AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG017839


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG017839 MtrunA17_Chr3g0144601 81.400 457 64 8 1 456 1 437 0.0 679
MsaG017839 MtrunA17_Chr3g0145531 81.400 457 64 8 1 456 1 437 0.0 671
MsaG017839 MtrunA17_Chr3g0082361 79.032 124 21 2 194 317 56 174 7.88e-59 191
MsaG017839 MtrunA17_Chr3g0107471 32.061 262 121 5 220 452 387 620 1.47e-29 121
MsaG017839 MtrunA17_Chr3g0107471 34.135 208 108 9 6 209 8 190 1.91e-17 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG017839 AT5G58340.2 25.984 381 247 13 89 450 81 445 5.71e-14 73.9
MsaG017839 AT5G58340.1 25.984 381 247 13 89 450 81 445 5.71e-14 73.9
MsaG017839 AT1G15720.1 28.571 371 191 17 89 450 81 386 3.06e-12 68.6

Find 111 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTCATCATTGTTAACATTT+AGG 0.186976 3:-113749118 None:intergenic
AAAGAAATAACCAACCATTA+TGG 0.218651 3:-113748344 None:intergenic
CTGCTTGGAGGTAGTGTTTA+GGG 0.228026 3:-113748062 None:intergenic
CTCTTGAATGGCTTTCCTTC+TGG 0.254243 3:-113748229 None:intergenic
TCCAAGCAGTTGACAGAATA+TGG 0.254939 3:+113748076 MsaT017839.1:CDS
TAAGTGAATCCCCGTTCTTT+TGG 0.273307 3:-113748932 None:intergenic
TAACTCCAAAATTGAGATTC+TGG 0.273343 3:+113748139 MsaT017839.1:CDS
GTCTGGCATACAAATAGAAT+TGG 0.288931 3:-113749000 None:intergenic
TGAGTACGAGCAGAACTATT+TGG 0.294065 3:-113749200 None:intergenic
AAAGACAATGGAAGGCTTAA+AGG 0.299896 3:+113748822 MsaT017839.1:CDS
ACTGCTTGGAGGTAGTGTTT+AGG 0.310482 3:-113748063 None:intergenic
TATAGAGAGTGAGCATATTA+AGG 0.313329 3:+113747759 MsaT017839.1:CDS
TCAGAATTGGAGAAGGAAAC+TGG 0.354877 3:+113749908 MsaT017839.1:intron
AAGAAATAACCAACCATTAT+GGG 0.366017 3:-113748343 None:intergenic
GCATCGCTAATAGGTGGATT+GGG 0.369444 3:-113747958 None:intergenic
CATCTTCCGATTATCGATTT+CGG 0.378562 3:-113747809 None:intergenic
GATGATGAACATCACTTTGA+TGG 0.379549 3:-113749163 None:intergenic
CCATTCATCGATAGATGCTT+TGG 0.387362 3:-113747872 None:intergenic
GATTTCATGGCATCGCTAAT+AGG 0.391784 3:-113747967 None:intergenic
TGATTTGATCGATGGATTGC+AGG 0.392480 3:+113749381 MsaT017839.1:CDS
GTAGACATAAGCAGATTTCA+TGG 0.396640 3:-113747980 None:intergenic
GGAAAGGTTAGGGTGGTGTT+TGG 0.397081 3:+113747708 MsaT017839.1:CDS
TGTTGTTGTTGTTGAGGTAA+TGG 0.400125 3:+113748860 MsaT017839.1:CDS
TTTGTATGCCAGACATTGTA+AGG 0.401380 3:+113749009 MsaT017839.1:CDS
GAAGAAGCTTTCTCCGTTGA+AGG 0.405658 3:+113749453 MsaT017839.1:CDS
CACCTGCACCTGCTGCTTCA+AGG 0.406135 3:-113748029 None:intergenic
GGAAGTTGCCTTCGTAAGAT+TGG 0.411891 3:-113749141 None:intergenic
GGTGGATTGGGGTTTGAAGA+AGG 0.411930 3:-113747946 None:intergenic
TGGTGTTTGGAATTCGTTCT+TGG 0.411975 3:+113747721 MsaT017839.1:CDS
GCTCAAAATCAATCCCATAA+TGG 0.413594 3:+113748330 MsaT017839.1:CDS
TTAACGAGGCCCAAAAGAAC+GGG 0.420375 3:+113748922 MsaT017839.1:CDS
TCCATATTCTGTCAACTGCT+TGG 0.421745 3:-113748077 None:intergenic
TTTAGGCAAGCATGTGGGTT+GGG 0.424815 3:-113749101 None:intergenic
GGCATCGCTAATAGGTGGAT+TGG 0.433127 3:-113747959 None:intergenic
AAAACTACTTCTAATTGATT+GGG 0.433610 3:+113747921 MsaT017839.1:CDS
GCATGTATCGTGAGTTGAAA+AGG 0.433870 3:-113748182 None:intergenic
GCAAATAACTTCTTCCCTCC+AGG 0.443932 3:-113748116 None:intergenic
TGGACAACAACTCATCTTCA+AGG 0.456297 3:-113747852 None:intergenic
AATGGGAAGAGGATAATCTA+AGG 0.459156 3:+113749527 MsaT017839.1:CDS
GGAGAAAGCTTCTTCCTCTC+TGG 0.461592 3:-113749445 None:intergenic
CACAAATCAGGAGCCACAAA+TGG 0.462731 3:+113749052 MsaT017839.1:CDS
TACTACTGTTGTTGTTGTTG+AGG 0.467147 3:+113748854 MsaT017839.1:CDS
TGGAGAAATTTGAAGCGGTC+TGG 0.467731 3:+113750066 MsaT017839.1:CDS
ATTTGAAAATGGAAAGGTTA+GGG 0.470688 3:+113747698 None:intergenic
ACATCAGACCTTACAATGTC+TGG 0.471043 3:-113749017 None:intergenic
GTACATTTGCATCTTTACTC+TGG 0.471288 3:-113749079 None:intergenic
AATTTGAAAATGGAAAGGTT+AGG 0.473595 3:+113747697 None:intergenic
GAAGATGAAAATGCTTCTGT+TGG 0.479184 3:+113747825 MsaT017839.1:CDS
TACCTTGAAGCAGCAGGTGC+AGG 0.480680 3:+113748027 MsaT017839.1:CDS
GCAACAGAGTGAAGAAAGGA+AGG 0.481758 3:-113748294 None:intergenic
GGCAATTGAAGACACAAATC+AGG 0.483604 3:+113749040 MsaT017839.1:CDS
CAGTCACCGAAATCGATAAT+CGG 0.485524 3:+113747803 MsaT017839.1:CDS
GATGCTCGGAATAACCTTGT+AGG 0.496320 3:+113748270 MsaT017839.1:CDS
TCTGGCATACAAATAGAATT+GGG 0.497185 3:-113748999 None:intergenic
ATATTCTGTCAACTGCTTGG+AGG 0.502799 3:-113748074 None:intergenic
CTATTTGGTTTCATCAAGCT+AGG 0.506498 3:-113749185 None:intergenic
AAGTACATACAGTTTAATTC+CGG 0.506549 3:-113749551 None:intergenic
ATGAAAATGCTTCTGTTGGA+AGG 0.511456 3:+113747829 MsaT017839.1:CDS
GTGGATTGGGGTTTGAAGAA+GGG 0.513396 3:-113747945 None:intergenic
CCAAAGCATCTATCGATGAA+TGG 0.516478 3:+113747872 MsaT017839.1:CDS
TGAAAAGGGAAGCATCGATT+CGG 0.518415 3:-113748167 None:intergenic
TTGATCGATGGATTGCAGGC+AGG 0.522304 3:+113749385 MsaT017839.1:CDS
TTGTCTTTGTCGAGTTCCAT+CGG 0.525502 3:-113748807 None:intergenic
AGCAGCAACAGAGTGAAGAA+AGG 0.532298 3:-113748298 None:intergenic
CATGTATCGTGAGTTGAAAA+GGG 0.536326 3:-113748181 None:intergenic
GATTGCAGGCAGGAACATCA+AGG 0.543132 3:+113749395 MsaT017839.1:CDS
TTCACTTAAATGCAATTCTG+TGG 0.545122 3:+113748947 MsaT017839.1:CDS
TTTGGTTCATACTCCTTCAA+CGG 0.551515 3:-113749466 None:intergenic
AAAATGGAGTCAATGGGAAG+AGG 0.556320 3:+113749516 MsaT017839.1:CDS
ATTTAGGCAAGCATGTGGGT+TGG 0.556821 3:-113749102 None:intergenic
TAGTGGGATGATTTGATCGA+TGG 0.557914 3:+113749373 MsaT017839.1:intron
AAAGGAATTTGAAAATGGAA+AGG 0.559315 3:+113747692 None:intergenic
GAACCGTAGGTTTCAAAACC+TGG 0.560313 3:+113748098 MsaT017839.1:CDS
ATGATGAACATCACTTTGAT+GGG 0.562151 3:-113749162 None:intergenic
GAAGAGGATAATCTAAGGAC+CGG 0.564580 3:+113749532 MsaT017839.1:CDS
GTTAACGAGGCCCAAAAGAA+CGG 0.567267 3:+113748921 MsaT017839.1:CDS
GAAGAAAGGAAGGGCCTACA+AGG 0.570430 3:-113748284 None:intergenic
CTTCATTGTCTGATACCAGA+AGG 0.585689 3:+113748214 MsaT017839.1:CDS
AACTCGACAAAGACAATGGA+AGG 0.587275 3:+113748814 MsaT017839.1:CDS
CAATGGAAGGCTTAAAGGCA+AGG 0.588132 3:+113748827 MsaT017839.1:CDS
TTGCTGTGGAATGTACCGTT+AGG 0.589094 3:+113748004 MsaT017839.1:CDS
TTCATGGCATCGCTAATAGG+TGG 0.591268 3:-113747964 None:intergenic
AGGTTGATTTGAAAGACAAG+TGG 0.593616 3:+113750046 MsaT017839.1:intron
TTGACAGAATATGGAACCGT+AGG 0.599653 3:+113748085 MsaT017839.1:CDS
CATCGCTAATAGGTGGATTG+GGG 0.601309 3:-113747957 None:intergenic
TGACTCTTTGCCAGTTAACG+AGG 0.601690 3:+113748908 MsaT017839.1:CDS
TGCTTATGTCTACATTGCTG+TGG 0.602167 3:+113747990 MsaT017839.1:CDS
TTAACATTTAGGCAAGCATG+TGG 0.604145 3:-113749107 None:intergenic
CTTGAAGCAGCAGGTGCAGG+TGG 0.604795 3:+113748030 MsaT017839.1:CDS
TCTCATATTAGAGTCTCCGA+TGG 0.606409 3:+113748791 MsaT017839.1:intron
ATTGCAGGCAGGAACATCAA+GGG 0.616311 3:+113749396 MsaT017839.1:CDS
GTTAGGTACCTTGAAGCAGC+AGG 0.617125 3:+113748021 MsaT017839.1:CDS
ATTATCGATTTCGGTGACTG+AGG 0.617150 3:-113747800 None:intergenic
ATGGAACTCGACAAAGACAA+TGG 0.617169 3:+113748810 MsaT017839.1:CDS
TGAAAATGGAAAGGTTAGGG+TGG 0.628807 3:+113747701 None:intergenic
CCTAAATGTTAACAATGATG+AGG 0.630277 3:+113749118 MsaT017839.1:CDS
TGCTGCTTCAAGGTACCTAA+CGG 0.634086 3:-113748019 None:intergenic
ATACAAATAGAATTGGGCAC+AGG 0.635848 3:-113748993 None:intergenic
ATGGATGCTTGAACTTCTCG+AGG 0.640307 3:+113747891 MsaT017839.1:CDS
TTGCAGGCAGGAACATCAAG+GGG 0.642905 3:+113749397 MsaT017839.1:CDS
TTCGTTTGCGTAGTCCAGAG+AGG 0.651598 3:+113749431 MsaT017839.1:CDS
CAACAGAGTGAAGAAAGGAA+GGG 0.656227 3:-113748293 None:intergenic
CGTAGGTTTCAAAACCTGGA+GGG 0.661614 3:+113748102 MsaT017839.1:CDS
CAGAAGGAAAGCCATTCAAG+AGG 0.668057 3:+113748230 MsaT017839.1:CDS
TAACATTTAGGCAAGCATGT+GGG 0.675244 3:-113749106 None:intergenic
ACAAGTGGAGAAATTTGAAG+CGG 0.678726 3:+113750061 MsaT017839.1:CDS
AGACATTGTAAGGTCTGATG+TGG 0.687030 3:+113749019 MsaT017839.1:CDS
CCGTAGGTTTCAAAACCTGG+AGG 0.690526 3:+113748101 MsaT017839.1:CDS
TAGTTCTGCTCGTACTCACG+AGG 0.692042 3:+113749205 MsaT017839.1:CDS
TGATGAGGCCAATCTTACGA+AGG 0.699645 3:+113749133 MsaT017839.1:CDS
TAACGAGGCCCAAAAGAACG+GGG 0.712659 3:+113748923 MsaT017839.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 113747706 113750098 113747706 ID=MsaG017839
Chr3 mRNA 113747706 113750098 113747706 ID=MsaT017839.1;Parent=MsaG017839
Chr3 exon 113747706 113748351 113747706 ID=MsaT017839.1.exon1;Parent=MsaT017839.1
Chr3 CDS 113747706 113748351 113747706 ID=cds.MsaT017839.1;Parent=MsaT017839.1
Chr3 exon 113748802 113749226 113748802 ID=MsaT017839.1.exon2;Parent=MsaT017839.1
Chr3 CDS 113748802 113749226 113748802 ID=cds.MsaT017839.1;Parent=MsaT017839.1
Chr3 exon 113749376 113749563 113749376 ID=MsaT017839.1.exon3;Parent=MsaT017839.1
Chr3 CDS 113749376 113749563 113749376 ID=cds.MsaT017839.1;Parent=MsaT017839.1
Chr3 exon 113749912 113749972 113749912 ID=MsaT017839.1.exon4;Parent=MsaT017839.1
Chr3 CDS 113749912 113749972 113749912 ID=cds.MsaT017839.1;Parent=MsaT017839.1
Chr3 exon 113750048 113750098 113750048 ID=MsaT017839.1.exon5;Parent=MsaT017839.1
Chr3 CDS 113750048 113750098 113750048 ID=cds.MsaT017839.1;Parent=MsaT017839.1
Gene Sequence

>MsaT017839.1

ATGGAAAGGTTAGGGTGGTGTTTGGAATTCGTTCTTGGACATTCTTCAACAAGTATAGAGAGTGAGCATATTAAGGAAATCTTGAAACTAAGCTCCTCAGTCACCGAAATCGATAATCGGAAGATGAAAATGCTTCTGTTGGAAGGCCTTGAAGATGAGTTGTTGTCCAAAGCATCTATCGATGAATGGATGCTTGAACTTCTCGAGGTATTCGAAAAACTACTTCTAATTGATTGGGACCCTTCTTCAAACCCCAATCCACCTATTAGCGATGCCATGAAATCTGCTTATGTCTACATTGCTGTGGAATGTACCGTTAGGTACCTTGAAGCAGCAGGTGCAGGTGGTATATCTAACCCTAAACACTACCTCCAAGCAGTTGACAGAATATGGAACCGTAGGTTTCAAAACCTGGAGGGAAGAAGTTATTTGCTAACTCCAAAATTGAGATTCTGGAAAAGCCGAATCGATGCTTCCCTTTTCAACTCACGATACATGCTCAAACTTGCTTCATTGTCTGATACCAGAAGGAAAGCCATTCAAGAGGTTCAACTTTTTTTGGAGGATGCTCGGAATAACCTTGTAGGCCCTTCCTTTCTTCACTCTGTTGCTGCTCCTTCTGCTGCTCAAAATCAATCCCATAATGAGTCTCCGATGGAACTCGACAAAGACAATGGAAGGCTTAAAGGCAAGGCTTCTACTACTGTTGTTGTTGTTGAGGTAATGGCTACATCAACCAGCTGTAGCAAAATTGACTCTTTGCCAGTTAACGAGGCCCAAAAGAACGGGGATTCACTTAAATGCAATTCTGTGGAGTTCAAAACATTTGCGAACGATCCTGTGCCCAATTCTATTTGTATGCCAGACATTGTAAGGTCTGATGTGGCAATTGAAGACACAAATCAGGAGCCACAAATGGAAAACCAGAGTAAAGATGCAAATGTACCCAACCCACATGCTTGCCTAAATGTTAACAATGATGAGGCCAATCTTACGAAGGCAACTTCCCATCAAAGTGATGTTCATCATCCTAGCTTGATGAAACCAAATAGTTCTGCTCGTACTCACGAGTGGGATGATTTGATCGATGGATTGCAGGCAGGAACATCAAGGGGCACAAGTAGAATTCGTTTGCGTAGTCCAGAGAGGAAGAAGCTTTCTCCGTTGAAGGAGTATGAACCAAAAAATATTACGAAAAGGAGAAAGAAAAAAAAATGGAGTCAATGGGAAGAGGATAATCTAAGGACCGGAATTAAACTAATTGGAGAAGGAAACTGGAAATCAATTCTTCGTTCTTATGAATTTGACGAAAGAACTGAAGTTGATTTGAAAGACAAGTGGAGAAATTTGAAGCGGTCTGGATGCCAATGA

Protein sequence

>MsaT017839.1

MERLGWCLEFVLGHSSTSIESEHIKEILKLSSSVTEIDNRKMKMLLLEGLEDELLSKASIDEWMLELLEVFEKLLLIDWDPSSNPNPPISDAMKSAYVYIAVECTVRYLEAAGAGGISNPKHYLQAVDRIWNRRFQNLEGRSYLLTPKLRFWKSRIDASLFNSRYMLKLASLSDTRRKAIQEVQLFLEDARNNLVGPSFLHSVAAPSAAQNQSHNESPMELDKDNGRLKGKASTTVVVVEVMATSTSCSKIDSLPVNEAQKNGDSLKCNSVEFKTFANDPVPNSICMPDIVRSDVAIEDTNQEPQMENQSKDANVPNPHACLNVNNDEANLTKATSHQSDVHHPSLMKPNSSARTHEWDDLIDGLQAGTSRGTSRIRLRSPERKKLSPLKEYEPKNITKRRKKKKWSQWEEDNLRTGIKLIGEGNWKSILRSYEFDERTEVDLKDKWRNLKRSGCQ*