AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0190000

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0190000 MtrunA17_Chr2g0279561 90.000 100 4 1 1 100 1 94 1.12e-39 127
Msa0190000 MtrunA17_Chr3g0087151 39.286 112 54 5 1 100 1 110 1.72e-13 63.9
Msa0190000 MtrunA17_Chr3g0087211 44.144 111 46 8 1 100 1 106 2.60e-11 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 31 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGGCTTCCATCAATTTC+TGG 0.176747 2_1:-5438532 Msa0190000:CDS
TGAGGCAAAGTTGGTACATT+AGG 0.250872 2_1:+5438347 None:intergenic
GGCAATTGTGGCTGTGTTAA+TGG 0.262929 2_1:+5438401 None:intergenic
GTTGGTACATTAGGGATTAC+TGG 0.335295 2_1:+5438356 None:intergenic
CCTCAGATTCCTACTGTTCC+TGG 0.365627 2_1:-5438302 Msa0190000:CDS
GAGGCAAAGTTGGTACATTA+GGG 0.367979 2_1:+5438348 None:intergenic
ATTACTGGAACACCTAAGTT+TGG 0.371975 2_1:+5438371 None:intergenic
ACTTTAGGTACTTATGGTTT+AGG 0.379485 2_1:+5438239 None:intergenic
CCACAAATTCCTCAGATTCC+TGG 0.389504 2_1:-5438275 Msa0190000:CDS
ACACCTAAGTTTGGAATTGT+TGG 0.404545 2_1:+5438380 None:intergenic
GGCAATGGCACTGGCAGATT+AGG 0.425870 2_1:+5438422 None:intergenic
AATTAATGACCAGAAATTGA+TGG 0.431474 2_1:+5438523 None:intergenic
TGAGGCACAGTTGGTATTTG+AGG 0.431733 2_1:+5438329 None:intergenic
TCATCAATGACAAGTATTGA+AGG 0.467180 2_1:-5438476 Msa0190000:CDS
TTGCCAACAATTCCAAACTT+AGG 0.468746 2_1:-5438383 Msa0190000:CDS
CCAGGAATCTGAGGAATTTG+TGG 0.472835 2_1:+5438275 None:intergenic
TTTGGAATTGTTGGCAATTG+TGG 0.474516 2_1:+5438389 None:intergenic
GTTGGTATTTGAGGCAAAGT+TGG 0.507961 2_1:+5438338 None:intergenic
GTAGGAATCTGAGGTATTTG+AGG 0.535890 2_1:+5438311 None:intergenic
TGTGTTAATGGCAATGGCAC+TGG 0.535953 2_1:+5438413 None:intergenic
TGAGGAATTTGTGGCACACC+AGG 0.542628 2_1:+5438284 None:intergenic
TGAGGTATTTGAGGCACAGT+TGG 0.543443 2_1:+5438320 None:intergenic
TTAGGCACACTAGGCACACC+AGG 0.574512 2_1:+5438257 None:intergenic
ACTTATGGTTTAGGCACACT+AGG 0.582264 2_1:+5438248 None:intergenic
CTAGGCACACCAGGAATCTG+AGG 0.592705 2_1:+5438266 None:intergenic
GGCACTGGCAGATTAGGTAG+TGG 0.603557 2_1:+5438428 None:intergenic
TGTGGCACACCAGGAACAGT+AGG 0.606684 2_1:+5438293 None:intergenic
CCAGGAACAGTAGGAATCTG+AGG 0.616707 2_1:+5438302 None:intergenic
TGTGGCTGTGTTAATGGCAA+TGG 0.622083 2_1:+5438407 None:intergenic
ACTGGCAGATTAGGTAGTGG+TGG 0.639353 2_1:+5438431 None:intergenic
GTAGTGGTGGCAACTCAACA+AGG 0.734703 2_1:+5438444 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATTAATGACCAGAAATTGA+TGG + chr2_1:5438260-5438279 None:intergenic 25.0%
!! TCATCAATGACAAGTATTGA+AGG - chr2_1:5438304-5438323 Msa0190000:CDS 30.0%
! TTTGGAATTGTTGGCAATTG+TGG + chr2_1:5438394-5438413 None:intergenic 35.0%
TTGCCAACAATTCCAAACTT+AGG - chr2_1:5438397-5438416 Msa0190000:CDS 35.0%
! ACACCTAAGTTTGGAATTGT+TGG + chr2_1:5438403-5438422 None:intergenic 35.0%
ATTACTGGAACACCTAAGTT+TGG + chr2_1:5438412-5438431 None:intergenic 35.0%
GTTGGTACATTAGGGATTAC+TGG + chr2_1:5438427-5438446 None:intergenic 40.0%
!! GAGGCAAAGTTGGTACATTA+GGG + chr2_1:5438435-5438454 None:intergenic 40.0%
!! TGAGGCAAAGTTGGTACATT+AGG + chr2_1:5438436-5438455 None:intergenic 40.0%
! GTTGGTATTTGAGGCAAAGT+TGG + chr2_1:5438445-5438464 None:intergenic 40.0%
! GTAGGAATCTGAGGTATTTG+AGG + chr2_1:5438472-5438491 None:intergenic 40.0%
TGTGTTAATGGCAATGGCAC+TGG + chr2_1:5438370-5438389 None:intergenic 45.0%
TGTGGCTGTGTTAATGGCAA+TGG + chr2_1:5438376-5438395 None:intergenic 45.0%
GGCAATTGTGGCTGTGTTAA+TGG + chr2_1:5438382-5438401 None:intergenic 45.0%
! TGAGGCACAGTTGGTATTTG+AGG + chr2_1:5438454-5438473 None:intergenic 45.0%
! TGAGGTATTTGAGGCACAGT+TGG + chr2_1:5438463-5438482 None:intergenic 45.0%
CCAGGAATCTGAGGAATTTG+TGG + chr2_1:5438508-5438527 None:intergenic 45.0%
CCACAAATTCCTCAGATTCC+TGG - chr2_1:5438505-5438524 Msa0190000:CDS 45.0%
GTAGTGGTGGCAACTCAACA+AGG + chr2_1:5438339-5438358 None:intergenic 50.0%
! ACTGGCAGATTAGGTAGTGG+TGG + chr2_1:5438352-5438371 None:intergenic 50.0%
CCAGGAACAGTAGGAATCTG+AGG + chr2_1:5438481-5438500 None:intergenic 50.0%
CCTCAGATTCCTACTGTTCC+TGG - chr2_1:5438478-5438497 Msa0190000:CDS 50.0%
TGAGGAATTTGTGGCACACC+AGG + chr2_1:5438499-5438518 None:intergenic 50.0%
!! GGCACTGGCAGATTAGGTAG+TGG + chr2_1:5438355-5438374 None:intergenic 55.0%
!! GGCAATGGCACTGGCAGATT+AGG + chr2_1:5438361-5438380 None:intergenic 55.0%
TGTGGCACACCAGGAACAGT+AGG + chr2_1:5438490-5438509 None:intergenic 55.0%
CTAGGCACACCAGGAATCTG+AGG + chr2_1:5438517-5438536 None:intergenic 55.0%
TTAGGCACACTAGGCACACC+AGG + chr2_1:5438526-5438545 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 5438250 5438552 5438250 ID=Msa0190000;Name=Msa0190000
chr2_1 mRNA 5438250 5438552 5438250 ID=Msa0190000-mRNA-1;Parent=Msa0190000;Name=Msa0190000-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|100
chr2_1 exon 5438250 5438552 5438250 ID=Msa0190000-mRNA-1:exon:2441;Parent=Msa0190000-mRNA-1
chr2_1 CDS 5438250 5438552 5438250 ID=Msa0190000-mRNA-1:cds;Parent=Msa0190000-mRNA-1
Gene Sequence

>Msa0190000

ATGGCTTCCATCAATTTCTGGTCATTAATTTTATCACTTCTACTCATAACATTTTCATCAATGACAAGTATTGAAGGAGCACGTAACCTTGTTGAGTTGCCACCACTACCTAATCTGCCAGTGCCATTGCCATTAACACAGCCACAATTGCCAACAATTCCAAACTTAGGTGTTCCAGTAATCCCTAATGTACCAACTTTGCCTCAAATACCAACTGTGCCTCAAATACCTCAGATTCCTACTGTTCCTGGTGTGCCACAAATTCCTCAGATTCCTGGTGTGCCTAGTGTGCCTAAACCATAA
Protein sequence

>Msa0190000

MASINFWSLILSLLLITFSSMTSIEGARNLVELPPLPNLPVPLPLTQPQLPTIPNLGVPVIPNVPTLPQIPTVPQIPQIPTVPGVPQIPQIPGVPSVPKP*