AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1221910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1221910 MtrunA17_Chr4g0076791 90.625 32 3 0 14 45 218 249 8.81e-14 65.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACTAGAATGCGATTCAATT+TGG 0.229510 8_1:+85877629 Msa1221910:CDS
TCAGAGGATTTGTACCTGGC+TGG 0.457541 8_1:-85877213 Msa1221900:intron
ACTAGGGATTTCAGCATGGT+TGG 0.492803 8_1:-85877495 Msa1221900:intron
AAACCATCTCTTTAGCCACT+TGG 0.496022 8_1:+85876966 None:intergenic
ACATAAACTAATCTTTCTGC+AGG 0.505085 8_1:+85877001 Msa1221910:CDS
ATCATTTGCCGTTAGAACAC+TGG 0.515238 8_1:+85877034 Msa1221910:CDS
TAATATAATTCTCAGCAACT+CGG 0.518851 8_1:-85877186 Msa1221900:intron
TGAGAAACTGTGCAGATCAC+AGG 0.531427 8_1:+85877517 Msa1221910:CDS
GTGACTAATGGTATCCACTT+AGG 0.539904 8_1:-85877675 Msa1221900:intron
GAATGCGATTCAATTTGGAC+AGG 0.545641 8_1:+85877634 Msa1221910:CDS
ATCTGCACAGTTTCTCACTA+GGG 0.559582 8_1:-85877511 Msa1221900:intron
AATTATATTAATATCCAGCC+AGG 0.566677 8_1:+85877199 Msa1221910:CDS
AATATAATTCTCAGCAACTC+GGG 0.573122 8_1:-85877185 Msa1221900:intron
GATCTGCACAGTTTCTCACT+AGG 0.574102 8_1:-85877512 Msa1221900:intron
ACTAATTTACCAGTCCTAAG+TGG 0.575067 8_1:+85877661 Msa1221910:CDS
TAATGGTATCCACTTAGGAC+TGG 0.589408 8_1:-85877670 Msa1221900:intron
ATGGGAGATGCAGACCCCAC+AGG 0.600097 8_1:+85877070 Msa1221910:CDS
TCTCACTAGGGATTTCAGCA+TGG 0.604577 8_1:-85877499 Msa1221900:intron
TGTTGAAACTCATTTCCAAG+TGG 0.644681 8_1:-85876981 Msa1221900:intron
GATCGTGTAGGATACAGAAG+AGG 0.682619 8_1:+85877597 Msa1221910:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTAATTGAGAAATATTTA+TGG - chr8_1:85877326-85877345 Msa1221900:intron 10.0%
!!! ATGTACATCTCATTTATTTT+TGG + chr8_1:85877112-85877131 Msa1221910:intron 20.0%
! TAATATAATTCTCAGCAACT+CGG - chr8_1:85877189-85877208 Msa1221900:intron 25.0%
! AATTATATTAATATCCAGCC+AGG + chr8_1:85877199-85877218 Msa1221910:CDS 25.0%
! AAAGAAGCAAAATGATCAAA+TGG + chr8_1:85877236-85877255 Msa1221910:intron 25.0%
! GTAGATATGAAAGATTAACT+TGG - chr8_1:85877451-85877470 Msa1221900:intron 25.0%
ACATAAACTAATCTTTCTGC+AGG + chr8_1:85877001-85877020 Msa1221910:CDS 30.0%
AATATAATTCTCAGCAACTC+GGG - chr8_1:85877188-85877207 Msa1221900:intron 30.0%
! ATCATTTTGCTTCTTTTCAG+AGG - chr8_1:85877232-85877251 Msa1221900:intron 30.0%
CTAAGACACTGTTAAAGTTA+TGG - chr8_1:85877550-85877569 Msa1221900:intron 30.0%
TGTTGAAACTCATTTCCAAG+TGG - chr8_1:85876984-85877003 Msa1221900:intron 35.0%
! TTTTCTGTCCAGTGTTCTAA+CGG - chr8_1:85877045-85877064 Msa1221900:intron 35.0%
! ATCTTTTCAGTTTGACCTGT+GGG - chr8_1:85877088-85877107 Msa1221900:intron 35.0%
AGCATTGTAAGTAGTTGACT+AGG - chr8_1:85877141-85877160 Msa1221900:intron 35.0%
!! ATAGCATGCAGTGCTTTTTA+CGG - chr8_1:85877364-85877383 Msa1221900:intron 35.0%
AAACCATTTCTTCAGTCACA+TGG + chr8_1:85877393-85877412 Msa1221910:intron 35.0%
TTTCCATGTGACTGAAGAAA+TGG - chr8_1:85877399-85877418 Msa1221900:intron 35.0%
CTAAGAAACAATGATCGTGT+AGG + chr8_1:85877585-85877604 Msa1221910:intron 35.0%
GACTAGAATGCGATTCAATT+TGG + chr8_1:85877629-85877648 Msa1221910:CDS 35.0%
ACTAATTTACCAGTCCTAAG+TGG + chr8_1:85877661-85877680 Msa1221910:CDS 35.0%
ATCATTTGCCGTTAGAACAC+TGG + chr8_1:85877034-85877053 Msa1221910:CDS 40.0%
ACTGGACAGAAAAACGCTAT+GGG + chr8_1:85877052-85877071 Msa1221910:CDS 40.0%
! TCTTTTCAGTTTGACCTGTG+GGG - chr8_1:85877087-85877106 Msa1221900:intron 40.0%
! CATCTTTTCAGTTTGACCTG+TGG - chr8_1:85877089-85877108 Msa1221900:intron 40.0%
! CTTTTCAGAGGATTTGTACC+TGG - chr8_1:85877220-85877239 Msa1221900:intron 40.0%
ATCTGCACAGTTTCTCACTA+GGG - chr8_1:85877514-85877533 Msa1221900:intron 40.0%
GAATGCGATTCAATTTGGAC+AGG + chr8_1:85877634-85877653 Msa1221910:CDS 40.0%
TAATGGTATCCACTTAGGAC+TGG - chr8_1:85877673-85877692 Msa1221900:intron 40.0%
CACTGGACAGAAAAACGCTA+TGG + chr8_1:85877051-85877070 Msa1221910:CDS 45.0%
ACTAGGGATTTCAGCATGGT+TGG - chr8_1:85877498-85877517 Msa1221900:intron 45.0%
TCTCACTAGGGATTTCAGCA+TGG - chr8_1:85877502-85877521 Msa1221900:intron 45.0%
GATCTGCACAGTTTCTCACT+AGG - chr8_1:85877515-85877534 Msa1221900:intron 45.0%
TGAGAAACTGTGCAGATCAC+AGG + chr8_1:85877517-85877536 Msa1221910:CDS 45.0%
GATCGTGTAGGATACAGAAG+AGG + chr8_1:85877597-85877616 Msa1221910:intron 45.0%
TCAGAGGATTTGTACCTGGC+TGG - chr8_1:85877216-85877235 Msa1221900:intron 50.0%
ATGGGAGATGCAGACCCCAC+AGG + chr8_1:85877070-85877089 Msa1221910:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 85876981 85877693 85876981 ID=Msa1221910;Name=Msa1221910
chr8_1 mRNA 85876981 85877693 85876981 ID=Msa1221910-mRNA-1;Parent=Msa1221910;Name=Msa1221910-mRNA-1;_AED=0.59;_eAED=0.62;_QI=0|0|0|0.75|0.66|0.75|4|0|100
chr8_1 exon 85876981 85877091 85876981 ID=Msa1221910-mRNA-1:exon:30854;Parent=Msa1221910-mRNA-1
chr8_1 exon 85877176 85877220 85877176 ID=Msa1221910-mRNA-1:exon:30855;Parent=Msa1221910-mRNA-1
chr8_1 exon 85877479 85877538 85877479 ID=Msa1221910-mRNA-1:exon:30856;Parent=Msa1221910-mRNA-1
chr8_1 exon 85877607 85877693 85877607 ID=Msa1221910-mRNA-1:exon:30857;Parent=Msa1221910-mRNA-1
chr8_1 CDS 85876981 85877091 85876981 ID=Msa1221910-mRNA-1:cds;Parent=Msa1221910-mRNA-1
chr8_1 CDS 85877176 85877220 85877176 ID=Msa1221910-mRNA-1:cds;Parent=Msa1221910-mRNA-1
chr8_1 CDS 85877479 85877538 85877479 ID=Msa1221910-mRNA-1:cds;Parent=Msa1221910-mRNA-1
chr8_1 CDS 85877607 85877693 85877607 ID=Msa1221910-mRNA-1:cds;Parent=Msa1221910-mRNA-1
Gene Sequence

>Msa1221910

CCACTTGGAAATGAGTTTCAACATAAACTAATCTTTCTGCAGGCTAACACTAAATCATTTGCCGTTAGAACACTGGACAGAAAAACGCTATGGGAGATGCAGACCCCACAGATTATCAAACCCGAGTTGCTGAGAATTATATTAATATCCAGCCAGATAACTTGTACTGCATCCAACCATGCTGAAATCCCTAGTGAGAAACTGTGCAGATCACAGGATACAGAAGAGGATACTAGAAGACTAGAATGCGATTCAATTTGGACAGGAAATACTAATTTACCAGTCCTAAGTGGATACCATTAG
Protein sequence

>Msa1221910

PLGNEFQHKLIFLQANTKSFAVRTLDRKTLWEMQTPQIIKPELLRIILISSQITCTASNHAEIPSEKLCRSQDTEEDTRRLECDSIWTGNTNLPVLSGYH*