AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1424970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1424970 MtrunA17_Chr4g0067271 99.099 111 1 0 1 111 1 111 2.86e-79 228
Msa1424970 MtrunA17_Chr2g0296031 76.364 110 24 2 1 109 1 109 1.25e-50 155
Msa1424970 MtrunA17_Chr1g0148141 65.138 109 36 2 1 109 1 107 5.72e-44 139
Msa1424970 MtrunA17_Chr2g0328221 49.600 125 48 5 1 111 1 124 2.25e-34 115
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1424970 AT5G24860.1 65.766 111 35 2 1 110 1 109 2.27e-47 147
Msa1424970 AT5G24860.3 65.766 111 35 2 1 110 37 145 6.66e-47 147
Msa1424970 AT5G24860.2 65.766 111 35 2 1 110 64 172 1.23e-46 148
Msa1424970 AT5G10625.1 61.818 110 41 1 1 109 1 110 5.97e-45 141
Msa1424970 AT4G31380.1 56.098 123 40 3 1 109 1 123 3.24e-41 132

Find 37 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATACACGGTGGAACGTTTA+TGG 0.252672 tig0025808:-36451 None:intergenic
ACAAGAACTATTTCCATGTT+AGG 0.272222 tig0025808:+36540 Msa1424970:CDS
TAAATATATGTCAGGGGTTT+GGG 0.311345 tig0025808:+36232 None:intergenic
TTGAGCTTGTTGAAGTCCTT+TGG 0.351336 tig0025808:-36485 None:intergenic
CTCTCACCTCCCTCACCTCC+AGG 0.355629 tig0025808:-36290 None:intergenic
ATAAATATATGTCAGGGGTT+TGG 0.360676 tig0025808:+36231 None:intergenic
TGGAACTGAAGCAGATGATC+AGG 0.409956 tig0025808:-36431 None:intergenic
GGGTTTGGGTATTTAAGAAC+GGG 0.413387 tig0025808:+36246 Msa1424970:CDS
TTGAAGAATAAATATATGTC+AGG 0.420226 tig0025808:+36224 None:intergenic
GAAGTGATAACTTCATTTGT+TGG 0.431867 tig0025808:-36350 None:intergenic
CTTGCGTTCTAGCACAGAAT+AGG 0.458659 tig0025808:-36372 None:intergenic
CAAGAACTATTTCCATGTTA+GGG 0.466756 tig0025808:+36541 Msa1424970:CDS
GTAGAGAACCCTGGAGGTGA+GGG 0.476799 tig0025808:+36281 Msa1424970:CDS
CAAGCTACAATCACTTGGTT+GGG 0.481409 tig0025808:+36391 Msa1424970:CDS
TAGTAGTGGTAGGAGTAGAA+AGG 0.485325 tig0025808:+36313 Msa1424970:CDS
GCAAGCTACAATCACTTGGT+TGG 0.494741 tig0025808:+36390 Msa1424970:CDS
GTATCTCATTTCTCTTCCAA+AGG 0.532666 tig0025808:+36469 Msa1424970:CDS
TGAAGAATAAATATATGTCA+GGG 0.534338 tig0025808:+36225 None:intergenic
GAGGGAGGTGAGAGTAGTAG+TGG 0.547254 tig0025808:+36299 Msa1424970:CDS
AGTAGAGAACCCTGGAGGTG+AGG 0.547801 tig0025808:+36280 Msa1424970:CDS
TCTACGACGTGTCCCTAACA+TGG 0.558804 tig0025808:-36553 None:intergenic
TATTTAAGAACGGGGTGGTG+AGG 0.566271 tig0025808:+36255 Msa1424970:CDS
GGGGTTTGGGTATTTAAGAA+CGG 0.569349 tig0025808:+36245 Msa1424970:CDS
GAGGTGAGAGTAGTAGTGGT+AGG 0.573664 tig0025808:+36303 Msa1424970:CDS
GAGAACCCTGGAGGTGAGGG+AGG 0.579970 tig0025808:+36284 Msa1424970:CDS
TCTCACCTCCCTCACCTCCA+GGG 0.583311 tig0025808:-36289 None:intergenic
GGTTTGGGTATTTAAGAACG+GGG 0.589791 tig0025808:+36247 Msa1424970:CDS
GACAATGTCATACATGTGCA+TGG 0.595835 tig0025808:-36510 None:intergenic
GAACGCAAGCTACAATCACT+TGG 0.612258 tig0025808:+36386 Msa1424970:CDS
ACAATGTCATACATGTGCAT+GGG 0.614527 tig0025808:-36509 None:intergenic
GAAGAATAAATATATGTCAG+GGG 0.621770 tig0025808:+36226 None:intergenic
GGAACTGAAGCAGATGATCA+GGG 0.633009 tig0025808:-36430 None:intergenic
TTGGGTATTTAAGAACGGGG+TGG 0.643727 tig0025808:+36250 Msa1424970:CDS
GTGAGGCTAGTAGAGAACCC+TGG 0.657276 tig0025808:+36272 Msa1424970:CDS
TGGAAGAGAAATGAGATACA+CGG 0.705052 tig0025808:-36465 None:intergenic
AAGAGAAATGAGATACACGG+TGG 0.764680 tig0025808:-36462 None:intergenic
AGGCTAGTAGAGAACCCTGG+AGG 0.779430 tig0025808:+36275 Msa1424970:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
GAAGTGATAACTTCATTTGT+TGG - tig0025808:36353-36372 None:intergenic 30.0%
ACAAGAACTATTTCCATGTT+AGG + tig0025808:36540-36559 Msa1424970:CDS 30.0%
CAAGAACTATTTCCATGTTA+GGG + tig0025808:36541-36560 Msa1424970:CDS 30.0%
TGGAAGAGAAATGAGATACA+CGG - tig0025808:36468-36487 None:intergenic 35.0%
GTATCTCATTTCTCTTCCAA+AGG + tig0025808:36469-36488 Msa1424970:CDS 35.0%
ACAATGTCATACATGTGCAT+GGG - tig0025808:36512-36531 None:intergenic 35.0%
GGGGTTTGGGTATTTAAGAA+CGG + tig0025808:36245-36264 Msa1424970:CDS 40.0%
GGGTTTGGGTATTTAAGAAC+GGG + tig0025808:36246-36265 Msa1424970:CDS 40.0%
GGTTTGGGTATTTAAGAACG+GGG + tig0025808:36247-36266 Msa1424970:CDS 40.0%
TAGTAGTGGTAGGAGTAGAA+AGG + tig0025808:36313-36332 Msa1424970:CDS 40.0%
CAAGCTACAATCACTTGGTT+GGG + tig0025808:36391-36410 Msa1424970:CDS 40.0%
AAGAGAAATGAGATACACGG+TGG - tig0025808:36465-36484 None:intergenic 40.0%
!! TTGAGCTTGTTGAAGTCCTT+TGG - tig0025808:36488-36507 None:intergenic 40.0%
GACAATGTCATACATGTGCA+TGG - tig0025808:36513-36532 None:intergenic 40.0%
TTGGGTATTTAAGAACGGGG+TGG + tig0025808:36250-36269 Msa1424970:CDS 45.0%
TATTTAAGAACGGGGTGGTG+AGG + tig0025808:36255-36274 Msa1424970:CDS 45.0%
CTTGCGTTCTAGCACAGAAT+AGG - tig0025808:36375-36394 None:intergenic 45.0%
GAACGCAAGCTACAATCACT+TGG + tig0025808:36386-36405 Msa1424970:CDS 45.0%
GCAAGCTACAATCACTTGGT+TGG + tig0025808:36390-36409 Msa1424970:CDS 45.0%
GGAACTGAAGCAGATGATCA+GGG - tig0025808:36433-36452 None:intergenic 45.0%
TGGAACTGAAGCAGATGATC+AGG - tig0025808:36434-36453 None:intergenic 45.0%
GATACACGGTGGAACGTTTA+TGG - tig0025808:36454-36473 None:intergenic 45.0%
GAGGTGAGAGTAGTAGTGGT+AGG + tig0025808:36303-36322 Msa1424970:CDS 50.0%
GTGAGGCTAGTAGAGAACCC+TGG + tig0025808:36272-36291 Msa1424970:CDS 55.0%
AGGCTAGTAGAGAACCCTGG+AGG + tig0025808:36275-36294 Msa1424970:CDS 55.0%
AGTAGAGAACCCTGGAGGTG+AGG + tig0025808:36280-36299 Msa1424970:CDS 55.0%
GTAGAGAACCCTGGAGGTGA+GGG + tig0025808:36281-36300 Msa1424970:CDS 55.0%
GAGGGAGGTGAGAGTAGTAG+TGG + tig0025808:36299-36318 Msa1424970:CDS 55.0%
TCTCACCTCCCTCACCTCCA+GGG - tig0025808:36292-36311 None:intergenic 60.0%
GAGAACCCTGGAGGTGAGGG+AGG + tig0025808:36284-36303 Msa1424970:CDS 65.0%
CTCTCACCTCCCTCACCTCC+AGG - tig0025808:36293-36312 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
tig0025808 gene 36239 36574 36239 ID=Msa1424970;Name=Msa1424970
tig0025808 mRNA 36239 36574 36239 ID=Msa1424970-mRNA-1;Parent=Msa1424970;Name=Msa1424970-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|111
tig0025808 exon 36239 36574 36239 ID=Msa1424970-mRNA-1:exon:4059;Parent=Msa1424970-mRNA-1
tig0025808 CDS 36239 36574 36239 ID=Msa1424970-mRNA-1:cds;Parent=Msa1424970-mRNA-1
Gene Sequence

>Msa1424970

ATGTCAGGGGTTTGGGTATTTAAGAACGGGGTGGTGAGGCTAGTAGAGAACCCTGGAGGTGAGGGAGGTGAGAGTAGTAGTGGTAGGAGTAGAAAGGTGCTTGTATACACACCAACAAATGAAGTTATCACTTCCTATTCTGTGCTAGAACGCAAGCTACAATCACTTGGTTGGGAACGTTATTATGATGACCCTGATCATCTGCTTCAGTTCCATAAACGTTCCACCGTGTATCTCATTTCTCTTCCAAAGGACTTCAACAAGCTCAAGCCCATGCACATGTATGACATTGTCGTCAAGAACAAGAACTATTTCCATGTTAGGGACACGTCGTAG
Protein sequence

>Msa1424970

MSGVWVFKNGVVRLVENPGGEGGESSSGRSRKVLVYTPTNEVITSYSVLERKLQSLGWERYYDDPDHLLQFHKRSTVYLISLPKDFNKLKPMHMYDIVVKNKNYFHVRDTS*