AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0110310

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0110310 MtrunA17_Chr7g0232811 90.783 217 16 1 11 223 275 491 1.12e-142 409
Msa0110310 MtrunA17_Chr7g0232841 89.908 218 17 2 11 223 263 480 6.07e-139 399
Msa0110310 MtrunA17_Chr7g0232981 79.263 217 27 2 11 223 266 468 7.29e-112 330
Msa0110310 MtrunA17_Chr7g0232871 92.727 110 8 0 62 171 1 110 9.95e-70 208
Msa0110310 MtrunA17_Chr5g0399801 43.651 252 95 5 5 223 804 1041 7.75e-57 194
Msa0110310 MtrunA17_Chr4g0003511 42.683 246 94 5 11 223 773 1004 3.42e-54 186
Msa0110310 MtrunA17_Chr4g0003501 42.683 246 92 5 11 223 678 907 7.26e-52 179
Msa0110310 MtrunA17_Chr7g0232751 94.366 71 4 0 153 223 1 71 9.99e-45 145
Msa0110310 MtrunA17_Chr1g0170651 31.418 261 100 5 1 223 284 503 2.53e-32 123
Msa0110310 MtrunA17_Chr8g0369301 28.287 251 132 5 7 223 482 718 1.86e-28 112
Msa0110310 MtrunA17_Chr3g0080761 30.980 255 116 8 12 222 376 614 4.57e-28 111
Msa0110310 MtrunA17_Chr7g0255181 32.389 247 106 8 12 219 436 660 1.52e-27 109
Msa0110310 MtrunA17_Chr8g0368901 28.063 253 128 7 8 223 503 738 2.39e-27 109
Msa0110310 MtrunA17_Chr8g0354821 30.159 252 119 9 12 222 403 638 1.13e-26 107
Msa0110310 MtrunA17_Chr8g0368911 27.600 250 133 7 8 223 496 731 3.70e-26 105
Msa0110310 MtrunA17_Chr5g0403241 36.913 149 65 3 76 222 1344 1465 1.44e-23 98.6
Msa0110310 MtrunA17_Chr1g0163051 27.530 247 129 7 12 223 396 627 2.16e-23 97.8
Msa0110310 MtrunA17_Chr3g0094881 25.692 253 130 7 12 223 369 604 2.79e-23 97.4
Msa0110310 MtrunA17_Chr7g0252211 30.830 253 124 8 12 223 467 709 7.76e-23 96.3
Msa0110310 MtrunA17_Chr6g0476111 31.765 255 121 9 11 223 403 646 1.79e-22 95.1
Msa0110310 MtrunA17_Chr4g0075321 35.099 151 65 3 76 222 901 1022 3.85e-22 94.4
Msa0110310 MtrunA17_Chr6g0467381 25.692 253 130 9 12 223 310 545 8.61e-22 93.2
Msa0110310 MtrunA17_Chr6g0467421 25.692 253 130 9 12 223 310 545 8.70e-22 93.2
Msa0110310 MtrunA17_Chr8g0373821 35.329 167 74 5 61 222 360 497 1.18e-21 92.8
Msa0110310 MtrunA17_Chr6g0467531 26.087 253 129 9 12 223 310 545 1.35e-21 92.4
Msa0110310 MtrunA17_Chr6g0476121 31.373 255 122 9 11 223 352 595 6.40e-21 90.9
Msa0110310 MtrunA17_Chr6g0467401 25.296 253 131 9 12 223 310 545 2.95e-20 88.6
Msa0110310 MtrunA17_Chr6g0467411 24.901 253 132 9 12 223 228 463 7.95e-20 87.4
Msa0110310 MtrunA17_Chr1g0163041 27.426 237 122 7 12 213 315 536 4.21e-18 82.4
Msa0110310 MtrunA17_Chr2g0306961 27.152 151 91 4 76 223 310 444 5.43e-16 76.3
Msa0110310 MtrunA17_Chr1g0190311 36.170 141 61 6 63 202 465 577 1.24e-14 72.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0110310 AT2G22740.2 42.339 248 93 6 12 223 509 742 6.89e-52 179
Msa0110310 AT2G22740.1 42.339 248 93 6 12 223 509 742 6.89e-52 179
Msa0110310 AT2G35160.5 40.164 244 74 5 12 223 507 710 2.45e-49 172
Msa0110310 AT2G35160.2 40.164 244 74 5 12 223 543 746 3.07e-49 172
Msa0110310 AT2G35160.3 40.164 244 74 5 12 223 543 746 3.07e-49 172
Msa0110310 AT2G35160.1 40.164 244 74 5 12 223 543 746 3.07e-49 172
Msa0110310 AT2G35160.4 40.164 244 74 5 12 223 543 746 3.07e-49 172
Msa0110310 AT5G04940.2 30.279 251 117 8 12 222 388 620 3.84e-25 103
Msa0110310 AT5G04940.1 30.279 251 117 8 12 222 388 620 3.84e-25 103
Msa0110310 AT5G13960.2 30.952 252 126 8 11 223 200 442 7.96e-25 102
Msa0110310 AT5G13960.1 30.952 252 126 8 11 223 334 576 8.58e-25 102
Msa0110310 AT1G73100.1 29.719 249 122 8 12 222 386 619 1.80e-24 101
Msa0110310 AT4G13460.1 27.126 247 132 5 12 223 386 619 1.13e-22 96.3
Msa0110310 AT4G13460.2 27.126 247 132 5 12 223 386 619 1.13e-22 96.3
Msa0110310 AT2G33290.1 24.900 249 134 6 12 223 388 620 2.16e-21 92.4
Msa0110310 AT2G33290.3 24.900 249 134 6 12 223 388 620 2.16e-21 92.4
Msa0110310 AT2G33290.4 24.900 249 134 6 12 223 388 620 2.16e-21 92.4
Msa0110310 AT2G33290.2 24.900 249 134 6 12 223 388 620 2.16e-21 92.4
Msa0110310 AT2G23740.1 33.333 147 73 3 76 222 1209 1330 1.52e-19 87.4
Msa0110310 AT2G23740.3 33.333 147 73 3 76 222 1216 1337 1.66e-19 87.4
Msa0110310 AT2G23740.6 33.333 147 73 3 76 222 1216 1337 1.66e-19 87.4
Msa0110310 AT2G23740.2 33.333 147 73 3 76 222 1216 1337 1.66e-19 87.4
Msa0110310 AT2G24740.1 26.316 247 138 6 1 219 470 700 1.49e-17 81.3
Msa0110310 AT1G17770.1 31.098 164 86 5 58 214 490 633 1.46e-16 78.6
Msa0110310 AT3G04380.6 35.714 140 60 5 63 201 257 367 1.91e-14 72.0
Msa0110310 AT3G04380.2 35.714 140 60 5 63 201 257 367 1.93e-14 72.0
Msa0110310 AT3G04380.4 35.714 140 60 5 63 201 284 394 2.03e-14 72.0
Msa0110310 AT3G04380.1 35.714 140 60 5 63 201 284 394 2.05e-14 72.0
Msa0110310 AT3G04380.5 35.714 140 60 5 63 201 241 351 2.19e-14 72.0
Msa0110310 AT3G04380.3 35.714 140 60 5 63 201 268 378 2.32e-14 72.0
Msa0110310 AT2G23740.4 32.258 124 59 3 76 199 1216 1314 1.12e-13 70.1
Msa0110310 AT2G23740.5 32.258 124 59 3 76 199 1216 1314 1.12e-13 70.1

Find 42 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCATTAGAAATATCTTTAT+AGG 0.206306 1_3:-23100249 None:intergenic
TTTACCACTTGAAGCTTCTA+AGG 0.221245 1_3:-23100714 None:intergenic
GATGAGTATTTATTTAATAT+TGG 0.247972 1_3:+23100611 Msa0110310:CDS
AACATTTCGAGCAAACAAAT+TGG 0.261209 1_3:-23100831 None:intergenic
CGAGTAATGTATTGAAAATA+TGG 0.296319 1_3:-23100323 None:intergenic
TCCTATAAAGATATTTCTAA+TGG 0.302242 1_3:+23100248 Msa0110310:CDS
ACAATTGATGCTGCTAAGTA+TGG 0.305938 1_3:+23100773 Msa0110310:CDS
TCAGAGAATGCAATTCCTTC+TGG 0.338329 1_3:+23100521 Msa0110310:CDS
GAATCTTCGAAAAGCCATTC+AGG 0.347836 1_3:-23100356 None:intergenic
CTCGTAACATTTATCCTGAA+TGG 0.372209 1_3:+23100342 Msa0110310:CDS
AGGTGAGATTATTGAAGATC+AGG 0.383100 1_3:+23100565 Msa0110310:CDS
TTCATATATGGTTGATAGTA+AGG 0.403159 1_3:+23100673 Msa0110310:CDS
ATGGGAAGAGGATTCATATA+TGG 0.412825 1_3:+23100661 Msa0110310:CDS
GTGGTTAATCGTATAGATTC+TGG 0.413281 1_3:+23100293 Msa0110310:CDS
ACAAATTGGGAGAACAACTA+TGG 0.427505 1_3:-23100817 None:intergenic
ACATTTCGAGCAAACAAATT+GGG 0.449844 1_3:-23100830 None:intergenic
ATACGATTAACCACACATAT+AGG 0.451047 1_3:-23100284 None:intergenic
TTCACAAGGTCTATAGTTCA+TGG 0.458760 1_3:+23100642 Msa0110310:CDS
CCCTCCACTCTTAAGAGCAC+AGG 0.461039 1_3:-23100417 None:intergenic
CAAGACTAAGGCGAAAGGAT+GGG 0.513493 1_3:+23100490 Msa0110310:CDS
GGTCTATAGTTCATGGGAAG+AGG 0.525490 1_3:+23100649 Msa0110310:CDS
TCAAGACTAAGGCGAAAGGA+TGG 0.530216 1_3:+23100489 Msa0110310:CDS
GCCTGTGCTCTTAAGAGTGG+AGG 0.530694 1_3:+23100416 Msa0110310:CDS
AGAAGCTTCAAGTGGTAAAG+AGG 0.540440 1_3:+23100718 Msa0110310:CDS
AAGACTAAGGCGAAAGGATG+GGG 0.542189 1_3:+23100491 Msa0110310:CDS
TTACCACTTGAAGCTTCTAA+GGG 0.542917 1_3:-23100713 None:intergenic
CTAAGTATGGTAACGTGGCA+AGG 0.558339 1_3:+23100786 Msa0110310:CDS
ATTGATGATCGATGTGATAG+TGG 0.558469 1_3:+23100743 Msa0110310:CDS
ACTATCACATCGATCATCAA+TGG 0.565161 1_3:-23100741 None:intergenic
TTTGCCTGTGCTCTTAAGAG+TGG 0.575325 1_3:+23100413 Msa0110310:CDS
CCTGTGCTCTTAAGAGTGGA+GGG 0.588175 1_3:+23100417 Msa0110310:CDS
TCACAAGGTCTATAGTTCAT+GGG 0.590256 1_3:+23100643 Msa0110310:CDS
TTTACAATGATGATGATCTG+AGG 0.599652 1_3:+23100855 Msa0110310:CDS
ATGATCGATGTGATAGTGGT+AGG 0.614728 1_3:+23100747 Msa0110310:CDS
TATTGGCAATTATATTCACA+AGG 0.615507 1_3:+23100628 Msa0110310:CDS
TAATCGTATAGATTCTGGCA+AGG 0.632162 1_3:+23100298 Msa0110310:CDS
TCACAAATAAAACTTCCAGA+AGG 0.644047 1_3:-23100536 None:intergenic
CAACCCTTAGAAGCTTCAAG+TGG 0.647600 1_3:+23100710 Msa0110310:CDS
AGAACATTTACGCCCAACAG+AGG 0.655904 1_3:-23100378 None:intergenic
GCTCATTCATGCATGATGTG+TGG 0.661940 1_3:-23100881 None:intergenic
AGAAGCTGTTCCTATATGTG+TGG 0.665038 1_3:+23100274 Msa0110310:CDS
TGCTGCTAAGTATGGTAACG+TGG 0.728265 1_3:+23100781 Msa0110310:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GATGAGTATTTATTTAATAT+TGG + chr1_3:23100611-23100630 Msa0110310:CDS 15.0%
!!! TCCTATAAAGATATTTCTAA+TGG + chr1_3:23100248-23100267 Msa0110310:CDS 20.0%
!! TCCATTAGAAATATCTTTAT+AGG - chr1_3:23100252-23100271 None:intergenic 20.0%
!!! AGTTTTATTTGTGAGTATTT+AGG + chr1_3:23100545-23100564 Msa0110310:CDS 20.0%
! CGAGTAATGTATTGAAAATA+TGG - chr1_3:23100326-23100345 None:intergenic 25.0%
!!! ATCTCATTTTTCTTTACTCT+AGG - chr1_3:23100449-23100468 None:intergenic 25.0%
! TATTGGCAATTATATTCACA+AGG + chr1_3:23100628-23100647 Msa0110310:CDS 25.0%
!!! TTCATATATGGTTGATAGTA+AGG + chr1_3:23100673-23100692 Msa0110310:CDS 25.0%
ATACGATTAACCACACATAT+AGG - chr1_3:23100287-23100306 None:intergenic 30.0%
!! GCTTCAAATTTTCAAGACTA+AGG + chr1_3:23100478-23100497 Msa0110310:CDS 30.0%
TCACAAATAAAACTTCCAGA+AGG - chr1_3:23100539-23100558 None:intergenic 30.0%
ACATTTCGAGCAAACAAATT+GGG - chr1_3:23100833-23100852 None:intergenic 30.0%
AACATTTCGAGCAAACAAAT+TGG - chr1_3:23100834-23100853 None:intergenic 30.0%
! TTTACAATGATGATGATCTG+AGG + chr1_3:23100855-23100874 Msa0110310:CDS 30.0%
GTGGTTAATCGTATAGATTC+TGG + chr1_3:23100293-23100312 Msa0110310:CDS 35.0%
TAATCGTATAGATTCTGGCA+AGG + chr1_3:23100298-23100317 Msa0110310:CDS 35.0%
CTCGTAACATTTATCCTGAA+TGG + chr1_3:23100342-23100361 Msa0110310:CDS 35.0%
! TTTTCGAAGATTCCTCTGTT+GGG + chr1_3:23100366-23100385 Msa0110310:CDS 35.0%
!! ATTTTCAAGACTAAGGCGAA+AGG + chr1_3:23100485-23100504 Msa0110310:CDS 35.0%
AGGTGAGATTATTGAAGATC+AGG + chr1_3:23100565-23100584 Msa0110310:CDS 35.0%
TTCACAAGGTCTATAGTTCA+TGG + chr1_3:23100642-23100661 Msa0110310:CDS 35.0%
TCACAAGGTCTATAGTTCAT+GGG + chr1_3:23100643-23100662 Msa0110310:CDS 35.0%
ATGGGAAGAGGATTCATATA+TGG + chr1_3:23100661-23100680 Msa0110310:CDS 35.0%
TTACCACTTGAAGCTTCTAA+GGG - chr1_3:23100716-23100735 None:intergenic 35.0%
TTTACCACTTGAAGCTTCTA+AGG - chr1_3:23100717-23100736 None:intergenic 35.0%
ACTATCACATCGATCATCAA+TGG - chr1_3:23100744-23100763 None:intergenic 35.0%
! ATTGATGATCGATGTGATAG+TGG + chr1_3:23100743-23100762 Msa0110310:CDS 35.0%
ACAATTGATGCTGCTAAGTA+TGG + chr1_3:23100773-23100792 Msa0110310:CDS 35.0%
ACAAATTGGGAGAACAACTA+TGG - chr1_3:23100820-23100839 None:intergenic 35.0%
AGAAGCTGTTCCTATATGTG+TGG + chr1_3:23100274-23100293 Msa0110310:CDS 40.0%
GAATCTTCGAAAAGCCATTC+AGG - chr1_3:23100359-23100378 None:intergenic 40.0%
! CTTTTCGAAGATTCCTCTGT+TGG + chr1_3:23100365-23100384 Msa0110310:CDS 40.0%
TCAGAGAATGCAATTCCTTC+TGG + chr1_3:23100521-23100540 Msa0110310:CDS 40.0%
AGAAGCTTCAAGTGGTAAAG+AGG + chr1_3:23100718-23100737 Msa0110310:CDS 40.0%
!! ATGATCGATGTGATAGTGGT+AGG + chr1_3:23100747-23100766 Msa0110310:CDS 40.0%
AGAACATTTACGCCCAACAG+AGG - chr1_3:23100381-23100400 None:intergenic 45.0%
TTTGCCTGTGCTCTTAAGAG+TGG + chr1_3:23100413-23100432 Msa0110310:CDS 45.0%
TCAAGACTAAGGCGAAAGGA+TGG + chr1_3:23100489-23100508 Msa0110310:CDS 45.0%
CAAGACTAAGGCGAAAGGAT+GGG + chr1_3:23100490-23100509 Msa0110310:CDS 45.0%
AAGACTAAGGCGAAAGGATG+GGG + chr1_3:23100491-23100510 Msa0110310:CDS 45.0%
GGTCTATAGTTCATGGGAAG+AGG + chr1_3:23100649-23100668 Msa0110310:CDS 45.0%
CAACCCTTAGAAGCTTCAAG+TGG + chr1_3:23100710-23100729 Msa0110310:CDS 45.0%
! TGCTGCTAAGTATGGTAACG+TGG + chr1_3:23100781-23100800 Msa0110310:CDS 45.0%
! CTAAGTATGGTAACGTGGCA+AGG + chr1_3:23100786-23100805 Msa0110310:CDS 45.0%
CCTGTGCTCTTAAGAGTGGA+GGG + chr1_3:23100417-23100436 Msa0110310:CDS 50.0%
GCCTGTGCTCTTAAGAGTGG+AGG + chr1_3:23100416-23100435 Msa0110310:CDS 55.0%
! CCCTCCACTCTTAAGAGCAC+AGG - chr1_3:23100420-23100439 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 23100224 23100901 23100224 ID=Msa0110310;Name=Msa0110310
chr1_3 mRNA 23100224 23100901 23100224 ID=Msa0110310-mRNA-1;Parent=Msa0110310;Name=Msa0110310-mRNA-1;_AED=0.16;_eAED=0.17;_QI=0|-1|0|1|-1|1|1|0|225
chr1_3 exon 23100224 23100901 23100224 ID=Msa0110310-mRNA-1:exon:8104;Parent=Msa0110310-mRNA-1
chr1_3 CDS 23100224 23100901 23100224 ID=Msa0110310-mRNA-1:cds;Parent=Msa0110310-mRNA-1
Gene Sequence

>Msa0110310

TTGGTTAATCGTAAAAGAAGCTGTTCCTATAAAGATATTTCTAATGGAAAAGAAGCTGTTCCTATATGTGTGGTTAATCGTATAGATTCTGGCAAGGTTCCATATTTTCAATACATTACTCGTAACATTTATCCTGAATGGCTTTTCGAAGATTCCTCTGTTGGGCGTAAATGTTCTGATTCAATGAAATTTGCCTGTGCTCTTAAGAGTGGAGGGAAAATTCCTAGAGTAAAGAAAAATGAGATTAAATTTAAGCTTCAAATTTTCAAGACTAAGGCGAAAGGATGGGGTGTGAGATCAGAGAATGCAATTCCTTCTGGAAGTTTTATTTGTGAGTATTTAGGTGAGATTATTGAAGATCAGGAAGCTTTGAAAATAGTTGATAATGATGAGTATTTATTTAATATTGGCAATTATATTCACAAGGTCTATAGTTCATGGGAAGAGGATTCATATATGGTTGATAGTAAGGAGATGAGTTCATATCAACCCTTAGAAGCTTCAAGTGGTAAAGAGGCCATTGATGATCGATGTGATAGTGGTAGGTTTACAATTGATGCTGCTAAGTATGGTAACGTGGCAAGGTTTATCAACCATAGTTGTTCTCCCAATTTGTTTGCTCGAAATGTTCTTTACAATGATGATGATCTGAGGATTCCACACATCATGCATGAATGA
Protein sequence

>Msa0110310

LVNRKRSCSYKDISNGKEAVPICVVNRIDSGKVPYFQYITRNIYPEWLFEDSSVGRKCSDSMKFACALKSGGKIPRVKKNEIKFKLQIFKTKAKGWGVRSENAIPSGSFICEYLGEIIEDQEALKIVDNDEYLFNIGNYIHKVYSSWEEDSYMVDSKEMSSYQPLEASSGKEAIDDRCDSGRFTIDAAKYGNVARFINHSCSPNLFARNVLYNDDDLRIPHIMHE*