AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG013305

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG013305 MtrunA17_Chr3g0094681 90.385 520 33 2 1 520 5 507 0.0 934
MsaG013305 MtrunA17_Chr5g0441991 58.577 548 187 10 2 519 6 543 0.0 565
MsaG013305 MtrunA17_Chr4g0046591 49.231 65 31 1 9 71 24 88 3.00e-12 69.7
MsaG013305 MtrunA17_Chr2g0282771 50.909 55 27 0 17 71 43 97 1.01e-11 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG013305 AT4G03250.1 39.488 547 255 19 2 519 7 506 4.38e-75 246
MsaG013305 AT1G28420.1 29.911 224 107 7 17 240 42 215 8.75e-18 87.8
MsaG013305 AT5G44180.2 49.153 59 30 0 13 71 16 74 4.84e-12 69.3
MsaG013305 AT5G44180.3 49.153 59 30 0 13 71 16 74 5.68e-12 69.3
MsaG013305 AT5G44180.1 49.153 59 30 0 13 71 16 74 5.68e-12 69.3

Find 128 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTATATCCCGTAGGATTTA+AGG 0.172559 3:-48219672 None:intergenic
CAAACTGCAAATCCAGTTAA+TGG 0.208185 3:+48219839 MsaT013305.1:CDS
CACCTTCCATTTGTAAATCT+TGG 0.234276 3:-48221181 None:intergenic
GCATAATTCCCGAATTTCTA+TGG 0.243108 3:+48221577 MsaT013305.1:CDS
CTTCAGAATCCATAGAAATT+CGG 0.270342 3:-48221586 None:intergenic
CTTGCATGATTCTGATTTCC+AGG 0.289398 3:+48221217 MsaT013305.1:CDS
TTTAGCCACGATTGCCTGTT+TGG 0.294997 3:-48220627 None:intergenic
TTCAGAATCCATAGAAATTC+GGG 0.310071 3:-48221585 None:intergenic
TTAGCCACGATTGCCTGTTT+GGG 0.323696 3:-48220626 None:intergenic
ACCATGACTCTCAACCTCTT+TGG 0.325414 3:-48219456 None:intergenic
CAAGACCGTGTCAGTGGACT+AGG 0.327708 3:+48219383 MsaT013305.1:CDS
TTTGGTGTTACGTGTCTATC+AGG 0.328315 3:-48219635 None:intergenic
GGCAAATGATTGGTATGAAT+TGG 0.347033 3:-48221290 None:intergenic
TAAAACCCCTGCACAGCTTA+TGG 0.357510 3:+48218943 MsaT013305.1:CDS
CTGTTTGGGGCAGAGTCCTC+TGG 0.364648 3:-48220612 None:intergenic
ATAGTAAACATACCATTAAC+TGG 0.371891 3:-48219851 None:intergenic
ACCTTCCATTTGTAAATCTT+GGG 0.373107 3:-48221180 None:intergenic
CCCTGCACAGCTTATGGCCT+TGG 0.376056 3:+48218949 MsaT013305.1:CDS
CCATGACTCTCAACCTCTTT+GGG 0.381347 3:-48219455 None:intergenic
CACTCAACCCATGGAGGAAC+TGG 0.387048 3:-48222397 None:intergenic
AGGACAGGATCCATATGATA+TGG 0.397603 3:+48219610 MsaT013305.1:CDS
ATGCATTGTATTTGAAGGTT+CGG 0.397770 3:-48221558 None:intergenic
TTATATCCCGTAGGATTTAA+GGG 0.406147 3:-48219671 None:intergenic
CTCGTGATAGCGATGATCAC+TGG 0.417810 3:-48221444 None:intergenic
CTTGGTTCAATCTCAGCAAA+AGG 0.421560 3:-48222212 None:intergenic
CTATCAGGCTCCATATCATA+TGG 0.429226 3:-48219620 None:intergenic
GCATGGTGAGTACAGGTGTT+TGG 0.431803 3:+48219430 MsaT013305.1:CDS
GATTTGAACGAAGACTCAAC+TGG 0.434272 3:+48221332 MsaT013305.1:CDS
CAGAGGACTCTGCCCCAAAC+AGG 0.437155 3:+48220613 MsaT013305.1:CDS
TCCAAGGCCATAAGCTGTGC+AGG 0.439233 3:-48218950 None:intergenic
TTGTTCTTTGTTGAATAAGC+TGG 0.441613 3:-48221253 None:intergenic
TTGCAGGAAGAAAAGTTCAA+TGG 0.441671 3:+48221738 MsaT013305.1:intron
TGCAGGAAGAAAAGTTCAAT+GGG 0.443717 3:+48221739 MsaT013305.1:intron
AAAGGTGAAGTATGTGCTAA+TGG 0.444429 3:+48219332 MsaT013305.1:CDS
GGGGAAGCACCATCTTATAA+TGG 0.447883 3:+48221353 MsaT013305.1:CDS
GTTCTTGCCAGGCAAATGAT+TGG 0.454021 3:-48221300 None:intergenic
TATCATATGGATCCTGTCCT+TGG 0.459663 3:-48219607 None:intergenic
TCAACTTTCATTTCCTCTGT+GGG 0.466436 3:-48219227 None:intergenic
GAATTATGCATTGTATTTGA+AGG 0.467902 3:-48221563 None:intergenic
AAAGAGAGGGGTTTGCATCA+TGG 0.471242 3:-48220581 None:intergenic
ACAAATGGAAGGTGGTGACT+TGG 0.472755 3:+48221190 MsaT013305.1:CDS
GATAGACACGTAACACCAAA+TGG 0.476346 3:+48219638 MsaT013305.1:CDS
TCAAAATCTACATTAAGTAG+TGG 0.476441 3:-48219788 None:intergenic
AAGGGTGGAAGAGCTCCATT+TGG 0.483958 3:-48219653 None:intergenic
ACTGCTGTTAAGAATCGGTT+AGG 0.488521 3:+48219743 MsaT013305.1:CDS
CTATAACTGCTGTTAAGAAT+CGG 0.491784 3:+48219738 MsaT013305.1:CDS
CTACTACATGGCTACAATAA+CGG 0.493623 3:+48221497 MsaT013305.1:CDS
GGCACTAGAAATCATAGAAT+AGG 0.497964 3:+48221374 MsaT013305.1:CDS
ATTCATACCAATCATTTGCC+TGG 0.506282 3:+48221293 MsaT013305.1:CDS
TTTCTAGTGCCATTATAAGA+TGG 0.507796 3:-48221362 None:intergenic
GGATCTGACTTCATAATCGC+CGG 0.509626 3:-48221473 None:intergenic
CCTACGGGATATAAACCATC+AGG 0.511765 3:+48219680 MsaT013305.1:CDS
CAAATGGAAGGTGGTGACTT+GGG 0.512635 3:+48221191 MsaT013305.1:CDS
TACAGAAAATGATAGTGAAA+CGG 0.512674 3:+48219535 MsaT013305.1:CDS
TCCACAGGAAAGTTCTTGCC+AGG 0.512885 3:-48221311 None:intergenic
TTCAACTTTCATTTCCTCTG+TGG 0.515681 3:-48219228 None:intergenic
CTATGGATTCTGAAGAAAGA+GGG 0.519430 3:+48221594 MsaT013305.1:CDS
GCTGGCGGGATTTCTTATCC+TGG 0.525159 3:-48221235 None:intergenic
TGATGAAACCAGTTCCTCCA+TGG 0.527407 3:+48222389 MsaT013305.1:CDS
GAGTCTTCGTTCAAATCCAC+AGG 0.528611 3:-48221326 None:intergenic
GCACTAAGCATGGTGAGTAC+AGG 0.530782 3:+48219423 MsaT013305.1:CDS
TGCAAAGATGAGCTACTCTC+AGG 0.534507 3:-48219569 None:intergenic
TTGACAGAAAAGCAAATCTC+GGG 0.535331 3:+48219269 MsaT013305.1:CDS
GTTGACAGAAAAGCAAATCT+CGG 0.536727 3:+48219268 MsaT013305.1:CDS
GTTTGAAATTCAAATGCCCC+TGG 0.538643 3:-48219821 None:intergenic
AAAGAATATCATGAGTCAGA+TGG 0.539635 3:+48221777 MsaT013305.1:CDS
TCTTCTAATTGCAACTCCAT+CGG 0.542711 3:-48218881 None:intergenic
TCCCAAGATTTACAAATGGA+AGG 0.543378 3:+48221179 MsaT013305.1:CDS
TCTTCCACCCTTAAATCCTA+CGG 0.548387 3:+48219664 MsaT013305.1:CDS
TAGCCACGATTGCCTGTTTG+GGG 0.550694 3:-48220625 None:intergenic
CAAAATCTACATTAAGTAGT+GGG 0.551836 3:-48219787 None:intergenic
AAGTTCCCAAGATTTACAAA+TGG 0.561294 3:+48221175 MsaT013305.1:CDS
CCAAGGCCATAAGCTGTGCA+GGG 0.562140 3:-48218949 None:intergenic
CTTCCACCCTTAAATCCTAC+GGG 0.562266 3:+48219665 MsaT013305.1:CDS
TCTATGGATTCTGAAGAAAG+AGG 0.562753 3:+48221593 MsaT013305.1:CDS
ACGGTATTATCTCCAAGGAC+AGG 0.562785 3:+48219595 MsaT013305.1:CDS
TTCTTTGTTGAATAAGCTGG+CGG 0.564732 3:-48221250 None:intergenic
AAGAAAGAGGGCTTTCTGAA+AGG 0.565873 3:+48221606 MsaT013305.1:CDS
TCTGGAGAATTTGAAAGAGA+GGG 0.566795 3:-48220594 None:intergenic
CTCTGGAGAATTTGAAAGAG+AGG 0.566877 3:-48220595 None:intergenic
GTAATGTGAAGAATGTACTA+AGG 0.567502 3:+48221519 MsaT013305.1:CDS
AAGAGGGCTTTCTGAAAGGA+TGG 0.567622 3:+48221610 MsaT013305.1:CDS
CAACTTTCATTTCCTCTGTG+GGG 0.569792 3:-48219226 None:intergenic
CTCACCACAGTTTCTCTCAA+AGG 0.571956 3:-48221810 None:intergenic
GCACTAAGCATGGTGTTGAA+AGG 0.573397 3:+48221396 MsaT013305.1:CDS
CTGGAGAATTTGAAAGAGAG+GGG 0.574144 3:-48220593 None:intergenic
GCCTGGCAAGAACTTTCCTG+TGG 0.575905 3:+48221310 MsaT013305.1:CDS
TCGTGATAGCGATGATCACT+GGG 0.576108 3:-48221443 None:intergenic
CCCAAAGAGGTTGAGAGTCA+TGG 0.576918 3:+48219455 MsaT013305.1:CDS
AGTCATCAGCACTCAACCCA+TGG 0.576920 3:-48222406 None:intergenic
CAAGAACGGTATTATCTCCA+AGG 0.580779 3:+48219590 MsaT013305.1:CDS
CTCTCTTTCAAATTCTCCAG+AGG 0.584967 3:+48220596 MsaT013305.1:CDS
AGAAGACAATACAACCTCTA+CGG 0.585953 3:+48218898 MsaT013305.1:CDS
CTGTTAAGAATCGGTTAGGA+AGG 0.588262 3:+48219747 MsaT013305.1:CDS
GATGAAACCAGTTCCTCCAT+GGG 0.588465 3:+48222390 MsaT013305.1:CDS
CAGGTGTTTGGATCCCAAAG+AGG 0.589068 3:+48219442 MsaT013305.1:CDS
GTAGCTCATCTTTGCAAGAA+CGG 0.592344 3:+48219576 MsaT013305.1:CDS
AAAGATAAGAGACTGATGAA+AGG 0.596779 3:+48219314 MsaT013305.1:CDS
ATTTGAACGAAGACTCAACT+GGG 0.598194 3:+48221333 MsaT013305.1:CDS
CTGCCCCAAACAGGCAATCG+TGG 0.602076 3:+48220622 MsaT013305.1:CDS
CATAGAATAGGCACTAAGCA+TGG 0.605322 3:+48221386 MsaT013305.1:CDS
AAGTCAGATCCACTACTACA+TGG 0.608206 3:+48221485 MsaT013305.1:CDS
GATCTGACTTCATAATCGCC+GGG 0.612811 3:-48221472 None:intergenic
CAGAAAAGCAAATCTCGGGA+TGG 0.614233 3:+48219273 MsaT013305.1:CDS
CAAGATTTACAAATGGAAGG+TGG 0.616333 3:+48221182 MsaT013305.1:CDS
TTATTGTAGCCATGTAGTAG+TGG 0.623018 3:-48221494 None:intergenic
GCTTTCTGAAAGGATGGCAA+AGG 0.632256 3:+48221616 MsaT013305.1:CDS
TCATGTGGAAGCACTAAGCA+TGG 0.632594 3:+48219413 MsaT013305.1:CDS
CAAGGCCATAAGCTGTGCAG+GGG 0.634076 3:-48218948 None:intergenic
TCATCCTCACTAAAGCTAGA+CGG 0.642459 3:-48222360 None:intergenic
AAGACCGTGTCAGTGGACTA+GGG 0.645299 3:+48219384 MsaT013305.1:CDS
TCTTTGTTGAATAAGCTGGC+GGG 0.646615 3:-48221249 None:intergenic
GTTGTTCAAGACCGTGTCAG+TGG 0.651661 3:+48219377 MsaT013305.1:CDS
CCTGATGGTTTATATCCCGT+AGG 0.652093 3:-48219680 None:intergenic
GTGAAGAATGTACTAAGGTG+TGG 0.652203 3:+48221524 MsaT013305.1:CDS
TGAAATTCAAATGCCCCTGG+AGG 0.656858 3:-48219818 None:intergenic
CTGGAAATCAGAATCATGCA+AGG 0.657071 3:-48221216 None:intergenic
CTTGCCCTAGTCCACTGACA+CGG 0.661193 3:-48219388 None:intergenic
GGACTAGGGCAAGATTCATG+TGG 0.663027 3:+48219398 MsaT013305.1:CDS
TCGCTATCACGAGAATAACC+CGG 0.675003 3:+48221454 MsaT013305.1:CDS
ATGATAATGTAGATCTGCTG+TGG 0.688279 3:+48222332 MsaT013305.1:intron
CATCAGCACTCAACCCATGG+AGG 0.702201 3:-48222403 None:intergenic
TATCCCGTAGGATTTAAGGG+TGG 0.709100 3:-48219668 None:intergenic
ATTGCCTTTGAGAGAAACTG+TGG 0.709138 3:+48221806 MsaT013305.1:CDS
GTTGCCGTCTAGCTTTAGTG+AGG 0.710155 3:+48222356 MsaT013305.1:CDS
TTGAACCAAGGAAAACTCAG+AGG 0.722923 3:+48222225 MsaT013305.1:CDS
TTTGAACGAAGACTCAACTG+GGG 0.776627 3:+48221334 MsaT013305.1:CDS
AGAGCACAAATACCCCACAG+AGG 0.803915 3:+48219214 MsaT013305.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 48218884 48222416 48218884 ID=MsaG013305
Chr3 mRNA 48218884 48222416 48218884 ID=MsaT013305.1;Parent=MsaG013305
Chr3 exon 48218884 48218986 48218884 ID=MsaT013305.1.exon1;Parent=MsaT013305.1
Chr3 CDS 48218884 48218986 48218884 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48219216 48219860 48219216 ID=MsaT013305.1.exon2;Parent=MsaT013305.1
Chr3 CDS 48219216 48219860 48219216 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48220574 48220653 48220574 ID=MsaT013305.1.exon3;Parent=MsaT013305.1
Chr3 CDS 48220574 48220653 48220574 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48221149 48221637 48221149 ID=MsaT013305.1.exon4;Parent=MsaT013305.1
Chr3 CDS 48221149 48221637 48221149 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48221744 48221827 48221744 ID=MsaT013305.1.exon5;Parent=MsaT013305.1
Chr3 CDS 48221744 48221827 48221744 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48222158 48222246 48222158 ID=MsaT013305.1.exon6;Parent=MsaT013305.1
Chr3 CDS 48222158 48222246 48222158 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Chr3 exon 48222344 48222416 48222344 ID=MsaT013305.1.exon7;Parent=MsaT013305.1
Chr3 CDS 48222344 48222416 48222344 ID=cds.MsaT013305.1;Parent=MsaT013305.1
Gene Sequence

>MsaT013305.1

ATGGAGTTGCAATTAGAAGACAATACAACCTCTACGGAGAAAAATAGTAAAAGAAAGCTTAAAACCCCTGCACAGCTTATGGCCTTGGAAAATTTTTATAACGAGCACAAATACCCCACAGAGGAAATGAAAGTTGAACTTGCTAATGAACTAGCGTTGACAGAAAAGCAAATCTCGGGATGGTTTTGTCACAGAAGGTTAAAAGATAAGAGACTGATGAAAGGTGAAGTATGTGCTAATGGACGACAAGATCGATCAAGTGTTGTTGTTCAAGACCGTGTCAGTGGACTAGGGCAAGATTCATGTGGAAGCACTAAGCATGGTGAGTACAGGTGTTTGGATCCCAAAGAGGTTGAGAGTCATGGTCTCTATAATCATGAAGTGTTAGTTGCAGATATGAAATATGTACATAGAAACCATTATACAGAAAATGATAGTGAAACGGATAACTCATCACCTGAGAGTAGCTCATCTTTGCAAGAACGGTATTATCTCCAAGGACAGGATCCATATGATATGGAGCCTGATAGACACGTAACACCAAATGGAGCTCTTCCACCCTTAAATCCTACGGGATATAAACCATCAGGATATTTAAAAGTGAAGAAAGAGATAGAGCATGCTGCTATAACTGCTGTTAAGAATCGGTTAGGAAGGTATTTTCTGGAAGATGGCCCACTACTTAATGTAGATTTTGATACAATTCCTCCAGGGGCATTTGAATTTCAAACTGCAAATCCAGTTAATGAAACATACCATGATGCAAACCCCTCTCTTTCAAATTCTCCAGAGGACTCTGCCCCAAACAGGCAATCGTGGCTAAACTCTAGATATGATTTACATATGAACAGATTAAGTTCCCAAGATTTACAAATGGAAGGTGGTGACTTGGGCTCCTTGCATGATTCTGATTTCCAGGATAAGAAATCCCGCCAGCTTATTCAACAAAGAACAAATTTTCAGGGTCGTCCAATTCATACCAATCATTTGCCTGGCAAGAACTTTCCTGTGGATTTGAACGAAGACTCAACTGGGGAAGCACCATCTTATAATGGCACTAGAAATCATAGAATAGGCACTAAGCATGGTGTTGAAAGGATGAGATCTGATTCTGCTTCTAATCCCAGTGATCATCGCTATCACGAGAATAACCCGGCGATTATGAAGTCAGATCCACTACTACATGGCTACAATAACGGTAATGTGAAGAATGTACTAAGGTGTGGATATATAAAATCCGAACCTTCAAATACAATGCATAATTCCCGAATTTCTATGGATTCTGAAGAAAGAGGGCTTTCTGAAAGGATGGCAAAGGAAGAAAAGTTCAATGGGACTAGAAAGATTAAAAAAGAATATCATGAGTCAGATGGAGTAAGATTGCCTTTGAGAGAAACTGTGGTTGCAAAGCGAGCTAAGTTTGATTTACTTCATCAATATCATATCAAACAAGAACCTTTTGCTGAGATTGAACCAAGGAAAACTCAGAGATCTGCTGTGGTGTTGCCGTCTAGCTTTAGTGAGGATGATGAAACTGATGAAACCAGTTCCTCCATGGGTTGA
Protein sequence

>MsaT013305.1

MELQLEDNTTSTEKNSKRKLKTPAQLMALENFYNEHKYPTEEMKVELANELALTEKQISGWFCHRRLKDKRLMKGEVCANGRQDRSSVVVQDRVSGLGQDSCGSTKHGEYRCLDPKEVESHGLYNHEVLVADMKYVHRNHYTENDSETDNSSPESSSSLQERYYLQGQDPYDMEPDRHVTPNGALPPLNPTGYKPSGYLKVKKEIEHAAITAVKNRLGRYFLEDGPLLNVDFDTIPPGAFEFQTANPVNETYHDANPSLSNSPEDSAPNRQSWLNSRYDLHMNRLSSQDLQMEGGDLGSLHDSDFQDKKSRQLIQQRTNFQGRPIHTNHLPGKNFPVDLNEDSTGEAPSYNGTRNHRIGTKHGVERMRSDSASNPSDHRYHENNPAIMKSDPLLHGYNNGNVKNVLRCGYIKSEPSNTMHNSRISMDSEERGLSERMAKEEKFNGTRKIKKEYHESDGVRLPLRETVVAKRAKFDLLHQYHIKQEPFAEIEPRKTQRSAVVLPSSFSEDDETDETSSSMG*