AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0677820


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0677820 MtrunA17_Chr4g0022631 100.000 59 0 0 6 64 232 290 1.83e-34 118
Msa0677820 MtrunA17_Chr2g0323531 81.034 58 11 0 6 63 229 286 5.27e-26 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0677820 AT2G20890.1 84.746 59 9 0 6 64 225 283 1.54e-27 100

Find 9 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCAATTCAACAGCTTTGTT+CGG 0.391152 4_4:-32404144 Msa0677820:intron
AAGGAGAATGCTGCATTCAT+TGG 0.397106 4_4:-32404360 None:intergenic
TCGCAATCTGCTTTCTAAGT+TGG 0.429863 4_4:-32404075 Msa0677820:CDS
GAAGAAGAAAATAGAAGAAA+GGG 0.446296 4_4:-32403504 Msa0677820:CDS
AGAAGAAGAAAATAGAAGAA+AGG 0.447419 4_4:-32403505 Msa0677820:CDS
AGAAAGGGCTGAACCACAAA+AGG 0.489128 4_4:-32403489 Msa0677820:CDS
TGCTCAAGGAATACATTGAC+AGG 0.514662 4_4:-32404037 Msa0677820:intron
TGAACCACAAAAGGCTAATG+AGG 0.552905 4_4:-32403480 Msa0677820:CDS
ACAAGCTAAAGAGCTGCTCA+AGG 0.612741 4_4:-32404051 Msa0677820:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TACATTCAAATATATATCAT+AGG + chr4_4:32403860-32403879 None:intergenic 15.0%
!!! CTATTATATTTTTCTGAAAA+AGG + chr4_4:32404132-32404151 None:intergenic 15.0%
!! TACATTCAAATATATATCAT+AGG + chr4_4:32403860-32403879 None:intergenic 15.0%
!!! CTATTATATTTTTCTGAAAA+AGG + chr4_4:32404132-32404151 None:intergenic 15.0%
!!! TTCATTGGTAATAAACATTT+AGG - chr4_4:32403474-32403493 Msa0677820:CDS 20.0%
!! AACTGAAAAACTTAGTAAAT+AGG + chr4_4:32404078-32404097 None:intergenic 20.0%
!!! TTCATTGGTAATAAACATTT+AGG - chr4_4:32403474-32403493 Msa0677820:CDS 20.0%
!! AACTGAAAAACTTAGTAAAT+AGG + chr4_4:32404078-32404097 None:intergenic 20.0%
!! TTGGTAATAAACATTTAGGA+TGG - chr4_4:32403478-32403497 Msa0677820:CDS 25.0%
!! GTGATCTCAATTTTATGAAA+AGG + chr4_4:32403989-32404008 None:intergenic 25.0%
! CTTCTAATTGAAAATTAAGC+TGG - chr4_4:32404049-32404068 Msa0677820:CDS 25.0%
!!! TTTACTAAGTTTTTCAGTTC+AGG - chr4_4:32404079-32404098 Msa0677820:CDS 25.0%
!!! TTACTAAGTTTTTCAGTTCA+GGG - chr4_4:32404080-32404099 Msa0677820:CDS 25.0%
! TCATAACATGTCGAAAATTT+AGG + chr4_4:32404232-32404251 None:intergenic 25.0%
!!! TGTTATGATTATAACTTGCT+TGG - chr4_4:32404244-32404263 Msa0677820:intron 25.0%
! AGAAGAAGAAAATAGAAGAA+AGG - chr4_4:32404314-32404333 Msa0677820:intron 25.0%
! GAAGAAGAAAATAGAAGAAA+GGG - chr4_4:32404315-32404334 Msa0677820:intron 25.0%
!! TTGGTAATAAACATTTAGGA+TGG - chr4_4:32403478-32403497 Msa0677820:CDS 25.0%
!! GTGATCTCAATTTTATGAAA+AGG + chr4_4:32403989-32404008 None:intergenic 25.0%
! CTTCTAATTGAAAATTAAGC+TGG - chr4_4:32404049-32404068 Msa0677820:CDS 25.0%
!!! TTTACTAAGTTTTTCAGTTC+AGG - chr4_4:32404079-32404098 Msa0677820:CDS 25.0%
!!! TTACTAAGTTTTTCAGTTCA+GGG - chr4_4:32404080-32404099 Msa0677820:CDS 25.0%
! TCATAACATGTCGAAAATTT+AGG + chr4_4:32404232-32404251 None:intergenic 25.0%
!!! TGTTATGATTATAACTTGCT+TGG - chr4_4:32404244-32404263 Msa0677820:intron 25.0%
! AGAAGAAGAAAATAGAAGAA+AGG - chr4_4:32404314-32404333 Msa0677820:intron 25.0%
! GAAGAAGAAAATAGAAGAAA+GGG - chr4_4:32404315-32404334 Msa0677820:intron 25.0%
ATATGACTATCATCAGACTA+TGG - chr4_4:32403552-32403571 Msa0677820:intron 30.0%
CCACACACAAAAATTATTAG+TGG + chr4_4:32403627-32403646 None:intergenic 30.0%
! CCACTAATAATTTTTGTGTG+TGG - chr4_4:32403624-32403643 Msa0677820:intron 30.0%
! TAATAATTTTTGTGTGTGGC+TGG - chr4_4:32403628-32403647 Msa0677820:intron 30.0%
! AATAATTTTTGTGTGTGGCT+GGG - chr4_4:32403629-32403648 Msa0677820:intron 30.0%
!! AAAAAGTGTTGATCGAGATT+TGG - chr4_4:32403714-32403733 Msa0677820:intron 30.0%
AACAACTTAATAGCATTGCA+AGG + chr4_4:32403818-32403837 None:intergenic 30.0%
! ATTAAGTTGTTCTCACTTCT+CGG - chr4_4:32403827-32403846 Msa0677820:intron 30.0%
TGAAGACTAAATGTAGCATA+TGG + chr4_4:32403905-32403924 None:intergenic 30.0%
GATTCAATCTTGAACTTCAA+GGG + chr4_4:32403952-32403971 None:intergenic 30.0%
AGATTCAATCTTGAACTTCA+AGG + chr4_4:32403953-32403972 None:intergenic 30.0%
! CATGTCGAAAATTTAGGTTA+AGG + chr4_4:32404226-32404245 None:intergenic 30.0%
!!! TTATAACTTGCTTGGTTTTG+CGG - chr4_4:32404252-32404271 Msa0677820:intron 30.0%
ATATGACTATCATCAGACTA+TGG - chr4_4:32403552-32403571 Msa0677820:intron 30.0%
CCACACACAAAAATTATTAG+TGG + chr4_4:32403627-32403646 None:intergenic 30.0%
! CCACTAATAATTTTTGTGTG+TGG - chr4_4:32403624-32403643 Msa0677820:intron 30.0%
! TAATAATTTTTGTGTGTGGC+TGG - chr4_4:32403628-32403647 Msa0677820:intron 30.0%
! AATAATTTTTGTGTGTGGCT+GGG - chr4_4:32403629-32403648 Msa0677820:intron 30.0%
!! AAAAAGTGTTGATCGAGATT+TGG - chr4_4:32403714-32403733 Msa0677820:intron 30.0%
AACAACTTAATAGCATTGCA+AGG + chr4_4:32403818-32403837 None:intergenic 30.0%
! ATTAAGTTGTTCTCACTTCT+CGG - chr4_4:32403827-32403846 Msa0677820:intron 30.0%
TGAAGACTAAATGTAGCATA+TGG + chr4_4:32403905-32403924 None:intergenic 30.0%
GATTCAATCTTGAACTTCAA+GGG + chr4_4:32403952-32403971 None:intergenic 30.0%
AGATTCAATCTTGAACTTCA+AGG + chr4_4:32403953-32403972 None:intergenic 30.0%
! CATGTCGAAAATTTAGGTTA+AGG + chr4_4:32404226-32404245 None:intergenic 30.0%
!!! TTATAACTTGCTTGGTTTTG+CGG - chr4_4:32404252-32404271 Msa0677820:intron 30.0%
! TTTAGGATGGACAAAATTGC+TGG - chr4_4:32403491-32403510 Msa0677820:CDS 35.0%
ATGGACAAAATTGCTGGTAA+AGG - chr4_4:32403497-32403516 Msa0677820:CDS 35.0%
!! GTCAATTCAACAGCTTTGTT+CGG - chr4_4:32403675-32403694 Msa0677820:intron 35.0%
! TTAAGTTGTTCTCACTTCTC+GGG - chr4_4:32403828-32403847 Msa0677820:intron 35.0%
!! AGTTTTTCAGTTCAGGGTTT+AGG - chr4_4:32404086-32404105 Msa0677820:CDS 35.0%
CTAGTGATATACTGAGAACT+TGG - chr4_4:32404162-32404181 Msa0677820:intron 35.0%
TTCGAATGATCTCTTACTTC+AGG - chr4_4:32404290-32404309 Msa0677820:intron 35.0%
TCGAATGATCTCTTACTTCA+GGG - chr4_4:32404291-32404310 Msa0677820:intron 35.0%
! TTTAGGATGGACAAAATTGC+TGG - chr4_4:32403491-32403510 Msa0677820:CDS 35.0%
ATGGACAAAATTGCTGGTAA+AGG - chr4_4:32403497-32403516 Msa0677820:CDS 35.0%
!! GTCAATTCAACAGCTTTGTT+CGG - chr4_4:32403675-32403694 Msa0677820:intron 35.0%
! TTAAGTTGTTCTCACTTCTC+GGG - chr4_4:32403828-32403847 Msa0677820:intron 35.0%
!! AGTTTTTCAGTTCAGGGTTT+AGG - chr4_4:32404086-32404105 Msa0677820:CDS 35.0%
CTAGTGATATACTGAGAACT+TGG - chr4_4:32404162-32404181 Msa0677820:intron 35.0%
TTCGAATGATCTCTTACTTC+AGG - chr4_4:32404290-32404309 Msa0677820:intron 35.0%
TCGAATGATCTCTTACTTCA+GGG - chr4_4:32404291-32404310 Msa0677820:intron 35.0%
TCGCAATCTGCTTTCTAAGT+TGG - chr4_4:32403744-32403763 Msa0677820:intron 40.0%
TGCTCAAGGAATACATTGAC+AGG - chr4_4:32403782-32403801 Msa0677820:intron 40.0%
TGAACCACAAAAGGCTAATG+AGG - chr4_4:32404339-32404358 Msa0677820:intron 40.0%
TCGCAATCTGCTTTCTAAGT+TGG - chr4_4:32403744-32403763 Msa0677820:intron 40.0%
TGCTCAAGGAATACATTGAC+AGG - chr4_4:32403782-32403801 Msa0677820:intron 40.0%
TGAACCACAAAAGGCTAATG+AGG - chr4_4:32404339-32404358 Msa0677820:intron 40.0%
ACAAGCTAAAGAGCTGCTCA+AGG - chr4_4:32403768-32403787 Msa0677820:intron 45.0%
AGAAAGGGCTGAACCACAAA+AGG - chr4_4:32404330-32404349 Msa0677820:intron 45.0%
!!! ATGGCCTCATTAGCCTTTTG+TGG + chr4_4:32404346-32404365 None:intergenic 45.0%
ACAAGCTAAAGAGCTGCTCA+AGG - chr4_4:32403768-32403787 Msa0677820:intron 45.0%
AGAAAGGGCTGAACCACAAA+AGG - chr4_4:32404330-32404349 Msa0677820:intron 45.0%
!!! ATGGCCTCATTAGCCTTTTG+TGG + chr4_4:32404346-32404365 None:intergenic 45.0%
!!! AACTTGCTTGGTTTTGCGGC+TGG - chr4_4:32404256-32404275 Msa0677820:intron 50.0%
!!! AACTTGCTTGGTTTTGCGGC+TGG - chr4_4:32404256-32404275 Msa0677820:intron 50.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 32403466 32404375 32403466 ID=Msa0677820;Name=Msa0677820
chr4_4 mRNA 32403466 32404375 32403466 ID=Msa0677820-mRNA-1;Parent=Msa0677820;Name=Msa0677820-mRNA-1;_AED=0.52;_eAED=0.52;_QI=0|0|0|0.66|0|0|3|0|64
chr4_4 exon 32404361 32404375 32404361 ID=Msa0677820-mRNA-1:exon:8013;Parent=Msa0677820-mRNA-1
chr4_4 exon 32404038 32404153 32404038 ID=Msa0677820-mRNA-1:exon:8012;Parent=Msa0677820-mRNA-1
chr4_4 exon 32403466 32403529 32403466 ID=Msa0677820-mRNA-1:exon:8011;Parent=Msa0677820-mRNA-1
chr4_4 CDS 32404361 32404375 32404361 ID=Msa0677820-mRNA-1:cds;Parent=Msa0677820-mRNA-1
chr4_4 CDS 32404038 32404153 32404038 ID=Msa0677820-mRNA-1:cds;Parent=Msa0677820-mRNA-1
chr4_4 CDS 32403466 32403529 32403466 ID=Msa0677820-mRNA-1:cds;Parent=Msa0677820-mRNA-1
Gene Sequence

>Msa0677820

ATGCTGCATTCATTGCTTTGTTCGGCTTTGAATATCAACAAAAAAAGTGTTGATCGAGATTTGGACGTGTATCGCAATCTGCTTTCTAAGTTGGTACAAGCTAAAGAGCTGCTCAAGGAATACATTGACAGGGAGAAGAAGAAAATAGAAGAAAGGGCTGAACCACAAAAGGCTAATGAGGCCATTTCAAAATGA

Protein sequence

>Msa0677820

MLHSLLCSALNINKKSVDRDLDVYRNLLSKLVQAKELLKEYIDREKKKIEERAEPQKANEAISK*