AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG046187

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG046187 MtrunA17_Chr4g0072481 97.075 547 16 0 1 547 1 547 0.0 1100
MsaG046187 MtrunA17_Chr3g0120751 21.951 410 278 12 142 518 63 463 3.96e-18 87.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG046187 AT2G18850.1 52.060 534 250 4 5 537 10 538 0.0 556
MsaG046187 AT2G18850.2 51.685 534 245 5 5 537 10 531 0.0 548
MsaG046187 AT3G07670.1 23.629 474 311 18 82 520 15 472 7.90e-21 96.3
MsaG046187 AT3G07670.2 24.528 318 200 11 234 520 26 334 1.94e-15 78.6

Find 118 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTGATTTAATTTCTGATTT+TGG 0.061221 8:-81549423 MsaT046187.1:CDS
TGGTCTTCCCTCTCCATTAT+TGG 0.251856 8:-81541238 MsaT046187.1:CDS
ATACATTATCTTCATGCTAT+TGG 0.253277 8:+81542255 None:intergenic
GTTTCAACTTCTTGCTGTAC+TGG 0.267684 8:-81540266 MsaT046187.1:CDS
TAATTTGCAGGATTGAGTTT+TGG 0.273161 8:-81545291 MsaT046187.1:intron
GTACTCCCTTCATATTGTTT+TGG 0.278110 8:+81549397 None:intergenic
CCGTATGATGTCATTCCTTT+AGG 0.285448 8:-81541509 MsaT046187.1:intron
GAAAATGAGCTAGAAGTTCT+TGG 0.287372 8:-81540819 MsaT046187.1:CDS
CTGAGACAATATTGCTGTTA+TGG 0.304721 8:-81547808 MsaT046187.1:CDS
GAGAGCCTCCAACTCATTCC+TGG 0.355681 8:+81549533 None:intergenic
TCAGAAATTACTACGATGTA+AGG 0.359589 8:-81549964 MsaT046187.1:intron
AATCACAGCATATTCTATTA+TGG 0.363717 8:-81541258 MsaT046187.1:CDS
AGTGCTCCTCAGGACCTTCT+TGG 0.369830 8:-81549911 MsaT046187.1:CDS
ACATGTTTGATACCTCTTGC+TGG 0.371762 8:-81542214 MsaT046187.1:CDS
TCCACAGTTGCAAGGAAACT+TGG 0.382837 8:-81540841 MsaT046187.1:intron
TGACGACATGATGGACAGTA+TGG 0.401765 8:-81540778 MsaT046187.1:CDS
ATCTCTGGAGGAAATATATC+AGG 0.406816 8:+81542322 None:intergenic
CTCCATTATTGGATCATCTT+CGG 0.411384 8:-81541227 MsaT046187.1:CDS
CTATCAAGACCATGCCGATC+TGG 0.413805 8:-81541614 MsaT046187.1:CDS
ATAGAATATGCTGTGATTGT+TGG 0.416388 8:+81541263 None:intergenic
CACCATGTGAGTCGTCCATT+TGG 0.419396 8:+81541302 None:intergenic
TGCCCACATATTACACACTA+TGG 0.422578 8:-81541674 MsaT046187.1:CDS
TTCTCCCAAGTGTAAATCTC+TGG 0.423678 8:+81542307 None:intergenic
CTCCGAAGATGATCCAATAA+TGG 0.426430 8:+81541225 None:intergenic
AATTTCAATGAATTTGTTGA+AGG 0.427682 8:+81541641 None:intergenic
GCTTGTGCTTGAAACTGATA+TGG 0.430090 8:-81549064 MsaT046187.1:intron
AGATGTTGAAGGAGCAGGCC+GGG 0.432091 8:-81549163 MsaT046187.1:CDS
GCAGGCCGGGGAATGATAGC+AGG 0.433260 8:-81549150 MsaT046187.1:CDS
AAAGTCTTTGTTTGCATCAC+AGG 0.436089 8:+81541192 None:intergenic
TTACTACGATGTAAGGGGTT+TGG 0.439522 8:-81549957 MsaT046187.1:CDS
AAGCTCCTCAGAAATGATAA+TGG 0.442652 8:+81549083 None:intergenic
TTTCAACTTCTTGCTGTACT+GGG 0.444329 8:-81540265 MsaT046187.1:CDS
CTCACATGGTGCGTGGTACC+TGG 0.452049 8:-81541290 MsaT046187.1:CDS
TCCTTTCTTTGATGAAAAGA+AGG 0.455845 8:-81550882 MsaT046187.1:intron
GAATGAACTGCACAAGTGTT+TGG 0.459339 8:-81540228 MsaT046187.1:CDS
TGTTTGGCTGAGGACATTGT+AGG 0.459596 8:-81540212 MsaT046187.1:CDS
ACCCTTGCAGGATGTTTGTA+TGG 0.460432 8:+81549460 None:intergenic
TTGGTTCCTGCTTTGTGCAA+TGG 0.460579 8:-81542349 MsaT046187.1:CDS
TTAATCTACACAGATGTTGA+AGG 0.462913 8:-81549174 MsaT046187.1:intron
ATACATCTCAAGTGCTCCTC+AGG 0.464633 8:-81549921 MsaT046187.1:CDS
AGGATAAACCTGTGTCCAAA+TGG 0.465266 8:-81541317 MsaT046187.1:CDS
TTGAGATGTATCCATTCCTT+GGG 0.465915 8:+81549933 None:intergenic
CTTGAGATGTATCCATTCCT+TGG 0.467813 8:+81549932 None:intergenic
GTGAAGTCGATCTTGATAAC+AGG 0.473430 8:-81540755 MsaT046187.1:intron
TTCTGATGTTGATTCTATTG+AGG 0.474846 8:-81541337 MsaT046187.1:CDS
TCAGTATCGTCTCTTGAAAG+AGG 0.476597 8:-81547846 MsaT046187.1:intron
GAGAAGAACACCTGATTGAG+TGG 0.477724 8:-81549350 MsaT046187.1:CDS
GCAGGGAAAGATCTAAAAGT+TGG 0.483249 8:-81549132 MsaT046187.1:CDS
TGGGGACCAAAACAATATGA+AGG 0.487327 8:-81549403 MsaT046187.1:CDS
GAAGAATGCTGCTTAAGCTA+TGG 0.488333 8:-81541590 MsaT046187.1:CDS
CGTCTCTTGAAAGAGGTTGA+TGG 0.489397 8:-81547839 MsaT046187.1:CDS
AGCAAGAAGTTGAAACAGAA+TGG 0.489908 8:+81540273 None:intergenic
GAAGCGATTACAATGCTAGA+TGG 0.490904 8:-81545264 MsaT046187.1:CDS
CCTAAAGGAATGACATCATA+CGG 0.505016 8:+81541509 None:intergenic
GCTGTGATTGTTGGAGAGCC+AGG 0.506463 8:+81541272 None:intergenic
CAGCCCCAGGAATGAGTTGG+AGG 0.515961 8:-81549538 MsaT046187.1:CDS
AGAGCCTCCAACTCATTCCT+GGG 0.519139 8:+81549534 None:intergenic
TCCTCCAGAGATTTACACTT+GGG 0.521467 8:-81542311 MsaT046187.1:CDS
TACACAGATGTTGAAGGAGC+AGG 0.521506 8:-81549168 MsaT046187.1:intron
AAAAGCCATGGTGTAAAGAC+AGG 0.525288 8:-81549324 MsaT046187.1:CDS
ACGATATCATTCATCCAAGA+AGG 0.525319 8:+81549897 None:intergenic
AAATGTAATAAAATGAGAGC+TGG 0.529710 8:+81541559 None:intergenic
GGAAAACCATTGCACAAAGC+AGG 0.530912 8:+81542343 None:intergenic
CAGAAATTACTACGATGTAA+GGG 0.531459 8:-81549963 MsaT046187.1:CDS
ATGTAAGGGGTTTGGTCCCA+AGG 0.532723 8:-81549949 MsaT046187.1:CDS
AGGGGTTTGGTCCCAAGGAA+TGG 0.533877 8:-81549944 MsaT046187.1:CDS
CGTGTCCATTATCATTTCTG+AGG 0.534034 8:-81549088 MsaT046187.1:CDS
CAGATGTTGAAGGAGCAGGC+CGG 0.534056 8:-81549164 MsaT046187.1:CDS
CTTTCCCTGCTATCATTCCC+CGG 0.534319 8:+81549145 None:intergenic
AAGAATGCTGCTTAAGCTAT+GGG 0.536764 8:-81541589 MsaT046187.1:CDS
TTCTCAGAGAAAGCTACACC+TGG 0.537382 8:-81540343 MsaT046187.1:intron
GCAAGAAGTTGAAACAGAAT+GGG 0.537385 8:+81540274 None:intergenic
TTACAGCCCCAGGAATGAGT+TGG 0.537964 8:-81549541 MsaT046187.1:CDS
AGCAGCATTCTTCTCCAGAT+CGG 0.542200 8:+81541600 None:intergenic
ACAACTAGAAAGTGATTTGT+CGG 0.544339 8:+81549491 None:intergenic
GCACTCCTCGTCACTATCCA+TGG 0.550146 8:+81550934 None:intergenic
AGAGATAATGCAATCAAGAC+AGG 0.553032 8:-81545226 MsaT046187.1:intron
AGACATCTTTGACGACATGA+TGG 0.557106 8:-81540787 MsaT046187.1:CDS
TTCCATACAAACATCCTGCA+AGG 0.560101 8:-81549462 MsaT046187.1:CDS
TGAGTCGTCCATTTGGACAC+AGG 0.564379 8:+81541309 None:intergenic
CATTATCTCTTCAAACAGCA+AGG 0.565535 8:+81545239 None:intergenic
CTCAGAAATGATAATGGACA+CGG 0.571725 8:+81549089 None:intergenic
GCATGCTCAGTATGATGAGT+TGG 0.574500 8:-81542368 MsaT046187.1:CDS
AGATGATCCAATAATGGAGA+GGG 0.579934 8:+81541231 None:intergenic
TTCCTCCAGAGATTTACACT+TGG 0.582164 8:-81542312 MsaT046187.1:CDS
TTGCCATAGTGTGTAATATG+TGG 0.582672 8:+81541671 None:intergenic
AGAAGAACACCTGATTGAGT+GGG 0.587488 8:-81549349 MsaT046187.1:CDS
AGAAATTACTACGATGTAAG+GGG 0.589340 8:-81549962 MsaT046187.1:CDS
GGGGACCAAAACAATATGAA+GGG 0.590986 8:-81549402 MsaT046187.1:CDS
TCCATACAAACATCCTGCAA+GGG 0.600641 8:-81549461 MsaT046187.1:CDS
ATGAAGATAATGTATTCAGA+TGG 0.601114 8:-81542247 MsaT046187.1:CDS
GATGTTGAAGGAGCAGGCCG+GGG 0.613770 8:-81549162 MsaT046187.1:CDS
TGATTAAGAAAGCCAGCAAG+AGG 0.615019 8:+81542202 None:intergenic
TCCCAAGTGTAAATCTCTGG+AGG 0.620554 8:+81542310 None:intergenic
TTAATCCTGTCTTTACACCA+TGG 0.622253 8:+81549319 None:intergenic
CATTCTTCTCCAGATCGGCA+TGG 0.630402 8:+81541605 None:intergenic
GAGCCTCCAACTCATTCCTG+GGG 0.630829 8:+81549535 None:intergenic
TGCTGAAGACGATGCCTCGG+TGG 0.645814 8:-81549568 MsaT046187.1:CDS
TGGACGACTCACATGGTGCG+TGG 0.646565 8:-81541297 MsaT046187.1:CDS
CTAAAGGAATGACATCATAC+GGG 0.653617 8:+81541510 None:intergenic
AGGATGTTTGTATGGAAATG+TGG 0.655140 8:+81549468 None:intergenic
TCAGAAATGATAATGGACAC+GGG 0.657279 8:+81549090 None:intergenic
TGCCATAGTGTGTAATATGT+GGG 0.660167 8:+81541672 None:intergenic
CAGGCCGGGGAATGATAGCA+GGG 0.660857 8:-81549149 MsaT046187.1:CDS
AAGATGATCCAATAATGGAG+AGG 0.665042 8:+81541230 None:intergenic
GTTCTTCTCTCTCACAACTG+TGG 0.667911 8:+81549364 None:intergenic
TGCAGCCATGGATAGTGACG+AGG 0.679797 8:-81550939 None:intergenic
GTCCAAATGGACGACTCACA+TGG 0.681562 8:-81541304 MsaT046187.1:CDS
TCTCAGAGAAAGCTACACCT+GGG 0.684262 8:-81540342 MsaT046187.1:intron
TCATACGGGTTGTCTCCTTG+AGG 0.685652 8:+81541524 None:intergenic
ATTGAGTGGGGTAAAAGCCA+TGG 0.686263 8:-81549336 MsaT046187.1:CDS
GACGACATGATGGACAGTAT+GGG 0.690308 8:-81540777 MsaT046187.1:CDS
GAAGAACACCTGATTGAGTG+GGG 0.693168 8:-81549348 MsaT046187.1:CDS
ACTGCACAAGTGTTTGGCTG+AGG 0.693657 8:-81540222 MsaT046187.1:CDS
ATTCATCCAAGAAGGTCCTG+AGG 0.699592 8:+81549905 None:intergenic
TGTATTCAGATGGAAAACTG+AGG 0.723155 8:-81542237 MsaT046187.1:CDS
AAGAATCATACAGTTAAACG+AGG 0.733021 8:-81549853 MsaT046187.1:intron
GGGGCTGTAAAACTCCACCG+AGG 0.821008 8:+81549554 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 81540208 81550954 81540208 ID=MsaG046187
Chr8 mRNA 81540208 81550954 81540208 ID=MsaT046187.1;Parent=MsaG046187
Chr8 exon 81540208 81540358 81540208 ID=MsaT046187.1.exon11;Parent=MsaT046187.1
Chr8 CDS 81540208 81540358 81540208 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81540756 81540856 81540756 ID=MsaT046187.1.exon10;Parent=MsaT046187.1
Chr8 CDS 81540756 81540856 81540756 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81541191 81541369 81541191 ID=MsaT046187.1.exon9;Parent=MsaT046187.1
Chr8 CDS 81541191 81541369 81541191 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81541510 81541699 81541510 ID=MsaT046187.1.exon8;Parent=MsaT046187.1
Chr8 CDS 81541510 81541699 81541510 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81542198 81542395 81542198 ID=MsaT046187.1.exon7;Parent=MsaT046187.1
Chr8 CDS 81542198 81542395 81542198 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81545227 81545303 81545227 ID=MsaT046187.1.exon6;Parent=MsaT046187.1
Chr8 CDS 81545227 81545303 81545227 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81547732 81547864 81547732 ID=MsaT046187.1.exon5;Parent=MsaT046187.1
Chr8 CDS 81547732 81547864 81547732 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81549065 81549183 81549065 ID=MsaT046187.1.exon4;Parent=MsaT046187.1
Chr8 CDS 81549065 81549183 81549065 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81549310 81549604 81549310 ID=MsaT046187.1.exon3;Parent=MsaT046187.1
Chr8 CDS 81549310 81549604 81549310 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81549854 81549982 81549854 ID=MsaT046187.1.exon2;Parent=MsaT046187.1
Chr8 CDS 81549854 81549982 81549854 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Chr8 exon 81550883 81550954 81550883 ID=MsaT046187.1.exon1;Parent=MsaT046187.1
Chr8 CDS 81550883 81550954 81550883 ID=cds.MsaT046187.1;Parent=MsaT046187.1
Gene Sequence

>MsaT046187.1

ATGGATAGTGACGAGGAGTGCTCAATTGTTCTTGAGTTATCTGAAAATGATCCTTTCTTTGATGAAAAGAAGAAATTACTACGATGTAAGGGGTTTGGTCCCAAGGAATGGATACATCTCAAGTGCTCCTCAGGACCTTCTTGGATGAATGATATCGTAAAGATCTTACTTCAGATTGCAAGAATCATACAGTTAAACGAGCTGGAACTCTATTTTGCTGAAGACGATGCCTCGGTGGAGTTTTACAGCCCCAGGAATGAGTTGGAGGCTCTCAATTCAATTGTTTCGCTCACCGACAAATCACTTTCTAGTTGTCCACATTTCCATACAAACATCCTGCAAGGGTTACAACAAAAGATTTTTGATTTAATTTCTGATTTTGGGGACCAAAACAATATGAAGGGAGTACTTGAAAAGTACCACAGTTGTGAGAGAGAAGAACACCTGATTGAGTGGGGTAAAAGCCATGGTGTAAAGACAGGATTAAAGATAGCTTATGTTGAAGGAGCAGGCCGGGGAATGATAGCAGGGAAAGATCTAAAAGTTGGAGATACTGCTATAGAGATTCCCGTGTCCATTATCATTTCTGAGGAGCTTGTGCTTGAAACTGATATGTATCGTCTCTTGAAAGAGGTTGATGGCATATCATCTGAGACAATATTGCTGTTATGGAGTATGAAAGAGAAGTACAACTGTGATTCAAAATTCAAAATTTACTTTGACACACTTCCAGAAAAATTTAATACAGGATTGAGTTTTGGGATTGAAGCGATTACAATGCTAGATGGAACCTTGCTGTTTGAAGAGATAATGCAATCAAGACAGCACTTGCATGCTCAGTATGATGAGTTGGTTCCTGCTTTGTGCAATGGTTTTCCTGATATATTTCCTCCAGAGATTTACACTTGGGAGAATTTTTTATGGGCTTGTGAACTTTGGTATTCCAATAGCATGAAGATAATGTATTCAGATGGAAAACTGAGGACATGTTTGATACCTCTTGCTGGCTTTCTTAATCATTCACTGTGCCCACATATTACACACTATGGCAAAGTAGATCCTTCAACAAATTCATTGAAATTTTGTCTATCAAGACCATGCCGATCTGGAGAAGAATGCTGCTTAAGCTATGGGAACTTCTCCAGCTCTCATTTTATTACATTTTATGGTTTCTTACCTCAAGGAGACAACCCGTATGATGTCATTCCTTTAGACATCGATAGTTCTGATGTTGATTCTATTGAGGATAAACCTGTGTCCAAATGGACGACTCACATGGTGCGTGGTACCTGGCTCTCCAACAATCACAGCATATTCTATTATGGTCTTCCCTCTCCATTATTGGATCATCTTCGGAGATCTCGAAGTCCTGTGATGCAAACAAAGACTTTCTTGCAAGGAAACTTGGAAAATGAGCTAGAAGTTCTTGGAGATCTCAAAGACATCTTTGACGACATGATGGACAGTATGGGTGAAGTCGATCTTGATAACAGAGAAAGCTACACCTGGGATGAAAAATTGGCTGTGGATTGTAAAAATCTACAAAGACGAATAGCCCATTCTGTTTCAACTTCTTGCTGTACTGGGATCAACATGTTGAAGAATGAACTGCACAAGTGTTTGGCTGAGGACATTGTAGGTTAA
Protein sequence

>MsaT046187.1

MDSDEECSIVLELSENDPFFDEKKKLLRCKGFGPKEWIHLKCSSGPSWMNDIVKILLQIARIIQLNELELYFAEDDASVEFYSPRNELEALNSIVSLTDKSLSSCPHFHTNILQGLQQKIFDLISDFGDQNNMKGVLEKYHSCEREEHLIEWGKSHGVKTGLKIAYVEGAGRGMIAGKDLKVGDTAIEIPVSIIISEELVLETDMYRLLKEVDGISSETILLLWSMKEKYNCDSKFKIYFDTLPEKFNTGLSFGIEAITMLDGTLLFEEIMQSRQHLHAQYDELVPALCNGFPDIFPPEIYTWENFLWACELWYSNSMKIMYSDGKLRTCLIPLAGFLNHSLCPHITHYGKVDPSTNSLKFCLSRPCRSGEECCLSYGNFSSSHFITFYGFLPQGDNPYDVIPLDIDSSDVDSIEDKPVSKWTTHMVRGTWLSNNHSIFYYGLPSPLLDHLRRSRSPVMQTKTFLQGNLENELEVLGDLKDIFDDMMDSMGEVDLDNRESYTWDEKLAVDCKNLQRRIAHSVSTSCCTGINMLKNELHKCLAEDIVG*