AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0307750

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0307750 MtrunA17_Chr2g0279561 90.000 100 4 1 1 100 1 94 1.26e-39 127
Msa0307750 MtrunA17_Chr3g0087151 38.393 112 55 5 1 100 1 110 4.27e-12 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGGCTTCCATCAATTTC+TGG 0.176747 2_4:-890401 Msa0307750:CDS
TGAGGCAAAGTTGGTACATT+AGG 0.250872 2_4:+890216 None:intergenic
GGCAATTGTGGCTGTGTTAA+TGG 0.262929 2_4:+890270 None:intergenic
CCTCAGATTCCTACTGTTCC+TGG 0.290936 2_4:-890171 Msa0307750:CDS
ACTTTAGGTGCTTATGGTTT+AGG 0.331666 2_4:+890108 None:intergenic
GTTGGTACATTAGGGATTAC+TGG 0.335295 2_4:+890225 None:intergenic
GAGGCAAAGTTGGTACATTA+GGG 0.367979 2_4:+890217 None:intergenic
ATTACTGGAACACCTAAGTT+TGG 0.371975 2_4:+890240 None:intergenic
CCACAAATTCCTCAGATTCC+TGG 0.389504 2_4:-890144 Msa0307750:CDS
AATGAATGACCAGAAATTGA+TGG 0.402882 2_4:+890392 None:intergenic
ACACCTAAGTTTGGAATTGT+TGG 0.404545 2_4:+890249 None:intergenic
GGCAATGGCACTGGCAGATT+AGG 0.425870 2_4:+890291 None:intergenic
TGAGGCACAGTTGGTATTTG+AGG 0.431733 2_4:+890198 None:intergenic
TCATCAATGACAAGTATTGA+AGG 0.467180 2_4:-890345 Msa0307750:CDS
TTGCCAACAATTCCAAACTT+AGG 0.468746 2_4:-890252 Msa0307750:CDS
CCAGGAATCTGAGGAATTTG+TGG 0.472835 2_4:+890144 None:intergenic
TTTGGAATTGTTGGCAATTG+TGG 0.474516 2_4:+890258 None:intergenic
GTTGGTATTTGAGGCAAAGT+TGG 0.507961 2_4:+890207 None:intergenic
TGAGGAATTTGAGGCACAGT+TGG 0.533770 2_4:+890189 None:intergenic
TGTGTTAATGGCAATGGCAC+TGG 0.535953 2_4:+890282 None:intergenic
GTAGGAATCTGAGGAATTTG+AGG 0.536589 2_4:+890180 None:intergenic
TGAGGAATTTGTGGCACACC+AGG 0.542628 2_4:+890153 None:intergenic
GCTTATGGTTTAGGCACACT+AGG 0.569725 2_4:+890117 None:intergenic
GAAAATGTTATGAGTAGAAG+TGG 0.572387 2_4:+890366 None:intergenic
TTAGGCACACTAGGCACACC+AGG 0.574512 2_4:+890126 None:intergenic
CTAGGCACACCAGGAATCTG+AGG 0.592705 2_4:+890135 None:intergenic
GGCACTGGCAGATTAGGTAG+TGG 0.603557 2_4:+890297 None:intergenic
TGTGGCACACCAGGAACAGT+AGG 0.606684 2_4:+890162 None:intergenic
CCAGGAACAGTAGGAATCTG+AGG 0.611409 2_4:+890171 None:intergenic
TGTGGCTGTGTTAATGGCAA+TGG 0.622083 2_4:+890276 None:intergenic
ACTGGCAGATTAGGTAGTGG+TGG 0.639353 2_4:+890300 None:intergenic
GTAGTGGTGGCAACTCAACA+AGG 0.734703 2_4:+890313 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AATGAATGACCAGAAATTGA+TGG + chr2_4:890129-890148 None:intergenic 30.0%
GAAAATGTTATGAGTAGAAG+TGG + chr2_4:890155-890174 None:intergenic 30.0%
!! TCATCAATGACAAGTATTGA+AGG - chr2_4:890173-890192 Msa0307750:CDS 30.0%
! TTTGGAATTGTTGGCAATTG+TGG + chr2_4:890263-890282 None:intergenic 35.0%
TTGCCAACAATTCCAAACTT+AGG - chr2_4:890266-890285 Msa0307750:CDS 35.0%
! ACACCTAAGTTTGGAATTGT+TGG + chr2_4:890272-890291 None:intergenic 35.0%
ATTACTGGAACACCTAAGTT+TGG + chr2_4:890281-890300 None:intergenic 35.0%
GTTGGTACATTAGGGATTAC+TGG + chr2_4:890296-890315 None:intergenic 40.0%
!! GAGGCAAAGTTGGTACATTA+GGG + chr2_4:890304-890323 None:intergenic 40.0%
!! TGAGGCAAAGTTGGTACATT+AGG + chr2_4:890305-890324 None:intergenic 40.0%
! GTTGGTATTTGAGGCAAAGT+TGG + chr2_4:890314-890333 None:intergenic 40.0%
GTAGGAATCTGAGGAATTTG+AGG + chr2_4:890341-890360 None:intergenic 40.0%
TGTGTTAATGGCAATGGCAC+TGG + chr2_4:890239-890258 None:intergenic 45.0%
TGTGGCTGTGTTAATGGCAA+TGG + chr2_4:890245-890264 None:intergenic 45.0%
GGCAATTGTGGCTGTGTTAA+TGG + chr2_4:890251-890270 None:intergenic 45.0%
! TGAGGCACAGTTGGTATTTG+AGG + chr2_4:890323-890342 None:intergenic 45.0%
! TGAGGAATTTGAGGCACAGT+TGG + chr2_4:890332-890351 None:intergenic 45.0%
CCAGGAATCTGAGGAATTTG+TGG + chr2_4:890377-890396 None:intergenic 45.0%
CCACAAATTCCTCAGATTCC+TGG - chr2_4:890374-890393 Msa0307750:CDS 45.0%
GTAGTGGTGGCAACTCAACA+AGG + chr2_4:890208-890227 None:intergenic 50.0%
! ACTGGCAGATTAGGTAGTGG+TGG + chr2_4:890221-890240 None:intergenic 50.0%
CCAGGAACAGTAGGAATCTG+AGG + chr2_4:890350-890369 None:intergenic 50.0%
CCTCAGATTCCTACTGTTCC+TGG - chr2_4:890347-890366 Msa0307750:CDS 50.0%
TGAGGAATTTGTGGCACACC+AGG + chr2_4:890368-890387 None:intergenic 50.0%
!! GGCACTGGCAGATTAGGTAG+TGG + chr2_4:890224-890243 None:intergenic 55.0%
!! GGCAATGGCACTGGCAGATT+AGG + chr2_4:890230-890249 None:intergenic 55.0%
TGTGGCACACCAGGAACAGT+AGG + chr2_4:890359-890378 None:intergenic 55.0%
CTAGGCACACCAGGAATCTG+AGG + chr2_4:890386-890405 None:intergenic 55.0%
TTAGGCACACTAGGCACACC+AGG + chr2_4:890395-890414 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr2_4 gene 890119 890421 890119 ID=Msa0307750;Name=Msa0307750
chr2_4 mRNA 890119 890421 890119 ID=Msa0307750-mRNA-1;Parent=Msa0307750;Name=Msa0307750-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|100
chr2_4 exon 890119 890421 890119 ID=Msa0307750-mRNA-1:exon:343;Parent=Msa0307750-mRNA-1
chr2_4 CDS 890119 890421 890119 ID=Msa0307750-mRNA-1:cds;Parent=Msa0307750-mRNA-1
Gene Sequence

>Msa0307750

ATGGCTTCCATCAATTTCTGGTCATTCATTTTACCACTTCTACTCATAACATTTTCATCAATGACAAGTATTGAAGGAGCACGTAACCTTGTTGAGTTGCCACCACTACCTAATCTGCCAGTGCCATTGCCATTAACACAGCCACAATTGCCAACAATTCCAAACTTAGGTGTTCCAGTAATCCCTAATGTACCAACTTTGCCTCAAATACCAACTGTGCCTCAAATTCCTCAGATTCCTACTGTTCCTGGTGTGCCACAAATTCCTCAGATTCCTGGTGTGCCTAGTGTGCCTAAACCATAA
Protein sequence

>Msa0307750

MASINFWSFILPLLLITFSSMTSIEGARNLVELPPLPNLPVPLPLTQPQLPTIPNLGVPVIPNVPTLPQIPTVPQIPQIPTVPGVPQIPQIPGVPSVPKP*