AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG015166


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG015166 MtrunA17_Chr3g0115061 90.000 470 24 1 1 447 1 470 0.0 865
MsaG015166 MtrunA17_Chr8g0375381 25.413 303 160 13 6 264 24 304 7.28e-14 73.2
MsaG015166 MtrunA17_Chr3g0128421 28.205 156 95 4 159 312 459 599 8.74e-12 67.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG015166 AT2G17900.1 64.399 441 153 1 12 448 40 480 0.0 612

Find 81 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCTTTAATATTGATTTC+AGG 0.234425 3:+83367933 None:intergenic
CTCTTACTAACCCACATTCT+TGG 0.284514 3:+83366402 None:intergenic
TGATCTTGATATAGGTATCT+TGG 0.355193 3:-83363990 MsaT015166.1:intron
ATCAATAGTTCCTTCACTAA+TGG 0.370780 3:+83363894 None:intergenic
GGTTTCTTGCTCCGCACAAC+TGG 0.393388 3:-83366598 MsaT015166.1:intron
CCAGCTGTTCACCCTTTGCT+TGG 0.395564 3:-83364487 MsaT015166.1:CDS
CGAGAAAATGCAATTCTAGA+AGG 0.401251 3:-83366649 MsaT015166.1:CDS
GCTCACGTTGTCAAGTTGTT+TGG 0.406177 3:-83368799 MsaT015166.1:CDS
GATGGCATACTTTGATAGAT+TGG 0.406419 3:+83365324 None:intergenic
TGGTTACCTGTGATTGATAA+TGG 0.407535 3:+83367710 None:intergenic
TGACAGTGAGTTAAGACCTC+TGG 0.417510 3:-83367757 MsaT015166.1:CDS
ATACTTGTGGAAAACTTGAA+TGG 0.426325 3:-83364453 MsaT015166.1:intron
CAAGTTAGTGGACGCATTAG+TGG 0.432256 3:-83368122 MsaT015166.1:CDS
TGCATCAAATTGATCGAGAA+AGG 0.433641 3:+83366063 None:intergenic
GAGTTAAGACCTCTGGGAAC+AGG 0.450124 3:-83367750 MsaT015166.1:CDS
CCAAGCAAAGGGTGAACAGC+TGG 0.455085 3:+83364487 None:intergenic
TTTGCAGTCATTAATGAAGC+TGG 0.455096 3:-83365388 MsaT015166.1:intron
GGGGACAAACACAAGTGAAT+AGG 0.464095 3:+83366816 None:intergenic
TGCTCAAACTTTATCTTCGA+AGG 0.464527 3:-83368451 MsaT015166.1:CDS
CTGTGCAACATGTGCCTAAA+GGG 0.466513 3:-83367552 MsaT015166.1:CDS
ATAGATACCTCAGTCCCTTT+AGG 0.485587 3:+83367538 None:intergenic
TTGAGTTGGAACACAAACAT+AGG 0.489336 3:+83368865 None:intergenic
TTGTTTCCATTATCAATCAC+AGG 0.492390 3:-83367716 MsaT015166.1:intron
GGCTTGCAATATTATACTTG+TGG 0.493062 3:-83364466 MsaT015166.1:CDS
CCTTAGTATATCCACTGCCT+TGG 0.497065 3:+83363938 None:intergenic
GAACACAAACATAGGGCTCT+TGG 0.499515 3:+83368873 None:intergenic
TTTGTAAGAGGCTTCTGCAC+GGG 0.511710 3:+83363857 None:intergenic
GATCATTCCAAGCACTGCTA+TGG 0.511797 3:-83368152 MsaT015166.1:CDS
TCTTAACTCACTGTCACAAA+TGG 0.513188 3:+83367764 None:intergenic
GTATTGCGGAACACCATGTC+AGG 0.515490 3:-83368777 MsaT015166.1:intron
GCGTTTCAATGCCAAGAATG+TGG 0.517194 3:-83366413 MsaT015166.1:CDS
TGTCAAGTTGTTTGGTATTG+CGG 0.517303 3:-83368791 MsaT015166.1:CDS
TAAATCATTGACCAAGGCAG+TGG 0.519906 3:-83363949 MsaT015166.1:CDS
AAGCACTGTGACTCGACAAA+AGG 0.521126 3:-83366855 MsaT015166.1:CDS
TTGTCCCCTCTGTTCTAAAG+TGG 0.523368 3:-83366801 MsaT015166.1:intron
GAAGGAACTATTGATGATGT+TGG 0.529169 3:-83363886 MsaT015166.1:CDS
CCAAGGCAGTGGATATACTA+AGG 0.529257 3:-83363938 MsaT015166.1:CDS
GCATCAAATTGATCGAGAAA+GGG 0.531480 3:+83366064 None:intergenic
ATAAGTTATATAGAGACAGC+TGG 0.532422 3:-83366878 MsaT015166.1:CDS
AGGATACTGCCACTAGAAGA+AGG 0.532430 3:+83366317 None:intergenic
AAGTACCACTTTAGAACAGA+GGG 0.532968 3:+83366796 None:intergenic
TGAGTTGGAACACAAACATA+GGG 0.536392 3:+83368866 None:intergenic
CATTAATGAAGCTGGAGTGT+TGG 0.537677 3:-83365380 MsaT015166.1:CDS
TGACATCAAAGAGGAGCAGC+TGG 0.537970 3:-83368003 MsaT015166.1:CDS
CTGCCTACCCAATTCAGTGT+TGG 0.538934 3:-83367605 MsaT015166.1:CDS
TAATATTGCAAGCCAAGCAA+AGG 0.544619 3:+83364475 None:intergenic
GCTTCTAAGCCTTCTTCTAG+TGG 0.547425 3:-83366326 MsaT015166.1:CDS
CGTTTCAATGCCAAGAATGT+GGG 0.549729 3:-83366412 MsaT015166.1:CDS
AAGTTTGAGCATCAACCGTA+TGG 0.550663 3:+83368463 None:intergenic
TAGTTGTCCATAGCAGTGCT+TGG 0.554117 3:+83368145 None:intergenic
TATGGACAACTACAAGTTAG+TGG 0.554822 3:-83368134 MsaT015166.1:CDS
CTTCGAAGGAAATTGCAAGA+TGG 0.560287 3:-83368437 MsaT015166.1:CDS
GACAGTGAGTTAAGACCTCT+GGG 0.564404 3:-83367756 MsaT015166.1:CDS
TGATTGATAATGGAAACAAC+AGG 0.566394 3:+83367720 None:intergenic
CATACTTTGATAGATTGGTA+TGG 0.571289 3:+83365329 None:intergenic
TTGAGCATCAACCGTATGGA+TGG 0.572598 3:+83368467 None:intergenic
TTGTACACTTAATACTGCAA+TGG 0.575595 3:-83367956 MsaT015166.1:CDS
TTGAATGTCAAGCACTCTCA+AGG 0.577097 3:-83368520 MsaT015166.1:CDS
AATATTGCAAGCCAAGCAAA+GGG 0.578542 3:+83364476 None:intergenic
AAGGAAATTGCAAGATGGCA+AGG 0.594988 3:-83368432 MsaT015166.1:intron
GCTGTGCAACATGTGCCTAA+AGG 0.597001 3:-83367553 MsaT015166.1:CDS
GCTGGTGTTGTATGCACAGA+TGG 0.598430 3:-83367985 MsaT015166.1:CDS
TTTAGGTCATACCAGTTGTG+CGG 0.607337 3:+83366587 None:intergenic
GACAACGTGAGCATTTGCTA+AGG 0.614070 3:+83368810 None:intergenic
TACAAAGACTCCATTAGTGA+AGG 0.622523 3:-83363904 MsaT015166.1:CDS
ATGTGGGTTAGTAAGAGACA+AGG 0.627932 3:-83366396 MsaT015166.1:CDS
CAATTTGATGCAAACACGAG+AGG 0.630016 3:-83366052 MsaT015166.1:CDS
ATTTGTAAGAGGCTTCTGCA+CGG 0.631187 3:+83363856 None:intergenic
AATCTGTTACACCATCCATA+CGG 0.635943 3:-83368478 MsaT015166.1:CDS
AAACCAACACTGAATTGGGT+AGG 0.637837 3:+83367602 None:intergenic
AAAGGATACAAAACCTGACA+TGG 0.639706 3:+83368764 None:intergenic
AGCTATTAAATCATTGACCA+AGG 0.641241 3:-83363955 MsaT015166.1:CDS
GATATACTAAGGATTACTCA+TGG 0.643148 3:-83363927 MsaT015166.1:CDS
GGAACTATTGATGATGTTGG+AGG 0.643675 3:-83363883 MsaT015166.1:CDS
AGACATGTCTGACATCAAAG+AGG 0.653286 3:-83368012 MsaT015166.1:CDS
ACATGTGCCTAAAGGGACTG+AGG 0.674349 3:-83367545 MsaT015166.1:intron
ATGATATTCAGAAATCGGAG+TGG 0.685347 3:-83368556 MsaT015166.1:intron
TAAGTACCACTTTAGAACAG+AGG 0.686937 3:+83366795 None:intergenic
TAGGTATCTTGGAGACACAG+AGG 0.736759 3:-83363979 MsaT015166.1:CDS
GGATACAATCCTGTTCCCAG+AGG 0.760315 3:+83367741 None:intergenic
AGTACCACTTTAGAACAGAG+GGG 0.783095 3:+83366797 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 83363836 83369104 83363836 ID=MsaG015166
Chr3 mRNA 83363836 83369104 83363836 ID=MsaT015166.1;Parent=MsaG015166
Chr3 exon 83363836 83363998 83363836 ID=MsaT015166.1.exon14;Parent=MsaT015166.1
Chr3 CDS 83363836 83363998 83363836 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83364454 83364517 83364454 ID=MsaT015166.1.exon13;Parent=MsaT015166.1
Chr3 CDS 83364454 83364517 83364454 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83365334 83365403 83365334 ID=MsaT015166.1.exon12;Parent=MsaT015166.1
Chr3 CDS 83365334 83365403 83365334 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83366041 83366147 83366041 ID=MsaT015166.1.exon11;Parent=MsaT015166.1
Chr3 CDS 83366041 83366147 83366041 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83366324 83366443 83366324 ID=MsaT015166.1.exon10;Parent=MsaT015166.1
Chr3 CDS 83366324 83366443 83366324 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83366599 83366689 83366599 ID=MsaT015166.1.exon9;Parent=MsaT015166.1
Chr3 CDS 83366599 83366689 83366599 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83366802 83366906 83366802 ID=MsaT015166.1.exon8;Parent=MsaT015166.1
Chr3 CDS 83366802 83366906 83366802 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83367546 83367627 83367546 ID=MsaT015166.1.exon7;Parent=MsaT015166.1
Chr3 CDS 83367546 83367627 83367546 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83367717 83367805 83367717 ID=MsaT015166.1.exon6;Parent=MsaT015166.1
Chr3 CDS 83367717 83367805 83367717 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83367914 83368032 83367914 ID=MsaT015166.1.exon5;Parent=MsaT015166.1
Chr3 CDS 83367914 83368032 83367914 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83368119 83368173 83368119 ID=MsaT015166.1.exon4;Parent=MsaT015166.1
Chr3 CDS 83368119 83368173 83368119 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83368433 83368567 83368433 ID=MsaT015166.1.exon3;Parent=MsaT015166.1
Chr3 CDS 83368433 83368567 83368433 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83368778 83368911 83368778 ID=MsaT015166.1.exon2;Parent=MsaT015166.1
Chr3 CDS 83368778 83368911 83368778 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Chr3 exon 83369074 83369104 83369074 ID=MsaT015166.1.exon1;Parent=MsaT015166.1
Chr3 CDS 83369074 83369104 83369074 ID=cds.MsaT015166.1;Parent=MsaT015166.1
Gene Sequence

>MsaT015166.1

ATGGAGGAATTGCAACAAGCACTGAAGAATTGGGAAGTGATTATTAGCCAAGAGCCCTATGTTTGTGTTCCAACTCAAAAAAGGTGTGATGGATGTTTCTCAACAACTAACCTTAGCAAATGCTCACGTTGTCAAGTTGTTTGGTATTGCGGAACACCATGTCAGAAATCGGAGTGGAAGTTGCATCGTCTTGAATGTCAAGCACTCTCAAGGCTAGACAACCATAAGAGAAAATCTGTTACACCATCCATACGGTTGATGCTCAAACTTTATCTTCGAAGGAAATTGCAAGATGGCAAGATCATTCCAAGCACTGCTATGGACAACTACAAGTTAGTGGACGCATTAGTGGCTCACATGTCTGACATCAAAGAGGAGCAGCTGGTGTTGTATGCACAGATGGCTAATCTTGTACACTTAATACTGCAATGGCCTGAAATCAATATTAAAGAGATTGCAGAAATTTTTTCCAAGTTTGCATGTAATGCGCATACCATTTGTGACAGTGAGTTAAGACCTCTGGGAACAGGATTGTATCCTGTTGTTTCCATTATCAATCACAGCTGCCTACCCAATTCAGTGTTGGTTTTTGAAGGAAGGGTAGCATCGGTACGTGCTGTGCAACATGTGCCTAAAGGGACTGAGGTATTGATAAGTTATATAGAGACAGCTGGAAGCACTGTGACTCGACAAAAGGCTCTCAGAGAGCAGTACCTATTCACTTGTGTTTGTCCCCTCTGTTCTAAAGTGGGTCAGTATGAAGATGTTCGAGAAAATGCAATTCTAGAAGGATACAGATGCAAAAATGAAACATGTGATGGTTTCTTGCTCCGCACAACTGATGGAAAAGCGTTTCAATGCCAAGAATGTGGGTTAGTAAGAGACAAGGAAGAGATAAAGCAAATTGCAACTGAAATAAAATTTCTATCAGAAGAAGCTTCTAAGCCTTCTTCTAGTGGCAATTATCATGAAGCTATTTCCATATATAAAATGATCGAGAAACTGCAAACAAAACTATATCACCCTTTCTCGATCAATTTGATGCAAACACGAGAGGCGATTTTGAAGTCATTAATGAAGCTGGAGTGTTGGAGAGAAGCTTTAGCATATTGCAAATTGACCATACCAATCTATCAAAGAGTGTATCCAGCTGTTCACCCTTTGCTTGGCTTGCAATATTATACTTGTGGAAAACTTGAATGGTATCTTGGAGACACAGAGGAAGCTATTAAATCATTGACCAAGGCAGTGGATATACTAAGGATTACTCATGGTACAAAGACTCCATTAGTGAAGGAACTATTGATGATGTTGGAGGAAGCCCGTGCAGAAGCCTCTTACAAATTGTCATCAAAAGAAGAGTAG

Protein sequence

>MsaT015166.1

MEELQQALKNWEVIISQEPYVCVPTQKRCDGCFSTTNLSKCSRCQVVWYCGTPCQKSEWKLHRLECQALSRLDNHKRKSVTPSIRLMLKLYLRRKLQDGKIIPSTAMDNYKLVDALVAHMSDIKEEQLVLYAQMANLVHLILQWPEINIKEIAEIFSKFACNAHTICDSELRPLGTGLYPVVSIINHSCLPNSVLVFEGRVASVRAVQHVPKGTEVLISYIETAGSTVTRQKALREQYLFTCVCPLCSKVGQYEDVRENAILEGYRCKNETCDGFLLRTTDGKAFQCQECGLVRDKEEIKQIATEIKFLSEEASKPSSSGNYHEAISIYKMIEKLQTKLYHPFSINLMQTREAILKSLMKLECWREALAYCKLTIPIYQRVYPAVHPLLGLQYYTCGKLEWYLGDTEEAIKSLTKAVDILRITHGTKTPLVKELLMMLEEARAEASYKLSSKEE*