AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0896780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0896780 MtrunA17_Chr6g0481891 91.388 209 11 1 1 209 1 202 7.77e-139 386
Msa0896780 MtrunA17_Chr8g0388871 69.892 186 54 2 22 206 1 185 1.04e-89 261
Msa0896780 MtrunA17_Chr1g0212091 48.515 202 104 0 3 204 18 219 2.84e-62 193
Msa0896780 MtrunA17_Chr1g0162171 50.000 180 85 1 29 203 41 220 9.44e-59 184
Msa0896780 MtrunA17_Chr1g0212181 45.500 200 96 2 4 203 29 215 1.12e-56 179
Msa0896780 MtrunA17_Chr1g0212171 47.399 173 91 0 34 206 49 221 1.31e-54 173
Msa0896780 MtrunA17_Chr1g0212121 46.154 195 101 2 13 206 27 218 1.01e-53 171
Msa0896780 MtrunA17_Chr7g0251801 41.718 163 95 0 41 203 112 274 1.22e-42 145
Msa0896780 MtrunA17_Chr1g0212111 56.637 113 49 0 96 208 47 159 4.59e-39 132
Msa0896780 MtrunA17_Chr3g0133221 37.662 154 95 1 50 203 103 255 8.36e-39 134
Msa0896780 MtrunA17_Chr8g0367701 37.107 159 99 1 45 203 110 267 2.76e-34 123
Msa0896780 MtrunA17_Chr2g0315771 37.500 160 99 1 45 203 66 225 2.32e-31 114
Msa0896780 MtrunA17_Chr1g0212131 53.571 56 26 0 148 203 6 61 4.17e-14 64.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0896780 AT5G08350.1 48.663 187 94 1 20 206 31 215 5.96e-56 177
Msa0896780 AT5G23370.1 50.526 190 91 2 20 208 31 218 7.14e-56 177
Msa0896780 AT5G23360.1 48.913 184 85 1 20 203 31 205 6.57e-53 169
Msa0896780 AT5G23350.1 50.000 182 88 2 23 203 34 213 3.86e-52 167
Msa0896780 AT5G13200.1 40.252 159 95 0 45 203 102 260 3.91e-40 138
Msa0896780 AT4G01600.3 37.931 174 107 1 32 204 13 186 4.99e-38 130
Msa0896780 AT4G01600.1 40.373 161 95 1 45 204 65 225 1.13e-37 130
Msa0896780 AT2G22475.1 36.875 160 98 2 45 203 134 291 1.49e-36 130
Msa0896780 AT4G01600.2 43.243 148 83 1 58 204 73 220 2.31e-36 127
Msa0896780 AT1G28200.1 38.037 163 99 2 41 203 94 254 1.23e-35 126
Msa0896780 AT1G28200.2 38.037 163 99 2 41 203 94 254 1.23e-35 126
Msa0896780 AT5G13200.2 41.509 106 62 0 45 150 102 207 7.97e-23 92.0
Msa0896780 AT2G22475.2 34.188 117 74 2 45 160 134 248 7.98e-19 82.0

Find 31 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAAGGATGGCTCTGAATTT+TGG 0.191579 6_1:+87559426 Msa0896780:CDS
AAAATAATATATTTGCTAAT+TGG 0.222651 6_1:-87557789 None:intergenic
GAATTTATTGGCCATGAAAA+TGG 0.230364 6_1:-87559498 None:intergenic
CAGATAAAGAAAACTCAAAT+AGG 0.238573 6_1:+87558069 Msa0896780:intron
AAAGCGGTTCTTACTTGTTA+TGG 0.266422 6_1:-87557965 None:intergenic
CATACTCTGATGAAGTCTTT+TGG 0.272298 6_1:+87557865 Msa0896780:exon
GTTATGGTTGCAGTGAAATT+AGG 0.306142 6_1:+87558443 Msa0896780:intron
TTGAAGGGTAAGTTAAGTTT+AGG 0.334682 6_1:+87558485 Msa0896780:CDS
CAAAAGACTTCATCAGAGTA+TGG 0.356576 6_1:-87557864 None:intergenic
ACCACAGCTGGTCCTATTGC+TGG 0.386738 6_1:+87558611 Msa0896780:CDS
TCTGCAGAATAGAAGCTTGT+AGG 0.416048 6_1:-87558680 None:intergenic
GGTTTCAAGATTACTTTGTA+AGG 0.428405 6_1:-87558722 None:intergenic
ATAAAGAGAATTCCAGCAAT+AGG 0.429382 6_1:-87558623 None:intergenic
AGATAAAGAAAACTCAAATA+GGG 0.461660 6_1:+87558070 Msa0896780:intron
TCTAGGAAAGTACTGAAGAA+AGG 0.464281 6_1:-87557747 None:intergenic
ATATATAGAAGTAGTGACTA+AGG 0.483276 6_1:+87559409 Msa0896780:CDS
ATGGAGGTTGAATCAGAAGT+TGG 0.483557 6_1:-87557946 None:intergenic
GGTGCTAAAATTATTCAAGA+AGG 0.492255 6_1:+87558506 Msa0896780:CDS
ATTATTCAAGAAGGTGGAAG+AGG 0.509163 6_1:+87558515 Msa0896780:CDS
TGCTATTTATATACCACAGC+TGG 0.515042 6_1:+87558599 Msa0896780:CDS
ACAAGCTTCTATTCTGCAGA+TGG 0.530966 6_1:+87558683 Msa0896780:CDS
GCTAAAATTATTCAAGAAGG+TGG 0.533103 6_1:+87558509 Msa0896780:CDS
ACCAATAGAGAAGATAAAAG+AGG 0.549360 6_1:+87559349 Msa0896780:CDS
GCATATAGTATTCATGAACA+TGG 0.551487 6_1:+87558122 Msa0896780:CDS
CAAATAGGGATTTCACAAGA+AGG 0.555465 6_1:+87558084 Msa0896780:CDS
GCGGTTCTTACTTGTTATGG+AGG 0.563314 6_1:-87557962 None:intergenic
AAATAGGGATTTCACAAGAA+GGG 0.576471 6_1:+87558085 Msa0896780:CDS
CAAGCTTCTATTCTGCAGAT+GGG 0.579988 6_1:+87558684 Msa0896780:CDS
ATAGAAGTAGTGACTAAGGA+TGG 0.592266 6_1:+87559413 Msa0896780:CDS
TCCAGCAATAGGACCAGCTG+TGG 0.636838 6_1:-87558612 None:intergenic
AAGCTTCTATTCTGCAGATG+GGG 0.642873 6_1:+87558685 Msa0896780:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAATAATATATTTGCTAAT+TGG - chr6_1:87557792-87557811 None:intergenic 10.0%
!!! ATTATTTTTGTTATTGTTTT+TGG + chr6_1:87557804-87557823 Msa0896780:five_prime_UTR 10.0%
!!! ATCTATATTTTTTTTGTATT+TGG - chr6_1:87558350-87558369 None:intergenic 10.0%
!!! AGTTAAATTATTTTCATATA+AGG - chr6_1:87558900-87558919 None:intergenic 10.0%
!! TAAAGGAAAAAAAAAAAAAG+CGG - chr6_1:87557984-87558003 None:intergenic 15.0%
!!! ATATTTTTTTTGTATTTGGT+CGG - chr6_1:87558346-87558365 None:intergenic 15.0%
!!! TTATTTTCTCAAATTATTAC+CGG + chr6_1:87558381-87558400 Msa0896780:intron 15.0%
!! GATAAAAATTCTATGAATTA+AGG - chr6_1:87559279-87559298 None:intergenic 15.0%
!! GATGAAATGAAAGAAATTAA+AGG - chr6_1:87558001-87558020 None:intergenic 20.0%
!! TATACCAATAACAAAGTAAA+AGG + chr6_1:87558027-87558046 Msa0896780:intron 20.0%
!!! AAAACCTTTTACTTTGTTAT+TGG - chr6_1:87558034-87558053 None:intergenic 20.0%
!! AGATAAAGAAAACTCAAATA+GGG + chr6_1:87558070-87558089 Msa0896780:intron 20.0%
!!! AACATTTTCAAGCATATTTT+TGG + chr6_1:87558539-87558558 Msa0896780:CDS 20.0%
!!! ACATTTTCAAGCATATTTTT+GGG + chr6_1:87558540-87558559 Msa0896780:CDS 20.0%
!! AAATAAGCTAATCAAAACAT+AGG - chr6_1:87558764-87558783 None:intergenic 20.0%
!! ATAAGCTGAAAATAGTTTAT+GGG - chr6_1:87559118-87559137 None:intergenic 20.0%
!! AATAAGCTGAAAATAGTTTA+TGG - chr6_1:87559119-87559138 None:intergenic 20.0%
!! CTGTTATAAATAGCTTTTCT+AGG - chr6_1:87557767-87557786 None:intergenic 25.0%
!!! ATAACAAAAAAGCATCTACT+CGG - chr6_1:87557898-87557917 None:intergenic 25.0%
!!! TTTTGAGGAAATTATCATCA+TGG - chr6_1:87557924-87557943 None:intergenic 25.0%
! CAGATAAAGAAAACTCAAAT+AGG + chr6_1:87558069-87558088 Msa0896780:intron 25.0%
! TCAAACTTTCAATTCAATCA+AGG + chr6_1:87558188-87558207 Msa0896780:intron 25.0%
! AGATTGTGACATAATCATAA+CGG - chr6_1:87558230-87558249 None:intergenic 25.0%
!!! TAAATTTTCTGAGACTTTGA+AGG + chr6_1:87558469-87558488 Msa0896780:CDS 25.0%
!!! AAATTTTCTGAGACTTTGAA+GGG + chr6_1:87558470-87558489 Msa0896780:CDS 25.0%
! CTCAAACAGACAATAAAAAA+TGG - chr6_1:87558787-87558806 None:intergenic 25.0%
!! ACTTATTTGAGATTATCTAC+TGG + chr6_1:87559038-87559057 Msa0896780:intron 25.0%
! ATTGCATTGTTCTGATATAA+AGG + chr6_1:87559304-87559323 Msa0896780:intron 25.0%
! ATATATAGAAGTAGTGACTA+AGG + chr6_1:87559409-87559428 Msa0896780:CDS 25.0%
AAATAGGGATTTCACAAGAA+GGG + chr6_1:87558085-87558104 Msa0896780:CDS 30.0%
GCATATAGTATTCATGAACA+TGG + chr6_1:87558122-87558141 Msa0896780:CDS 30.0%
AAATCTTTCATGTGAAGTGT+CGG - chr6_1:87558299-87558318 None:intergenic 30.0%
TTGAAGGGTAAGTTAAGTTT+AGG + chr6_1:87558485-87558504 Msa0896780:CDS 30.0%
GGTGCTAAAATTATTCAAGA+AGG + chr6_1:87558506-87558525 Msa0896780:CDS 30.0%
GCTAAAATTATTCAAGAAGG+TGG + chr6_1:87558509-87558528 Msa0896780:CDS 30.0%
ATAAAGAGAATTCCAGCAAT+AGG - chr6_1:87558626-87558645 None:intergenic 30.0%
! GCAAAATGCAACTTTTACAT+TGG - chr6_1:87558651-87558670 None:intergenic 30.0%
GGTTTCAAGATTACTTTGTA+AGG - chr6_1:87558725-87558744 None:intergenic 30.0%
ATAGGATTTGAGCTTAAAGT+TGG - chr6_1:87558746-87558765 None:intergenic 30.0%
! AATAAGCGGAAAACAACTTT+TGG - chr6_1:87558839-87558858 None:intergenic 30.0%
CTGTAGCTTATGAAAATAAG+CGG - chr6_1:87558853-87558872 None:intergenic 30.0%
TCAAATAAGTCAACTCAAAC+AGG - chr6_1:87559028-87559047 None:intergenic 30.0%
TTAAACTCTCACAAACAATC+TGG - chr6_1:87559076-87559095 None:intergenic 30.0%
TATAAAGGTTCTTGTAATGC+AGG + chr6_1:87559319-87559338 Msa0896780:intron 30.0%
ACCAATAGAGAAGATAAAAG+AGG + chr6_1:87559349-87559368 Msa0896780:CDS 30.0%
! ACCTCTTTTATCTTCTCTAT+TGG - chr6_1:87559353-87559372 None:intergenic 30.0%
!! TTTGGTTCATGGGATTTTTA+AGG + chr6_1:87559444-87559463 Msa0896780:CDS 30.0%
!!! TCTCAATAATGCCATTTTCA+TGG + chr6_1:87559487-87559506 Msa0896780:CDS 30.0%
GAATTTATTGGCCATGAAAA+TGG - chr6_1:87559501-87559520 None:intergenic 30.0%
!! TCTAGGAAAGTACTGAAGAA+AGG - chr6_1:87557750-87557769 None:intergenic 35.0%
CAAAAGACTTCATCAGAGTA+TGG - chr6_1:87557867-87557886 None:intergenic 35.0%
! CATACTCTGATGAAGTCTTT+TGG + chr6_1:87557865-87557884 Msa0896780:exon 35.0%
! AATCAGAAGTTGGAGTTTTG+AGG - chr6_1:87557939-87557958 None:intergenic 35.0%
! AAAGCGGTTCTTACTTGTTA+TGG - chr6_1:87557968-87557987 None:intergenic 35.0%
CAAATAGGGATTTCACAAGA+AGG + chr6_1:87558084-87558103 Msa0896780:CDS 35.0%
TGTGAATGAAACACTGAAAC+CGG - chr6_1:87558403-87558422 None:intergenic 35.0%
GTTATGGTTGCAGTGAAATT+AGG + chr6_1:87558443-87558462 Msa0896780:intron 35.0%
ATTATTCAAGAAGGTGGAAG+AGG + chr6_1:87558515-87558534 Msa0896780:CDS 35.0%
!!! CATATTTTTGGGATGCAAGA+GGG + chr6_1:87558551-87558570 Msa0896780:CDS 35.0%
! TGCTATTTATATACCACAGC+TGG + chr6_1:87558599-87558618 Msa0896780:CDS 35.0%
! AAGTTGCATTTTGCAGTGAA+AGG + chr6_1:87558657-87558676 Msa0896780:CDS 35.0%
!! CGCTTATTTTCATAAGCTAC+AGG + chr6_1:87558851-87558870 Msa0896780:intron 35.0%
ATAGAAGTAGTGACTAAGGA+TGG + chr6_1:87559413-87559432 Msa0896780:CDS 35.0%
!! AAAAAAGCATCTACTCGGAG+AGG - chr6_1:87557893-87557912 None:intergenic 40.0%
ATGGAGGTTGAATCAGAAGT+TGG - chr6_1:87557949-87557968 None:intergenic 40.0%
ATTCACAGTTGTTGACCTTG+TGG + chr6_1:87558416-87558435 Msa0896780:intron 40.0%
TTGACCTTGTGGTTGTGTTA+TGG + chr6_1:87558427-87558446 Msa0896780:intron 40.0%
!!! GCATATTTTTGGGATGCAAG+AGG + chr6_1:87558550-87558569 Msa0896780:CDS 40.0%
TCTGCAGAATAGAAGCTTGT+AGG - chr6_1:87558683-87558702 None:intergenic 40.0%
ACAAGCTTCTATTCTGCAGA+TGG + chr6_1:87558683-87558702 Msa0896780:CDS 40.0%
CAAGCTTCTATTCTGCAGAT+GGG + chr6_1:87558684-87558703 Msa0896780:CDS 40.0%
AAGCTTCTATTCTGCAGATG+GGG + chr6_1:87558685-87558704 Msa0896780:CDS 40.0%
TGTTTACTCAACCAAAGCCT+TGG + chr6_1:87559000-87559019 Msa0896780:intron 40.0%
GTTTACTCAACCAAAGCCTT+GGG + chr6_1:87559001-87559020 Msa0896780:intron 40.0%
AGCTTATTTCCACAAGCTCT+CGG + chr6_1:87559131-87559150 Msa0896780:intron 40.0%
!!! CTAAGGATGGCTCTGAATTT+TGG + chr6_1:87559426-87559445 Msa0896780:CDS 40.0%
!!! TGGCTCTGAATTTTGGTTCA+TGG + chr6_1:87559433-87559452 Msa0896780:CDS 40.0%
!!! GGCTCTGAATTTTGGTTCAT+GGG + chr6_1:87559434-87559453 Msa0896780:CDS 40.0%
!! GCGGTTCTTACTTGTTATGG+AGG - chr6_1:87557965-87557984 None:intergenic 45.0%
!! TTGGTCGGTGTCACACATAT+TGG - chr6_1:87558331-87558350 None:intergenic 45.0%
GCAACCATAACACAACCACA+AGG - chr6_1:87558434-87558453 None:intergenic 45.0%
! AAGCTATTTCCGAGAGCTTG+TGG - chr6_1:87559143-87559162 None:intergenic 45.0%
TCAAACAGGTCCCAAGGCTT+TGG - chr6_1:87559014-87559033 None:intergenic 50.0%
GTCAACTCAAACAGGTCCCA+AGG - chr6_1:87559020-87559039 None:intergenic 50.0%
ACCACAGCTGGTCCTATTGC+TGG + chr6_1:87558611-87558630 Msa0896780:CDS 55.0%
TCCAGCAATAGGACCAGCTG+TGG - chr6_1:87558615-87558634 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 87557747 87559523 87557747 ID=Msa0896780;Name=Msa0896780
chr6_1 mRNA 87557747 87559523 87557747 ID=Msa0896780-mRNA-1;Parent=Msa0896780;Name=Msa0896780-mRNA-1;_AED=0.09;_eAED=0.09;_QI=127|1|0.75|1|1|1|4|0|209
chr6_1 exon 87557747 87557973 87557747 ID=Msa0896780-mRNA-1:exon:14794;Parent=Msa0896780-mRNA-1
chr6_1 exon 87558072 87558143 87558072 ID=Msa0896780-mRNA-1:exon:14795;Parent=Msa0896780-mRNA-1
chr6_1 exon 87558456 87558730 87558456 ID=Msa0896780-mRNA-1:exon:14796;Parent=Msa0896780-mRNA-1
chr6_1 exon 87559341 87559523 87559341 ID=Msa0896780-mRNA-1:exon:14797;Parent=Msa0896780-mRNA-1
chr6_1 five_prime_UTR 87557747 87557873 87557747 ID=Msa0896780-mRNA-1:five_prime_utr;Parent=Msa0896780-mRNA-1
chr6_1 CDS 87557874 87557973 87557874 ID=Msa0896780-mRNA-1:cds;Parent=Msa0896780-mRNA-1
chr6_1 CDS 87558072 87558143 87558072 ID=Msa0896780-mRNA-1:cds;Parent=Msa0896780-mRNA-1
chr6_1 CDS 87558456 87558730 87558456 ID=Msa0896780-mRNA-1:cds;Parent=Msa0896780-mRNA-1
chr6_1 CDS 87559341 87559523 87559341 ID=Msa0896780-mRNA-1:cds;Parent=Msa0896780-mRNA-1
Gene Sequence

>Msa0896780

ATGAAGTCTTTTGGAGCCTCTCCGAGTAGATGCTTTTTTGTTATTGACCATGATGATAATTTCCTCAAAACTCCAACTTCTGATTCAACCTCCATAACAAATAAAGAAAACTCAAATAGGGATTTCACAAGAAGGGAAAGAAGCAGTTTTGCATATAGTATTCATGAACATGTGAAATTAGGTTCTAAATTTTCTGAGACTTTGAAGGGTAAGTTAAGTTTAGGTGCTAAAATTATTCAAGAAGGTGGAAGAGGTAACATTTTCAAGCATATTTTTGGGATGCAAGAGGGAGAGAAACTCTTGAAAGCTTCTCAGTGCTATTTATATACCACAGCTGGTCCTATTGCTGGAATTCTCTTTATCTCCAATGTAAAAGTTGCATTTTGCAGTGAAAGGCCTACAAGCTTCTATTCTGCAGATGGGGACTTAGTAAAAGCACCTTACAAAGTTTTGATACCAATAGAGAAGATAAAAGAGGTGAATGAAAGCATGAATGTGAACAAGCTAGAACAGAAATATATAGAAGTAGTGACTAAGGATGGCTCTGAATTTTGGTTCATGGGATTTTTAAGGTATGAGAAAGCTATCAAGAATCTCAATAATGCCATTTTCATGGCCAATAAATTCTGA

Protein sequence

>Msa0896780

MKSFGASPSRCFFVIDHDDNFLKTPTSDSTSITNKENSNRDFTRRERSSFAYSIHEHVKLGSKFSETLKGKLSLGAKIIQEGGRGNIFKHIFGMQEGEKLLKASQCYLYTTAGPIAGILFISNVKVAFCSERPTSFYSADGDLVKAPYKVLIPIEKIKEVNESMNVNKLEQKYIEVVTKDGSEFWFMGFLRYEKAIKNLNNAIFMANKF*