AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0252970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0252970 MtrunA17_Chr2g0311861 88.136 59 7 0 1 59 289 347 1.18e-31 111
Msa0252970 MtrunA17_Chr2g0311831 76.271 59 14 0 1 59 313 371 7.42e-27 99.4
Msa0252970 MtrunA17_Chr8g0336761 66.102 59 20 0 1 59 306 364 3.65e-23 89.4
Msa0252970 MtrunA17_Chr2g0311761 67.797 59 19 0 1 59 314 372 5.04e-23 89.0
Msa0252970 MtrunA17_Chr8g0348081 66.102 59 20 0 1 59 306 364 2.82e-22 86.7
Msa0252970 MtrunA17_Chr8g0336841 59.322 59 24 0 1 59 33 91 3.07e-22 81.3
Msa0252970 MtrunA17_Chr8g0336781 64.407 59 21 0 1 59 342 400 3.16e-22 87.0
Msa0252970 MtrunA17_Chr8g0336801 61.017 59 23 0 1 59 98 156 4.46e-22 82.4
Msa0252970 MtrunA17_Chr8g0336861 65.000 60 20 1 1 59 307 366 5.34e-22 85.9
Msa0252970 MtrunA17_Chr8g0336851 62.712 59 22 0 1 59 306 364 5.83e-22 85.9
Msa0252970 MtrunA17_Chr8g0336631 61.017 59 23 0 1 59 307 365 2.82e-20 81.3
Msa0252970 MtrunA17_Chr8g0336871 62.500 56 21 0 1 56 116 171 9.28e-20 77.0
Msa0252970 MtrunA17_Chr2g0311921 57.627 59 25 0 1 59 300 358 1.13e-19 79.7
Msa0252970 MtrunA17_Chr7g0236011 71.739 46 13 0 14 59 328 373 2.50e-17 73.2
Msa0252970 MtrunA17_Chr8g0336751 65.217 46 16 0 14 59 352 397 1.67e-16 71.2
Msa0252970 MtrunA17_Chr7g0225881 69.565 46 14 0 14 59 325 370 2.02e-16 70.9
Msa0252970 MtrunA17_Chr4g0066991 63.265 49 18 0 11 59 305 353 2.27e-16 70.5
Msa0252970 MtrunA17_Chr7g0235951 63.043 46 17 0 14 59 328 373 1.04e-15 68.9
Msa0252970 MtrunA17_Chr1g0167951 58.696 46 19 0 14 59 310 355 5.19e-15 66.6
Msa0252970 MtrunA17_Chr8g0335411 63.043 46 17 0 14 59 328 373 7.21e-15 66.2
Msa0252970 MtrunA17_Chr6g0472861 63.043 46 17 0 14 59 328 373 1.06e-14 65.9
Msa0252970 MtrunA17_Chr8g0354241 50.000 60 29 1 1 59 315 374 2.82e-14 64.7
Msa0252970 MtrunA17_Chr4g0066121 52.542 59 27 1 2 59 308 366 6.02e-14 63.9
Msa0252970 MtrunA17_Chr2g0311741 62.222 45 16 1 15 59 284 327 1.39e-13 62.8
Msa0252970 MtrunA17_Chr8g0364471 57.143 49 21 0 11 59 325 373 1.41e-13 62.8
Msa0252970 MtrunA17_Chr1g0187811 53.704 54 22 1 9 59 440 493 2.16e-13 62.4
Msa0252970 MtrunA17_Chr1g0187831 55.102 49 22 0 10 58 325 373 4.30e-13 61.6
Msa0252970 MtrunA17_Chr7g0235981 58.696 46 19 0 14 59 282 327 1.07e-12 60.1
Msa0252970 MtrunA17_Chr8g0354261 48.333 60 30 1 1 59 315 374 1.39e-12 60.1
Msa0252970 MtrunA17_Chr1g0167931 45.763 59 32 0 1 59 260 318 3.80e-12 58.5
Msa0252970 MtrunA17_Chr1g0187821 58.696 46 19 0 14 59 325 370 4.43e-12 58.5
Msa0252970 MtrunA17_Chr2g0311701 59.574 47 18 1 13 59 330 375 1.09e-11 57.4
Msa0252970 MtrunA17_Chr4g0055591 54.348 46 21 0 14 59 316 361 2.29e-11 56.6
Msa0252970 MtrunA17_Chr1g0184241 42.623 61 26 1 8 59 307 367 3.73e-11 55.8
Msa0252970 MtrunA17_Chr1g0167961 44.068 59 33 0 1 59 314 372 7.72e-11 55.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0252970 AT1G06650.2 59.322 59 24 0 1 59 311 369 3.01e-20 81.6
Msa0252970 AT1G06645.1 62.000 50 19 0 10 59 330 379 1.47e-17 74.3
Msa0252970 AT1G06640.1 52.542 59 28 0 1 59 311 369 5.90e-16 69.7
Msa0252970 AT1G06620.1 45.763 59 32 0 1 59 307 365 7.02e-14 63.9
Msa0252970 AT2G30830.1 55.319 47 21 0 13 59 312 358 1.28e-13 63.2
Msa0252970 AT1G04380.1 45.763 59 32 0 1 59 287 345 2.54e-13 62.4
Msa0252970 AT5G59530.1 50.000 50 25 0 10 59 315 364 1.51e-12 60.5
Msa0252970 AT2G30840.1 50.980 51 25 0 9 59 312 362 6.84e-12 58.5
Msa0252970 AT2G30840.3 50.980 51 25 0 9 59 306 356 7.58e-12 58.2
Msa0252970 AT1G04350.1 50.000 50 25 0 10 59 311 360 1.88e-11 57.4
Msa0252970 AT5G59540.1 44.000 50 28 0 10 59 317 366 3.37e-11 56.6

Find 8 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TACAATGCAAAAGGGCTTGA+TGG 0.364835 2_2:-44546896 Msa0252970:CDS
AAAGTGGTTTCTCTGTATCT+TGG 0.427856 2_2:+44546938 None:intergenic
GTAGCCTACTACAATGCAAA+AGG 0.455727 2_2:-44546905 Msa0252970:CDS
GTGGTTTCTCTGTATCTTGG+AGG 0.498258 2_2:+44546941 None:intergenic
TGGTTTCTCTGTATCTTGGA+GGG 0.506798 2_2:+44546942 None:intergenic
GGCTACGAAATCTGCAAAAG+TGG 0.540121 2_2:+44546922 None:intergenic
TAGCCTACTACAATGCAAAA+GGG 0.606591 2_2:-44546904 Msa0252970:CDS
ATGAAATGGCTTGTGTGCCA+AGG 0.659120 2_2:-44547305 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TCTGATAACAATTCTTTTAT+AGG + chr2_2:44547197-44547216 None:intergenic 20.0%
ATCATATTCCTGTGATTGTA+AGG - chr2_2:44546940-44546959 Msa0252970:CDS 30.0%
! AGAGTACTAGCAAATACTAT+TGG - chr2_2:44547107-44547126 Msa0252970:intron 30.0%
!!! TATCTGTTGCATCTTTTTTC+AGG - chr2_2:44547138-44547157 Msa0252970:intron 30.0%
!!! ATCTGTTGCATCTTTTTTCA+GGG - chr2_2:44547139-44547158 Msa0252970:intron 30.0%
!!! TAGATTTTTTCTTGTGCTCT+AGG + chr2_2:44547170-44547189 None:intergenic 30.0%
AGAGCACAAGAAAAAATCTA+TGG - chr2_2:44547170-44547189 Msa0252970:intron 30.0%
TATTCAGCATCAACATACCT+TGG + chr2_2:44546880-44546899 None:intergenic 35.0%
TCACAATTTGAAGATGCAAG+AGG + chr2_2:44546912-44546931 None:intergenic 35.0%
TGCATCTTCAAATTGTGATG+AGG - chr2_2:44546914-44546933 Msa0252970:CDS 35.0%
AAAGATGCAACAGATACTCT+TGG + chr2_2:44547134-44547153 None:intergenic 35.0%
AAAGTGGTTTCTCTGTATCT+TGG + chr2_2:44547230-44547249 None:intergenic 35.0%
TAGCCTACTACAATGCAAAA+GGG - chr2_2:44547261-44547280 Msa0252970:intron 35.0%
! GCTTTTCACCTTACAATCAC+AGG + chr2_2:44546951-44546970 None:intergenic 40.0%
TGGTTTCTCTGTATCTTGGA+GGG + chr2_2:44547226-44547245 None:intergenic 40.0%
GTAGCCTACTACAATGCAAA+AGG - chr2_2:44547260-44547279 Msa0252970:intron 40.0%
! AAGCCCTTTTGCATTGTAGT+AGG + chr2_2:44547267-44547286 None:intergenic 40.0%
TACAATGCAAAAGGGCTTGA+TGG - chr2_2:44547269-44547288 Msa0252970:intron 40.0%
!!! GTTGCATCTTTTTTCAGGGC+AGG - chr2_2:44547143-44547162 Msa0252970:intron 45.0%
GTGGTTTCTCTGTATCTTGG+AGG + chr2_2:44547227-44547246 None:intergenic 45.0%
GGCTACGAAATCTGCAAAAG+TGG + chr2_2:44547246-44547265 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 44546865 44547322 44546865 ID=Msa0252970;Name=Msa0252970
chr2_2 mRNA 44546865 44547322 44546865 ID=Msa0252970-mRNA-1;Parent=Msa0252970;Name=Msa0252970-mRNA-1;_AED=0.50;_eAED=0.51;_QI=0|0|0|0.5|1|1|2|0|59
chr2_2 exon 44547306 44547322 44547306 ID=Msa0252970-mRNA-1:exon:13683;Parent=Msa0252970-mRNA-1
chr2_2 exon 44546865 44547027 44546865 ID=Msa0252970-mRNA-1:exon:13682;Parent=Msa0252970-mRNA-1
chr2_2 CDS 44547306 44547322 44547306 ID=Msa0252970-mRNA-1:cds;Parent=Msa0252970-mRNA-1
chr2_2 CDS 44546865 44547027 44546865 ID=Msa0252970-mRNA-1:cds;Parent=Msa0252970-mRNA-1
Gene Sequence

>Msa0252970

ATGGCTTGTGTGCCAAGGGCAGGTCCTAGAGCACAAGAAAAAATCTATGGACCTATAAAAGAATTGTTATCAGAAGACAACCCTCCAAGATACAGAGAAACCACTTTTGCAGATTTCGTAGCCTACTACAATGCAAAAGGGCTTGATGGCATCTCAGCTCTTGAACATTTCAAGCTTTGA
Protein sequence

>Msa0252970

MACVPRAGPRAQEKIYGPIKELLSEDNPPRYRETTFADFVAYYNAKGLDGISALEHFKL*