AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1218600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218600 MtrunA17_Chr4g0068191 96.667 60 2 0 1 60 1 60 1.93e-37 118
Msa1218600 MtrunA17_Chr4g0068181 93.333 60 4 0 1 60 1 60 1.32e-36 116
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1218600 AT3G06680.1 83.333 60 10 0 1 60 23 82 9.79e-31 102
Msa1218600 AT3G06700.1 83.333 60 10 0 1 60 1 60 1.58e-30 101
Msa1218600 AT3G06700.2 83.333 60 10 0 1 60 1 60 1.58e-30 101
Msa1218600 AT3G06700.3 83.333 60 10 0 1 60 1 60 1.58e-30 101
Msa1218600 AT3G06680.2 83.333 60 10 0 1 60 1 60 2.30e-30 101
Msa1218600 AT3G06680.3 83.333 60 10 0 1 60 1 60 2.30e-30 101

Find 20 sgRNAs with CRISPR-Local

Find 52 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGTACTCTGTTAACACTTT+TGG 0.202166 8_1:+81238799 Msa1218600:three_prime_UTR
GAAAACCCTAGCTGCATCTT+TGG 0.270324 8_1:+81238346 None:intergenic
GCTGCATCTTTGGAAGAATT+AGG 0.286020 8_1:+81238356 Msa1218600:five_prime_UTR
AGAATTGATATTCTGAATTC+TGG 0.329535 8_1:-81238872 None:intergenic
GAAGTGTGACGATGCCTCTT+TGG 0.332537 8_1:-81238465 None:intergenic
CATGCTTCCTTGCATACCTC+TGG 0.395718 8_1:-81238615 None:intergenic
GTAAAGTGTCGATCTCTAAT+CGG 0.398848 8_1:+81238669 Msa1218600:exon
TTTATAATTCAAGTTATGTA+TGG 0.401074 8_1:+81238717 Msa1218600:three_prime_UTR
TCTTGTGAGCTTTGTAAGAC+TGG 0.419661 8_1:-81238428 None:intergenic
ATGATTAATACATACCCCTT+TGG 0.426914 8_1:-81238490 None:intergenic
ATCGTCACACTTCAACCAAA+GGG 0.488627 8_1:+81238475 Msa1218600:CDS
TAAAGTGTCGATCTCTAATC+GGG 0.518145 8_1:+81238670 Msa1218600:exon
ATTCTTCCAAAGATGCAGCT+AGG 0.530379 8_1:-81238352 None:intergenic
TCTTACAAAGCTCACAAGAA+TGG 0.532217 8_1:+81238432 Msa1218600:CDS
GGTTTATCGAATTTCAGAGA+TGG 0.592629 8_1:+81238377 Msa1218600:exon
CATCGTCACACTTCAACCAA+AGG 0.595920 8_1:+81238474 Msa1218600:CDS
TGAGGAACCAGAGGTATGCA+AGG 0.602234 8_1:+81238608 Msa1218600:CDS
ATGGCATCAAGAAGCCAAAG+AGG 0.631544 8_1:+81238451 Msa1218600:CDS
TTTGTAAGACTGGTTGTGAG+CGG 0.659865 8_1:-81238418 None:intergenic
TCGTCACACTTCAACCAAAG+GGG 0.708509 8_1:+81238476 Msa1218600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATAATTCAAGTTATGTA+TGG + chr8_1:81238717-81238736 Msa1218600:three_prime_UTR 15.0%
!!! TTTATAATTCAAGTTATGTA+TGG + chr8_1:81238717-81238736 Msa1218600:three_prime_UTR 15.0%
!!! TATGTTCGACAATATTTTGA+TGG + chr8_1:81238754-81238773 Msa1218600:three_prime_UTR 25.0%
! AGAATTGATATTCTGAATTC+TGG - chr8_1:81238875-81238894 None:intergenic 25.0%
!!! TATGTTCGACAATATTTTGA+TGG + chr8_1:81238754-81238773 Msa1218600:three_prime_UTR 25.0%
! AGAATTGATATTCTGAATTC+TGG - chr8_1:81238875-81238894 None:intergenic 25.0%
ATGATTAATACATACCCCTT+TGG - chr8_1:81238493-81238512 None:intergenic 30.0%
TCAATCGTTTGAAAAATCAG+AGG - chr8_1:81238519-81238538 None:intergenic 30.0%
! AGTACTCTGTTAACACTTTT+GGG + chr8_1:81238800-81238819 Msa1218600:three_prime_UTR 30.0%
ATGATTAATACATACCCCTT+TGG - chr8_1:81238493-81238512 None:intergenic 30.0%
TCAATCGTTTGAAAAATCAG+AGG - chr8_1:81238519-81238538 None:intergenic 30.0%
! AGTACTCTGTTAACACTTTT+GGG + chr8_1:81238800-81238819 Msa1218600:three_prime_UTR 30.0%
GGTTTATCGAATTTCAGAGA+TGG + chr8_1:81238377-81238396 Msa1218600:exon 35.0%
TCTTACAAAGCTCACAAGAA+TGG + chr8_1:81238432-81238451 Msa1218600:CDS 35.0%
CTGTGATTGAATACTGTAGA+TGG + chr8_1:81238573-81238592 Msa1218600:intron 35.0%
! AGATGGATCCAAAGTTTTTG+AGG + chr8_1:81238590-81238609 Msa1218600:intron 35.0%
! AGGAAGCATGACAAGAAAAA+TGG + chr8_1:81238628-81238647 Msa1218600:CDS 35.0%
!! GTAAAGTGTCGATCTCTAAT+CGG + chr8_1:81238669-81238688 Msa1218600:exon 35.0%
!! TAAAGTGTCGATCTCTAATC+GGG + chr8_1:81238670-81238689 Msa1218600:exon 35.0%
! CAGTACTCTGTTAACACTTT+TGG + chr8_1:81238799-81238818 Msa1218600:three_prime_UTR 35.0%
GGTTTATCGAATTTCAGAGA+TGG + chr8_1:81238377-81238396 Msa1218600:exon 35.0%
TCTTACAAAGCTCACAAGAA+TGG + chr8_1:81238432-81238451 Msa1218600:CDS 35.0%
CTGTGATTGAATACTGTAGA+TGG + chr8_1:81238573-81238592 Msa1218600:intron 35.0%
! AGATGGATCCAAAGTTTTTG+AGG + chr8_1:81238590-81238609 Msa1218600:intron 35.0%
! AGGAAGCATGACAAGAAAAA+TGG + chr8_1:81238628-81238647 Msa1218600:CDS 35.0%
!! GTAAAGTGTCGATCTCTAAT+CGG + chr8_1:81238669-81238688 Msa1218600:exon 35.0%
!! TAAAGTGTCGATCTCTAATC+GGG + chr8_1:81238670-81238689 Msa1218600:exon 35.0%
! CAGTACTCTGTTAACACTTT+TGG + chr8_1:81238799-81238818 Msa1218600:three_prime_UTR 35.0%
! GCTGCATCTTTGGAAGAATT+AGG + chr8_1:81238356-81238375 Msa1218600:five_prime_UTR 40.0%
! TTTGTAAGACTGGTTGTGAG+CGG - chr8_1:81238421-81238440 None:intergenic 40.0%
! TCTTGTGAGCTTTGTAAGAC+TGG - chr8_1:81238431-81238450 None:intergenic 40.0%
ATCGTCACACTTCAACCAAA+GGG + chr8_1:81238475-81238494 Msa1218600:CDS 40.0%
! CTCTGGTTCCTCAAAAACTT+TGG - chr8_1:81238601-81238620 None:intergenic 40.0%
!! CAAAGTTTTTGAGGAACCAG+AGG + chr8_1:81238599-81238618 Msa1218600:CDS 40.0%
! GCTGCATCTTTGGAAGAATT+AGG + chr8_1:81238356-81238375 Msa1218600:five_prime_UTR 40.0%
! TTTGTAAGACTGGTTGTGAG+CGG - chr8_1:81238421-81238440 None:intergenic 40.0%
! TCTTGTGAGCTTTGTAAGAC+TGG - chr8_1:81238431-81238450 None:intergenic 40.0%
ATCGTCACACTTCAACCAAA+GGG + chr8_1:81238475-81238494 Msa1218600:CDS 40.0%
! CTCTGGTTCCTCAAAAACTT+TGG - chr8_1:81238601-81238620 None:intergenic 40.0%
!! CAAAGTTTTTGAGGAACCAG+AGG + chr8_1:81238599-81238618 Msa1218600:CDS 40.0%
ATGGCATCAAGAAGCCAAAG+AGG + chr8_1:81238451-81238470 Msa1218600:CDS 45.0%
CATCGTCACACTTCAACCAA+AGG + chr8_1:81238474-81238493 Msa1218600:CDS 45.0%
TCGTCACACTTCAACCAAAG+GGG + chr8_1:81238476-81238495 Msa1218600:CDS 45.0%
ATGGCATCAAGAAGCCAAAG+AGG + chr8_1:81238451-81238470 Msa1218600:CDS 45.0%
CATCGTCACACTTCAACCAA+AGG + chr8_1:81238474-81238493 Msa1218600:CDS 45.0%
TCGTCACACTTCAACCAAAG+GGG + chr8_1:81238476-81238495 Msa1218600:CDS 45.0%
GAAGTGTGACGATGCCTCTT+TGG - chr8_1:81238468-81238487 None:intergenic 50.0%
! TGAGGAACCAGAGGTATGCA+AGG + chr8_1:81238608-81238627 Msa1218600:CDS 50.0%
CATGCTTCCTTGCATACCTC+TGG - chr8_1:81238618-81238637 None:intergenic 50.0%
GAAGTGTGACGATGCCTCTT+TGG - chr8_1:81238468-81238487 None:intergenic 50.0%
! TGAGGAACCAGAGGTATGCA+AGG + chr8_1:81238608-81238627 Msa1218600:CDS 50.0%
CATGCTTCCTTGCATACCTC+TGG - chr8_1:81238618-81238637 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 81238355 81238902 81238355 ID=Msa1218600;Name=Msa1218600
chr8_1 mRNA 81238355 81238902 81238355 ID=Msa1218600-mRNA-1;Parent=Msa1218600;Name=Msa1218600-mRNA-1;_AED=0.30;_eAED=0.30;_QI=41|1|1|1|1|1|2|230|60
chr8_1 exon 81238355 81238497 81238355 ID=Msa1218600-mRNA-1:exon:28708;Parent=Msa1218600-mRNA-1
chr8_1 exon 81238592 81238902 81238592 ID=Msa1218600-mRNA-1:exon:28709;Parent=Msa1218600-mRNA-1
chr8_1 five_prime_UTR 81238355 81238395 81238355 ID=Msa1218600-mRNA-1:five_prime_utr;Parent=Msa1218600-mRNA-1
chr8_1 CDS 81238396 81238497 81238396 ID=Msa1218600-mRNA-1:cds;Parent=Msa1218600-mRNA-1
chr8_1 CDS 81238592 81238672 81238592 ID=Msa1218600-mRNA-1:cds;Parent=Msa1218600-mRNA-1
chr8_1 three_prime_UTR 81238673 81238902 81238673 ID=Msa1218600-mRNA-1:three_prime_utr;Parent=Msa1218600-mRNA-1
Gene Sequence

>Msa1218600

ATGGCGAAATCGAAGAATCACACCGCTCACAACCAGTCTTACAAAGCTCACAAGAATGGCATCAAGAAGCCAAAGAGGCATCGTCACACTTCAACCAAAGGGATGGATCCAAAGTTTTTGAGGAACCAGAGGTATGCAAGGAAGCATGACAAGAAAAATGGTGAAATTGCAGAAGAAGAGTAA

Protein sequence

>Msa1218600

MAKSKNHTAHNQSYKAHKNGIKKPKRHRHTSTKGMDPKFLRNQRYARKHDKKNGEIAEEE*