AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0645340

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0645340 MtrunA17_Chr5g0410931 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr5g0410951 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr8g0383851 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr8g0383781 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr8g0390361 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr2g0295191 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr7g0237661 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr4g0033041 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr7g0218971 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr4g0046301 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr8g0364801 100.000 136 0 0 1 136 1 136 3.79e-96 272
Msa0645340 MtrunA17_Chr4g0054161 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0645340 MtrunA17_Chr8g0363741 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0645340 MtrunA17_Chr1g0156021 97.059 136 4 0 1 136 1 136 2.60e-93 265
Msa0645340 MtrunA17_Chr4g0054151 97.059 136 4 0 1 136 4 139 2.61e-93 265
Msa0645340 MtrunA17_Chr8g0388121 96.324 136 5 0 1 136 1 136 1.09e-92 264
Msa0645340 MtrunA17_Chr2g0319141 89.706 136 14 0 1 136 1 136 1.10e-86 248
Msa0645340 MtrunA17_Chr2g0319151 89.706 136 14 0 1 136 1 136 1.10e-86 248
Msa0645340 MtrunA17_Chr2g0319131 85.616 146 11 1 1 136 1 146 1.38e-82 238
Msa0645340 MtrunA17_Chr2g0319121 84.559 136 19 2 1 135 1 135 5.82e-75 219
Msa0645340 MtrunA17_Chr7g0218961 86.607 112 15 0 25 136 2 113 8.01e-66 195
Msa0645340 MtrunA17_Chr7g0222991 67.164 134 43 1 1 134 10 142 5.47e-56 171
Msa0645340 MtrunA17_Chr5g0407311 67.241 116 35 2 1 116 1 113 1.29e-45 144
Msa0645340 MtrunA17_Chr7g0223001 58.647 133 41 3 3 134 27 146 5.46e-43 139
Msa0645340 MtrunA17_Chr7g0240791 100.000 66 0 0 1 66 1 66 9.61e-41 133
Msa0645340 MtrunA17_Chr8g0347231 55.102 98 43 1 37 133 28 125 3.80e-30 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0645340 AT1G09200.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0645340 AT5G65360.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0645340 AT5G10390.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0645340 AT5G10400.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0645340 AT3G27360.1 99.265 136 1 0 1 136 1 136 1.62e-95 271
Msa0645340 AT4G40030.3 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40030.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40030.4 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT5G10980.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40040.2 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40040.3 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40040.1 97.059 136 4 0 1 136 1 136 3.59e-93 265
Msa0645340 AT4G40030.2 97.059 136 4 0 1 136 29 164 7.05e-93 266
Msa0645340 AT5G65350.1 94.853 136 7 0 1 136 1 136 5.30e-91 260
Msa0645340 AT1G75600.1 93.382 136 9 0 1 136 1 136 1.25e-89 256
Msa0645340 AT1G13370.1 93.382 136 9 0 1 136 1 136 5.55e-89 254
Msa0645340 AT1G19890.1 89.781 137 13 1 1 136 1 137 1.07e-83 241
Msa0645340 AT5G12910.1 71.111 135 34 2 1 135 1 130 9.90e-67 198
Msa0645340 AT1G01370.2 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0645340 AT1G01370.1 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0645340 AT1G01370.4 53.982 113 49 2 24 134 63 174 2.97e-31 110
Msa0645340 AT1G01370.3 53.982 113 49 2 24 134 63 174 2.97e-31 110

Find 41 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGGTGGCAGGGGCGGATTTC+CGG 0.134660 4_3:+50318489 None:intergenic
TTCTTCACTCCGCCGGTGGC+AGG 0.276212 4_3:+50318476 None:intergenic
CTGAATATCCTTGGGCATAA+TGG 0.311342 4_3:+50318211 None:intergenic
TTCACGAAGTGCGACGGTTC+CGG 0.340741 4_3:+50318436 None:intergenic
TCACGAAGTGCGACGGTTCC+GGG 0.351546 4_3:+50318437 None:intergenic
GGTGGCAGGGGCGGATTTCC+GGG 0.352082 4_3:+50318490 None:intergenic
GAGCGGAAACAGCGCTGCTC+TGG 0.355901 4_3:+50318312 None:intergenic
AATCAGAGGCGAGAGGGCTT+AGG 0.382682 4_3:-50318177 None:intergenic
TCTTGCAAGCTGAATATCCT+TGG 0.414477 4_3:+50318202 None:intergenic
ATCAGAGGCGAGAGGGCTTA+GGG 0.424667 4_3:-50318176 None:intergenic
TCTTCACTCCGCCGGTGGCA+GGG 0.430381 4_3:+50318477 None:intergenic
CGGAAATCCGCCCCTGCCAC+CGG 0.446613 4_3:-50318488 Msa0645340:CDS
CTTCACTCCGCCGGTGGCAG+GGG 0.448918 4_3:+50318478 None:intergenic
CACGAACAAGACGTTGGAAT+GGG 0.458543 4_3:+50318369 None:intergenic
CTTGCAAGCTGAATATCCTT+GGG 0.468025 4_3:+50318203 None:intergenic
CACTCCGCCGGTGGCAGGGG+CGG 0.471645 4_3:+50318481 None:intergenic
AAACAGCGCTGCTCTGGAAA+CGG 0.476540 4_3:+50318318 None:intergenic
CGACGGTTCCGGGACGGAAA+CGG 0.513929 4_3:+50318447 None:intergenic
GCTGCTGAAGCTTATCTCGT+TGG 0.533530 4_3:-50318281 Msa0645340:CDS
AAACCTCACCGTTTCCGTCC+CGG 0.544193 4_3:-50318455 Msa0645340:CDS
GCGGATTTCACGAAGTGCGA+CGG 0.544208 4_3:+50318430 None:intergenic
TCTTGTTCGTGAAATCGCTC+AGG 0.549771 4_3:-50318357 Msa0645340:CDS
GTGAGGTTTCTTCACTCCGC+CGG 0.553823 4_3:+50318469 None:intergenic
TCACGAACAAGACGTTGGAA+TGG 0.558382 4_3:+50318368 None:intergenic
AGGTTTCTTCACTCCGCCGG+TGG 0.571477 4_3:+50318472 None:intergenic
GGCAGGGGCGGATTTCCGGG+CGG 0.573268 4_3:+50318493 None:intergenic
TTCAGCAGCTTCTTGAAGAG+CGG 0.576635 4_3:+50318295 None:intergenic
AAGAAGAATCAGAGGCGAGA+GGG 0.597241 4_3:-50318183 Msa0645340:CDS
AAATCCGCCCCTGCCACCGG+CGG 0.597314 4_3:-50318485 Msa0645340:CDS
GAGAGTTACCATTATGCCCA+AGG 0.602637 4_3:-50318219 Msa0645340:CDS
CAAACCGCTCGCAAATCCAC+CGG 0.612149 4_3:-50318551 Msa0645340:CDS
AGCATGAATAGCGCAAAGGT+TGG 0.613099 4_3:+50318244 None:intergenic
CGATTTCACGAACAAGACGT+TGG 0.613448 4_3:+50318363 None:intergenic
AACTTGCCACAAAAGCCGCC+CGG 0.618659 4_3:-50318508 Msa0645340:CDS
TCCTCCGGTGGATTTGCGAG+CGG 0.642208 4_3:+50318547 None:intergenic
CAAGAAGAATCAGAGGCGAG+AGG 0.648850 4_3:-50318184 Msa0645340:CDS
GAAGTGCGACGGTTCCGGGA+CGG 0.649162 4_3:+50318441 None:intergenic
TCTTAGCATGAATAGCGCAA+AGG 0.658330 4_3:+50318240 None:intergenic
CAGCTTGCAAGAAGAATCAG+AGG 0.660238 4_3:-50318191 Msa0645340:CDS
ACCGCTCGCAAATCCACCGG+AGG 0.664410 4_3:-50318548 Msa0645340:CDS
GTTCCGGGACGGAAACGGTG+AGG 0.671031 4_3:+50318452 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTGTGGCAAGTTGTTTTCT+TGG + chr4_3:50318229-50318248 None:intergenic 35.0%
!!! CTGTGCTTTTTTGGTATTTG+CGG + chr4_3:50318336-50318355 None:intergenic 35.0%
!!! TTTTCTTGGTGCTTTTCCTC+CGG + chr4_3:50318215-50318234 None:intergenic 40.0%
!!! TGAGAAGCTCTGTGCTTTTT+TGG + chr4_3:50318345-50318364 None:intergenic 40.0%
TCTTAGCATGAATAGCGCAA+AGG + chr4_3:50318507-50318526 None:intergenic 40.0%
CTGAATATCCTTGGGCATAA+TGG + chr4_3:50318536-50318555 None:intergenic 40.0%
CTTGCAAGCTGAATATCCTT+GGG + chr4_3:50318544-50318563 None:intergenic 40.0%
TCTTGCAAGCTGAATATCCT+TGG + chr4_3:50318545-50318564 None:intergenic 40.0%
! GACGTTGGAATGGGAGTTTT+CGG + chr4_3:50318369-50318388 None:intergenic 45.0%
CACGAACAAGACGTTGGAAT+GGG + chr4_3:50318378-50318397 None:intergenic 45.0%
TCACGAACAAGACGTTGGAA+TGG + chr4_3:50318379-50318398 None:intergenic 45.0%
CGATTTCACGAACAAGACGT+TGG + chr4_3:50318384-50318403 None:intergenic 45.0%
TCTTGTTCGTGAAATCGCTC+AGG - chr4_3:50318387-50318406 Msa0645340:CDS 45.0%
TTCAGCAGCTTCTTGAAGAG+CGG + chr4_3:50318452-50318471 None:intergenic 45.0%
AGCATGAATAGCGCAAAGGT+TGG + chr4_3:50318503-50318522 None:intergenic 45.0%
GAGAGTTACCATTATGCCCA+AGG - chr4_3:50318525-50318544 Msa0645340:CDS 45.0%
CAGCTTGCAAGAAGAATCAG+AGG - chr4_3:50318553-50318572 Msa0645340:CDS 45.0%
AAGAAGAATCAGAGGCGAGA+GGG - chr4_3:50318561-50318580 Msa0645340:CDS 45.0%
!! AAACAGCGCTGCTCTGGAAA+CGG + chr4_3:50318429-50318448 None:intergenic 50.0%
GCTGCTGAAGCTTATCTCGT+TGG - chr4_3:50318463-50318482 Msa0645340:CDS 50.0%
CAAGAAGAATCAGAGGCGAG+AGG - chr4_3:50318560-50318579 Msa0645340:CDS 50.0%
CAAACCGCTCGCAAATCCAC+CGG - chr4_3:50318193-50318212 Msa0645340:CDS 55.0%
!!! TCTTGGTGCTTTTCCTCCGG+TGG + chr4_3:50318212-50318231 None:intergenic 55.0%
AACTTGCCACAAAAGCCGCC+CGG - chr4_3:50318236-50318255 Msa0645340:CDS 55.0%
GTGAGGTTTCTTCACTCCGC+CGG + chr4_3:50318278-50318297 None:intergenic 55.0%
AAACCTCACCGTTTCCGTCC+CGG - chr4_3:50318289-50318308 Msa0645340:CDS 55.0%
TTCACGAAGTGCGACGGTTC+CGG + chr4_3:50318311-50318330 None:intergenic 55.0%
GCGGATTTCACGAAGTGCGA+CGG + chr4_3:50318317-50318336 None:intergenic 55.0%
! TCCTCCGGTGGATTTGCGAG+CGG + chr4_3:50318200-50318219 None:intergenic 60.0%
! GGATTTCCGGGCGGCTTTTG+TGG + chr4_3:50318245-50318264 None:intergenic 60.0%
AGGTTTCTTCACTCCGCCGG+TGG + chr4_3:50318275-50318294 None:intergenic 60.0%
TCACGAAGTGCGACGGTTCC+GGG + chr4_3:50318310-50318329 None:intergenic 60.0%
ACCGCTCGCAAATCCACCGG+AGG - chr4_3:50318196-50318215 Msa0645340:CDS 65.0%
TCTTCACTCCGCCGGTGGCA+GGG + chr4_3:50318270-50318289 None:intergenic 65.0%
TTCTTCACTCCGCCGGTGGC+AGG + chr4_3:50318271-50318290 None:intergenic 65.0%
GTTCCGGGACGGAAACGGTG+AGG + chr4_3:50318295-50318314 None:intergenic 65.0%
CGACGGTTCCGGGACGGAAA+CGG + chr4_3:50318300-50318319 None:intergenic 65.0%
GAAGTGCGACGGTTCCGGGA+CGG + chr4_3:50318306-50318325 None:intergenic 65.0%
GAGCGGAAACAGCGCTGCTC+TGG + chr4_3:50318435-50318454 None:intergenic 65.0%
! GGTGGCAGGGGCGGATTTCC+GGG + chr4_3:50318257-50318276 None:intergenic 70.0%
! CGGTGGCAGGGGCGGATTTC+CGG + chr4_3:50318258-50318277 None:intergenic 70.0%
CGGAAATCCGCCCCTGCCAC+CGG - chr4_3:50318256-50318275 Msa0645340:CDS 70.0%
AAATCCGCCCCTGCCACCGG+CGG - chr4_3:50318259-50318278 Msa0645340:CDS 70.0%
CTTCACTCCGCCGGTGGCAG+GGG + chr4_3:50318269-50318288 None:intergenic 70.0%
! GGCAGGGGCGGATTTCCGGG+CGG + chr4_3:50318254-50318273 None:intergenic 75.0%
! CACTCCGCCGGTGGCAGGGG+CGG + chr4_3:50318266-50318285 None:intergenic 80.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 50318178 50318588 50318178 ID=Msa0645340;Name=Msa0645340
chr4_3 mRNA 50318178 50318588 50318178 ID=Msa0645340-mRNA-1;Parent=Msa0645340;Name=Msa0645340-mRNA-1;_AED=0.41;_eAED=0.41;_QI=0|-1|0|1|-1|1|1|0|136
chr4_3 exon 50318178 50318588 50318178 ID=Msa0645340-mRNA-1:exon:12008;Parent=Msa0645340-mRNA-1
chr4_3 CDS 50318178 50318588 50318178 ID=Msa0645340-mRNA-1:cds;Parent=Msa0645340-mRNA-1
Gene Sequence

>Msa0645340

ATGGCGCGTACAAAGCAAACCGCTCGCAAATCCACCGGAGGAAAAGCACCAAGAAAACAACTTGCCACAAAAGCCGCCCGGAAATCCGCCCCTGCCACCGGCGGAGTGAAGAAACCTCACCGTTTCCGTCCCGGAACCGTCGCACTTCGTGAAATCCGCAAATACCAAAAAAGCACAGAGCTTCTCATCCGAAAACTCCCATTCCAACGTCTTGTTCGTGAAATCGCTCAGGATTTCAAAACTGATCTCCGTTTCCAGAGCAGCGCTGTTTCCGCTCTTCAAGAAGCTGCTGAAGCTTATCTCGTTGGACTCTTTGAAGATACCAACCTTTGCGCTATTCATGCTAAGAGAGTTACCATTATGCCCAAGGATATTCAGCTTGCAAGAAGAATCAGAGGCGAGAGGGCTTAG
Protein sequence

>Msa0645340

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVSALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA*