0.407535 1.3:+75793202 MS.gene71851:CDS
CTAAATTTGCCATTATCAAA+CGG 0.468003 1.3:+75794103 MS.gene71851:CDS
CCCAGAAAGAGGAAAACTCT+TGG 0.478273 1.3:-75793162 None:intergenic
GTCAGCAACTCTCTTCTGGC+AGG 0.495054 1.3:-75793362 None:intergenic
GTCAATTGTGGTGAATGTAT+TGG 0.498672 1.3:+75793987 MS.gene71851:CDS
ATAATGGCAAATTTAGGGGA+AGG 0.529849 1.3:-75794096 None:intergenic
TATAATTACTAATTAACCAC+TGG 0.531693 1.3:-75794139 None:intergenic
GCAAGACTAGTCCCAGAAAG+AGG 0.539833 1.3:-75793173 None:intergenic
GGTGAATGTATTGGAAAAGA+AGG 0.579398 1.3:+75793996 MS.gene71851:CDS
CGGATATTCCGCTCATCCAG+TGG 0.579718 1.3:+75794123 MS.gene71851:CDS
TTTGATAATGGCAAATTTAG+GGG 0.595724 1.3:-75794100 None:intergenic
CTAATTAACCACTGGATGAG+CGG 0.609688 1.3:-75794131 None:intergenic
AGCAGAGACAGAGTCAATTG+TGG 0.625282 1.3:+75793975 MS.gene71851:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAAATAACAATAATTGTA+AGG - chr1.3:75793733-75793752 None:intergenic 15.0%
!! TCTATATATATAGTGTTTAA+TGG + chr1.3:75793278-75793297 MS.gene71851:intron 15.0%
!! AAAACTCAAAATACAGTAAA+AGG - chr1.3:75793242-75793261 None:intergenic 20.0%
!! GACATTATTACAAAAATGAA+TGG + chr1.3:75793382-75793401 MS.gene71851:CDS 20.0%
!!! CATTTTTGTTCTGTTAAATA+AGG + chr1.3:75793425-75793444 MS.gene71851:intron 20.0%
! AAATAAGGAGATATCATGTA+TGG + chr1.3:75793440-75793459 MS.gene71851:intron 25.0%
! CTAAATTTGCCATTATCAAA+CGG + chr1.3:75794103-75794122 MS.gene71851:CDS 25.0%
! CTGCTGAAAAATTATAGATA+CGG - chr1.3:75793960-75793979 None:intergenic 25.0%
! TGCTGAAAAATTATAGATAC+GGG - chr1.3:75793959-75793978 None:intergenic 25.0%
!! TCTTTCACTGATTATATACA+TGG + chr1.3:75793788-75793807 MS.gene71851:intron 25.0%
!!! GTTTGATAATGGCAAATTTA+GGG - chr1.3:75794104-75794123 None:intergenic 25.0%
!!! TTTGATAATGGCAAATTTAG+GGG - chr1.3:75794103-75794122 None:intergenic 25.0%
AGAAGGTGATACTTACATTT+AGG + chr1.3:75794013-75794032 MS.gene71851:CDS 30.0%
AGGATATCAAAAACAACTGT+TGG + chr1.3:75794033-75794052 MS.gene71851:CDS 30.0%
CTGAAAAATTATAGATACGG+GGG - chr1.3:75793957-75793976 None:intergenic 30.0%
GCTGAAAAATTATAGATACG+GGG - chr1.3:75793958-75793977 None:intergenic 30.0%
!! CGTTTGATAATGGCAAATTT+AGG - chr1.3:75794105-75794124 None:intergenic 30.0%
ATAATGGCAAATTTAGGGGA+AGG - chr1.3:75794099-75794118 None:intergenic 35.0%
CAAGCTAGAGGAATGTTATA+GGG + chr1.3:75793664-75793683 MS.gene71851:intron 35.0%
CAGTAGCAACATAAACAGTA+AGG - chr1.3:75793610-75793629 None:intergenic 35.0%
GGTGAATGTATTGGAAAAGA+AGG + chr1.3:75793996-75794015 MS.gene71851:CDS 35.0%
GTCAATTGTGGTGAATGTAT+TGG + chr1.3:75793987-75794006 MS.gene71851:CDS 35.0%
TCTATTTGCTTTGCAAGAAG+AGG + chr1.3:75793552-75793571 MS.gene71851:intron 35.0%
TCTTCTTGCAAAGCAAATAG+AGG - chr1.3:75793553-75793572 None:intergenic 35.0%
!! GTGATTGTTTTGTTGAGAAC+AGG + chr1.3:75793300-75793319 MS.gene71851:intron 35.0%
AAGGAGATATCATGTATGGC+TGG + chr1.3:75793444-75793463 MS.gene71851:intron 40.0%
AGAGGTTAAAGAAGACAGAG+AGG + chr1.3:75793570-75793589 MS.gene71851:intron 40.0%
GCAAGCTAGAGGAATGTTAT+AGG + chr1.3:75793663-75793682 MS.gene71851:intron 40.0%
GCGGAATATCCGTTTGATAA+TGG - chr1.3:75794115-75794134 None:intergenic 40.0%
GGTTCAAAACTACATACCAG+TGG - chr1.3:75793221-75793240 None:intergenic 40.0%
TAATGTCAGCAACTCTCTTC+TGG - chr1.3:75793369-75793388 None:intergenic 40.0%
! ATAAGCCCTGCATGTGTTTT+TGG + chr1.3:75793638-75793657 MS.gene71851:intron 40.0%
! CCAAGAGTTTTCCTCTTTCT+GGG + chr1.3:75793162-75793181 MS.gene71851:CDS 40.0%
! TCCAAGAGTTTTCCTCTTTC+TGG + chr1.3:75793161-75793180 MS.gene71851:CDS 40.0%
AGCAGAGACAGAGTCAATTG+TGG + chr1.3:75793975-75793994 MS.gene71851:intron 45.0%
CCCAGAAAGAGGAAAACTCT+TGG - chr1.3:75793165-75793184 None:intergenic 45.0%
TGCAGCCAAAAACACATGCA+GGG - chr1.3:75793646-75793665 None:intergenic 45.0%
TTGCAGCCAAAAACACATGC+AGG - chr1.3:75793647-75793666 None:intergenic 45.0%
!! GGGGAAGGAGTCTTGTTTAA+TGG - chr1.3:75794084-75794103 None:intergenic 45.0%
!! GTTTTGTTGAGAACAGGTGC+AGG + chr1.3:75793306-75793325 MS.gene71851:intron 45.0%
!! TGGGACTAGTCTTGCATCTT+TGG + chr1.3:75793181-75793200 MS.gene71851:CDS 45.0%
!!! TGTTTTTGGCTGCAAGCTAG+AGG + chr1.3:75793652-75793671 MS.gene71851:intron 45.0%
GACAGAGAGGAAAAGAGCTG+TGG + chr1.3:75793583-75793602 MS.gene71851:intron 50.0%
! GCAAGACTAGTCCCAGAAAG+AGG - chr1.3:75793176-75793195 None:intergenic 50.0%
CGGATATTCCGCTCATCCAG+TGG + chr1.3:75794123-75794142 MS.gene71851:CDS 55.0%
GGAGTCTTTGTCACTGCCAC+TGG + chr1.3:75793202-75793221 MS.gene71851:CDS 55.0%
GTCAGCAACTCTCTTCTGGC+AGG - chr1.3:75793365-75793384 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr1.3 gene 75793158 75794149 75793158 ID=MS.gene71851
chr1.3 mRNA 75793158 75794149 75793158 ID=MS.gene71851.t1;Parent=MS.gene71851
chr1.3 exon 75793158 75793223 75793158 ID=MS.gene71851.t1.exon1;Parent=MS.gene71851.t1
chr1.3 CDS 75793158 75793223 75793158 ID=cds.MS.gene71851.t1;Parent=MS.gene71851.t1
chr1.3 exon 75793322 75793403 75793322 ID=MS.gene71851.t1.exon2;Parent=MS.gene71851.t1
chr1.3 CDS 75793322 75793403 75793322 ID=cds.MS.gene71851.t1;Parent=MS.gene71851.t1
chr1.3 exon 75793977 75794149 75793977 ID=MS.gene71851.t1.exon3;Parent=MS.gene71851.t1
chr1.3 CDS 75793977 75794149 75793977 ID=cds.MS.gene71851.t1;Parent=MS.gene71851.t1
Gene Sequence

>MS.gene71851

ATGTCCAAGAGTTTTCCTCTTTCTGGGACTAGTCTTGCATCTTTGGAGTCTTTGTCACTGCCACTGGTATGTAGTTTTGAACCTTTTACTGTATTTTGAGTTTTGAAATGAGCTTGAATTTCTATATATATAGTGTTTAATGGTGATTGTTTTGTTGAGAACAGGTGCAGGAAGTTGTTCTTTCAGCAGATATGCAATGTGAAACCTGCCAGAAGAGAGTTGCTGACATTATTACAAAAATGAATGGTAGTAAGCTTGTTTCTGTATCATTTTTGTTCTGTTAAATAAGGAGATATCATGTATGGCTGGCTATATGTGTTGCACATGATTGAGAAATTGTTGATTGATTTTAATGCTCTATGTGAAAATTGCTTTCTTCAAATCTCAATATTCCTCTATTTGCTTTGCAAGAAGAGGTTAAAGAAGACAGAGAGGAAAAGAGCTGTGGTCCTTACTGTTTATGTTGCTACTGTATAATTTATAAGCCCTGCATGTGTTTTTGGCTGCAAGCTAGAGGAATGTTATAGGGCTATAGTGCTGATATCTATGACTTAAATTACTGTTATTATTTACCTTACAATTATTGTTATTTACTGTTAAATCTTCTGTTTTTTTTAGAAACTTTATTTATCTTTCACTGATTATATACATGGTATCTTATAAGATATCTGAACTTATGATTCTGATGTGAGTTTAGCAGAACTTAGTATAAAACACATTTTCTGTTTTATACTAAAGTGTAATGAATTTTGTGATGATGTTTATGTTATTTCTCTTGTTAGCTCTAATACATGTTCCCCCGTATCTATAATTTTTCAGCAGAGACAGAGTCAATTGTGGTGAATGTATTGGAAAAGAAGGTGATACTTACATTTAGGATATCAAAAACAACTGTTGGTAAATTAATCTCAAAGAAAGTTACGCCATTAAACAAGACTCCTTCCCCTAAATTTGCCATTATCAAACGGATATTCCGCTCATCCAGTGGTTAA
Protein sequence

>MS.gene71851.t1

MSKSFPLSGTSLASLESLSLPLVQEVVLSADMQCETCQKRVADIITKMNAETESIVVNVLEKKVILTFRISKTTVGKLISKKVTPLNKTPSPKFAIIKRIFRSSSG