AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG042486

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042486 MtrunA17_Chr5g0433621 93.805 339 21 0 1 339 1 339 0.0 674
MsaG042486 MtrunA17_Chr1g0188461 26.667 285 177 10 52 315 33 306 1.38e-13 72.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG042486 AT5G17240.1 63.037 349 119 4 1 348 1 340 3.98e-160 459
MsaG042486 AT5G17240.2 65.328 274 89 3 76 348 1 269 6.65e-130 379

Find 78 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTAGTCATTAAAGCAGATTT+TGG 0.219025 8:+22810472 None:intergenic
GTCGGACGCCTTGCATATTC+TGG 0.219534 8:-22806838 MsaT042486.1:CDS
CTCTTCTCTCTCCTCTGTTC+AGG 0.231576 8:-22810398 MsaT042486.1:intron
CAACACTCTCTTTCCTCTCT+TGG 0.235733 8:-22810761 MsaT042486.1:CDS
AACATTTAAGGCATGGCTTT+GGG 0.315162 8:-22808306 MsaT042486.1:CDS
CACTTCTACTTCATGGTCTA+AGG 0.325752 8:-22806952 MsaT042486.1:CDS
CTATGTACACTTCTACTTCA+TGG 0.363522 8:-22806959 MsaT042486.1:CDS
TGGGCAACCCTCATAATAAA+AGG 0.372047 8:-22806867 MsaT042486.1:CDS
TAACATTTAAGGCATGGCTT+TGG 0.385694 8:-22808307 MsaT042486.1:CDS
TAATTAAACAAGTCACCAAC+AGG 0.396024 8:+22807568 None:intergenic
GAAAGAAGCTCATGCCTTGA+TGG 0.398662 8:-22808357 MsaT042486.1:CDS
AGTCATAACTTTGCGGCAAA+TGG 0.404610 8:+22808605 None:intergenic
GCACCTGGAGAGGACCTATC+TGG 0.423204 8:-22807541 MsaT042486.1:CDS
AGAATGTTGCAGTAGAGGTT+TGG 0.444175 8:-22810539 MsaT042486.1:intron
CAATCAAATGGAGACAAGAA+TGG 0.446355 8:-22807496 MsaT042486.1:CDS
GAATGTTGCAGTAGAGGTTT+GGG 0.448690 8:-22810538 MsaT042486.1:intron
CTTGTTATACGAAGTTGGTA+AGG 0.457725 8:-22808659 MsaT042486.1:CDS
GTTTGCTTGTTATACGAAGT+TGG 0.462021 8:-22808664 MsaT042486.1:CDS
AGGAAAGAGAGTGTTGAGAA+TGG 0.462418 8:+22810768 None:intergenic
TATGACTTGCTAGCCATGTT+TGG 0.465171 8:-22808589 MsaT042486.1:CDS
ATGGCTTTGGGCTGCTGCAA+CGG 0.467154 8:-22808294 MsaT042486.1:intron
CTACCTTTCCTCACTCTGGC+GGG 0.467292 8:-22810721 MsaT042486.1:intron
GTGCTGTGAGAGATCTTAAG+AGG 0.468743 8:-22810516 MsaT042486.1:CDS
CACCAGGTTCTATTATGCTA+TGG 0.472726 8:-22807071 MsaT042486.1:intron
TGCGGCAAATGGACGAGGTA+AGG 0.498856 8:+22808616 None:intergenic
GCTAGGACAAATTACAAGAA+AGG 0.501930 8:-22807385 MsaT042486.1:CDS
AAATTACAAGAAAGGCGATC+AGG 0.502432 8:-22807377 MsaT042486.1:intron
AAACATCAGTTCTTCCATCA+AGG 0.504879 8:+22808343 None:intergenic
AGCTATGTCTTGCTGTGAAT+AGG 0.511400 8:-22810423 MsaT042486.1:CDS
TTGGTAAGGGAAAGACTTCA+AGG 0.512774 8:-22808645 MsaT042486.1:CDS
GTTTCTACCTTTCCTCACTC+TGG 0.514945 8:-22810725 MsaT042486.1:CDS
AAGAGAGTGTTGAGAATGGT+CGG 0.528406 8:+22810772 None:intergenic
GCTGGTTGTTTATGCCCTGT+TGG 0.537691 8:-22807583 MsaT042486.1:CDS
AACTTTGCGGCAAATGGACG+AGG 0.537904 8:+22808611 None:intergenic
GCTAGCAAGTCATAACTTTG+CGG 0.538816 8:+22808598 None:intergenic
AAGAACATGGAAGGTTTGAA+AGG 0.542145 8:-22810847 MsaT042486.1:CDS
TACTAGCTGCGTTACGACTG+TGG 0.542432 8:-22806887 MsaT042486.1:CDS
TTTCTCAAATTCACCAAACA+TGG 0.542605 8:+22808576 None:intergenic
GAAGTAGAAGTGTACATAGC+AGG 0.549201 8:+22806963 None:intergenic
AAGAACTGATGTTTAAGCCT+CGG 0.551132 8:-22808334 MsaT042486.1:CDS
CTCAGAGACTAACTGATGGT+GGG 0.556902 8:-22807441 MsaT042486.1:CDS
TTGTTTAATTACGATGCACC+TGG 0.559289 8:-22807556 MsaT042486.1:CDS
ATACCAGATAGGTCCTCTCC+AGG 0.561435 8:+22807538 None:intergenic
ATCAGGTGGATGAAGCTATG+TGG 0.568564 8:-22808418 MsaT042486.1:intron
TTTGAGCTTCTTGAACACTA+CGG 0.569876 8:-22807035 MsaT042486.1:CDS
GTGTACATAGCAGGTTCCAA+AGG 0.569923 8:+22806972 None:intergenic
TCTACCTTTCCTCACTCTGG+CGG 0.572108 8:-22810722 MsaT042486.1:CDS
CTCGGACATTGCATATACCA+TGG 0.573706 8:-22807612 MsaT042486.1:CDS
CTACGTCGTCAATACCAGAT+AGG 0.574667 8:+22807527 None:intergenic
TTGTTATACGAAGTTGGTAA+GGG 0.583923 8:-22808658 MsaT042486.1:CDS
TCAGGTGGATGAAGCTATGT+GGG 0.588137 8:-22808417 MsaT042486.1:intron
TCGGACATTGCATATACCAT+GGG 0.588653 8:-22807611 MsaT042486.1:CDS
GGTTTGAAAGGTTCTTAACA+TGG 0.589973 8:-22810835 MsaT042486.1:CDS
TTGTTGAATCTGATATTCCA+AGG 0.592444 8:+22810804 None:intergenic
TCTCAGAGACTAACTGATGG+TGG 0.592968 8:-22807442 MsaT042486.1:CDS
GCCAGTTACCCGCCAGAGTG+AGG 0.593667 8:+22810713 None:intergenic
TAGAAGATGGAACAAGAACA+TGG 0.594815 8:-22810860 None:intergenic
TAATTACGATGCACCTGGAG+AGG 0.595408 8:-22807551 MsaT042486.1:CDS
TGCTGTGAGAGATCTTAAGA+GGG 0.596123 8:-22810515 MsaT042486.1:CDS
TGTACATAGCAGGTTCCAAA+GGG 0.596868 8:+22806973 None:intergenic
TAACAGAGACTGAACTTGCA+GGG 0.598802 8:+22808549 None:intergenic
CATTCTCAGAGACTAACTGA+TGG 0.601638 8:-22807445 MsaT042486.1:CDS
CATATACCATGGGATGAAGC+TGG 0.602506 8:-22807601 MsaT042486.1:CDS
AGATGGAACAAGAACATGGA+AGG 0.604086 8:-22810856 MsaT042486.1:CDS
CATAATAAAAGGAGGTCTGT+CGG 0.606789 8:-22806856 MsaT042486.1:CDS
AAATGGAGACAAGAATGGAA+TGG 0.608545 8:-22807491 MsaT042486.1:CDS
GCAGAGAGAATGACCAAGAG+AGG 0.631070 8:+22810748 None:intergenic
AAACAACCAGCTTCATCCCA+TGG 0.633574 8:+22807595 None:intergenic
ACTAGCTGCGTTACGACTGT+GGG 0.639311 8:-22806886 MsaT042486.1:CDS
GTTGAGAACCAGAATATGCA+AGG 0.639829 8:+22806830 None:intergenic
TTAACATGGACATCACACCT+TGG 0.645130 8:-22810821 MsaT042486.1:CDS
TCACTCTATATCCATCCCAA+CGG 0.653728 8:-22806927 MsaT042486.1:CDS
TTACCCGCCAGAGTGAGGAA+AGG 0.662573 8:+22810718 None:intergenic
GCAGCTAGTAGCGCAAACGA+AGG 0.670133 8:+22806900 None:intergenic
GCAACCCTCATAATAAAAGG+AGG 0.692096 8:-22806864 MsaT042486.1:CDS
GCTGTGAGAGATCTTAAGAG+GGG 0.713261 8:-22810514 MsaT042486.1:CDS
AATTAAACAAGTCACCAACA+GGG 0.716642 8:+22807569 None:intergenic
GTAAGGGAAAGACTTCAAGG+TGG 0.809146 8:-22808642 MsaT042486.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr8 gene 22806800 22810876 22806800 ID=MsaG042486
Chr8 mRNA 22806800 22810876 22806800 ID=MsaT042486.1;Parent=MsaG042486
Chr8 exon 22806800 22807087 22806800 ID=MsaT042486.1.exon6;Parent=MsaT042486.1
Chr8 CDS 22806800 22807087 22806800 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Chr8 exon 22807378 22807641 22807378 ID=MsaT042486.1.exon5;Parent=MsaT042486.1
Chr8 CDS 22807378 22807641 22807378 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Chr8 exon 22808295 22808435 22808295 ID=MsaT042486.1.exon4;Parent=MsaT042486.1
Chr8 CDS 22808295 22808435 22808295 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Chr8 exon 22808564 22808695 22808564 ID=MsaT042486.1.exon3;Parent=MsaT042486.1
Chr8 CDS 22808564 22808695 22808564 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Chr8 exon 22810399 22810549 22810399 ID=MsaT042486.1.exon2;Parent=MsaT042486.1
Chr8 CDS 22810399 22810549 22810399 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Chr8 exon 22810722 22810876 22810722 ID=MsaT042486.1.exon1;Parent=MsaT042486.1
Chr8 CDS 22810722 22810876 22810722 ID=cds.MsaT042486.1;Parent=MsaT042486.1
Gene Sequence

>MsaT042486.1

ATGGAACAAGAACATGGAAGGTTTGAAAGGTTCTTAACATGGACATCACACCTTGGAATATCAGATTCAACAACAACAAACACCGACCATTCTCAACACTCTCTTTCCTCTCTTGGTCATTCTCTCTGCGTTTCTACCTTTCCTCACTCTGGCGGTAGAGGTTTGGGTGCTGTGAGAGATCTTAAGAGGGGAGAAATTATTCTCAGAGTTCCAAAATCTGCTTTAATGACTAGTGAGAGTGTTATTATTGAAGATAAGAAGCTATGTCTTGCTGTGAATAGGCACTCTTCTCTCTCCTCTGTTCAGATATTGACTGTTTGCTTGTTATACGAAGTTGGTAAGGGAAAGACTTCAAGGTGGCATCCTTACCTCGTCCATTTGCCGCAAAGTTATGACTTGCTAGCCATGTTTGGTGAATTTGAGAAACAAGCCCTGCAAGTGGATGAAGCTATGTGGGTCACAGAAAAAGCTGTACAAAAAGCTAAATCAGAATGGAAAGAAGCTCATGCCTTGATGGAAGAACTGATGTTTAAGCCTCGGTTTTTAACATTTAAGGCATGGCTTTGGGCTGCTGCAACGATATCTTCTCGGACATTGCATATACCATGGGATGAAGCTGGTTGTTTATGCCCTGTTGGTGACTTGTTTAATTACGATGCACCTGGAGAGGACCTATCTGGTATTGACGACGTAGATAATTTTCAATCAAATGGAGACAAGAATGGAATGGTAGACGAAGAGCATATTGATTTTCATTCTCAGAGACTAACTGATGGTGGGTTTGAAGAAGATGCTAATGCATATTGCTTTTATGCTAGGACAAATTACAAGAAAGGCGATCAGGTTCTATTATGCTATGGAACATATACAAATTTTGAGCTTCTTGAACACTACGGATTTCTCTTACAAGAAAATCCAAATGACAAAATTTTCATCCCTTTGGAACCTGCTATGTACACTTCTACTTCATGGTCTAAGGAATCACTCTATATCCATCCCAACGGAAAACCTTCGTTTGCGCTACTAGCTGCGTTACGACTGTGGGCAACCCTCATAATAAAAGGAGGTCTGTCGGACGCCTTGCATATTCTGGTTCTCAACTGTCTGCTGACAATGAAATCATCGTTATGA
Protein sequence

>MsaT042486.1

MEQEHGRFERFLTWTSHLGISDSTTTNTDHSQHSLSSLGHSLCVSTFPHSGGRGLGAVRDLKRGEIILRVPKSALMTSESVIIEDKKLCLAVNRHSSLSSVQILTVCLLYEVGKGKTSRWHPYLVHLPQSYDLLAMFGEFEKQALQVDEAMWVTEKAVQKAKSEWKEAHALMEELMFKPRFLTFKAWLWAAATISSRTLHIPWDEAGCLCPVGDLFNYDAPGEDLSGIDDVDNFQSNGDKNGMVDEEHIDFHSQRLTDGGFEEDANAYCFYARTNYKKGDQVLLCYGTYTNFELLEHYGFLLQENPNDKIFIPLEPAMYTSTSWSKESLYIHPNGKPSFALLAALRLWATLIIKGGLSDALHILVLNCLLTMKSSL*