AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0428010


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0428010 MtrunA17_Chr3g0130641 95.556 90 4 0 1 90 388 477 8.40e-55 176
Msa0428010 MtrunA17_Chr3g0125081 66.667 90 30 0 1 90 390 479 4.83e-40 137
Msa0428010 MtrunA17_Chr3g0130661 68.966 87 27 0 1 87 92 178 9.46e-40 129
Msa0428010 MtrunA17_Chr3g0125101 65.556 90 31 0 1 90 391 480 7.67e-39 134
Msa0428010 MtrunA17_Chr3g0125091 64.444 90 32 0 1 90 391 480 1.52e-37 130
Msa0428010 MtrunA17_Chr8g0384661 62.500 88 33 0 3 90 407 494 2.00e-36 127
Msa0428010 MtrunA17_Chr4g0037201 58.889 90 37 0 1 90 423 512 1.55e-35 125
Msa0428010 MtrunA17_Chr1g0159761 58.889 90 37 0 1 90 386 475 1.34e-30 112
Msa0428010 MtrunA17_Chr1g0206821 56.180 89 39 0 1 89 442 530 1.08e-29 109
Msa0428010 MtrunA17_Chr1g0206851 52.874 87 41 0 1 87 292 378 1.77e-29 107
Msa0428010 MtrunA17_Chr3g0130651 73.563 87 23 0 1 87 379 465 1.89e-28 105
Msa0428010 MtrunA17_Chr3g0140761 47.191 89 47 0 1 89 393 481 9.84e-27 101
Msa0428010 MtrunA17_Chr1g0206871 49.438 89 45 0 1 89 382 470 1.74e-26 100
Msa0428010 MtrunA17_Chr1g0146491 48.315 89 46 0 1 89 383 471 7.69e-26 99.0
Msa0428010 MtrunA17_Chr1g0206831 54.321 81 37 0 1 81 255 335 9.49e-26 97.4
Msa0428010 MtrunA17_Chr5g0447221 54.430 79 36 0 1 79 385 463 2.53e-25 97.4
Msa0428010 MtrunA17_Chr3g0140531 47.674 86 45 0 1 86 382 467 1.30e-24 95.5
Msa0428010 MtrunA17_Chr3g0103251 51.899 79 38 0 1 79 292 370 6.39e-24 92.8
Msa0428010 MtrunA17_Chr3g0103231 51.899 79 38 0 1 79 379 457 7.79e-24 93.2
Msa0428010 MtrunA17_Chr3g0140541 47.500 80 42 0 7 86 387 466 6.51e-23 90.9
Msa0428010 MtrunA17_Chr3g0103211 48.101 79 41 0 1 79 379 457 1.31e-22 89.7
Msa0428010 MtrunA17_Chr3g0103221 49.367 79 40 0 1 79 386 464 1.38e-22 89.7
Msa0428010 MtrunA17_Chr1g0146391 45.977 87 47 0 1 87 368 454 1.94e-21 86.7
Msa0428010 MtrunA17_Chr1g0146331 42.529 87 50 0 1 87 377 463 3.32e-21 85.9
Msa0428010 MtrunA17_Chr2g0293331 41.379 87 51 0 1 87 368 454 7.28e-20 82.0
Msa0428010 MtrunA17_Chr1g0146411 39.286 84 51 0 3 86 386 469 2.96e-19 80.5
Msa0428010 MtrunA17_Chr3g0103271 46.667 75 40 0 4 78 387 461 1.01e-18 79.0
Msa0428010 MtrunA17_Chr5g0447231 34.211 76 50 0 4 79 385 460 1.55e-15 70.1
Msa0428010 MtrunA17_Chr1g0184721 34.444 90 55 1 1 86 348 437 8.59e-12 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0428010 AT1G44100.1 60.000 90 36 0 1 90 391 480 4.89e-37 129
Msa0428010 AT5G09220.1 61.111 90 35 0 1 90 404 493 9.26e-37 129
Msa0428010 AT5G63850.1 57.778 90 38 0 1 90 377 466 6.12e-35 124
Msa0428010 AT1G77380.1 62.222 90 34 0 1 90 387 476 4.27e-33 119
Msa0428010 AT5G49630.1 56.818 88 38 0 1 88 393 480 7.26e-30 110
Msa0428010 AT1G58360.1 53.333 90 42 0 1 90 395 484 1.95e-29 109
Msa0428010 AT1G10010.1 53.409 88 41 0 1 88 386 473 5.33e-29 107
Msa0428010 AT1G10010.2 53.409 88 41 0 1 88 387 474 5.42e-29 107
Msa0428010 AT5G23810.1 55.172 58 26 0 1 58 386 443 8.88e-17 73.9

Find 22 sgRNAs with CRISPR-Local

Find 23 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCATTTAGAACTCCATTT+TGG 0.108522 3_2:-78735091 None:intergenic
TCCTTTCTTTAATGATGTTC+TGG 0.137749 3_2:+78734991 Msa0428010:CDS
TTCTTGGAGCAGTGGGATTT+TGG 0.180772 3_2:+78735017 Msa0428010:CDS
AATGATGTTCTGGGATTTCT+TGG 0.212555 3_2:+78735001 Msa0428010:CDS
ACTGGATAATAAACTGTTAA+AGG 0.224075 3_2:-78735040 None:intergenic
CCTTTCTTTAATGATGTTCT+GGG 0.306108 3_2:+78734992 Msa0428010:CDS
TCCCAAAATGGAGTTCTAAA+TGG 0.320619 3_2:+78735089 Msa0428010:CDS
TGAATGGCTTGTAATGCTTT+AGG 0.330057 3_2:-78735195 None:intergenic
GTATCAGTTGTGGCTGCTCT+TGG 0.389248 3_2:+78735148 Msa0428010:CDS
CTTTAGGTCCTCTATAATAC+TGG 0.396377 3_2:-78735179 None:intergenic
CTGGGATTTCTTGGAGCAGT+GGG 0.412618 3_2:+78735010 Msa0428010:CDS
TGCAAAGGAAGATCCCAAAA+TGG 0.417168 3_2:+78735077 Msa0428010:CDS
ACATTGCAACAAAAGTAGTT+AGG 0.463138 3_2:-78734964 None:intergenic
CCCAGAACATCATTAAAGAA+AGG 0.503059 3_2:-78734992 None:intergenic
CTCAACCGCCAGTATTATAG+AGG 0.511484 3_2:+78735171 Msa0428010:CDS
ATGCTTTATTGTATCAGTTG+TGG 0.512651 3_2:+78735138 Msa0428010:CDS
GCTCAATACTCTGAGCTGAA+TGG 0.555896 3_2:-78735211 None:intergenic
TCTGGGATTTCTTGGAGCAG+TGG 0.566045 3_2:+78735009 Msa0428010:CDS
TTTAACAGTTTATTATCCAG+TGG 0.568524 3_2:+78735042 Msa0428010:CDS
TGCAAGATATACATCTCCAC+TGG 0.575990 3_2:-78735058 None:intergenic
TGGAGATGTATATCTTGCAA+AGG 0.629124 3_2:+78735062 Msa0428010:CDS
TAGGTCCTCTATAATACTGG+CGG 0.635831 3_2:-78735176 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ACTGGATAATAAACTGTTAA+AGG - chr3_2:78735043-78735062 None:intergenic 25.0%
! TTTAACAGTTTATTATCCAG+TGG + chr3_2:78735042-78735061 Msa0428010:CDS 25.0%
ACATTGCAACAAAAGTAGTT+AGG - chr3_2:78734967-78734986 None:intergenic 30.0%
TCCTTTCTTTAATGATGTTC+TGG + chr3_2:78734991-78735010 Msa0428010:CDS 30.0%
CCTTTCTTTAATGATGTTCT+GGG + chr3_2:78734992-78735011 Msa0428010:CDS 30.0%
!! TCCATTTAGAACTCCATTTT+GGG - chr3_2:78735093-78735112 None:intergenic 30.0%
!! ATCCATTTAGAACTCCATTT+TGG - chr3_2:78735094-78735113 None:intergenic 30.0%
!!! GAGTTCTAAATGGATTTTGT+TGG + chr3_2:78735099-78735118 Msa0428010:CDS 30.0%
! ATGCTTTATTGTATCAGTTG+TGG + chr3_2:78735138-78735157 Msa0428010:CDS 30.0%
CCCAGAACATCATTAAAGAA+AGG - chr3_2:78734995-78735014 None:intergenic 35.0%
!! AATGATGTTCTGGGATTTCT+TGG + chr3_2:78735001-78735020 Msa0428010:CDS 35.0%
TGGAGATGTATATCTTGCAA+AGG + chr3_2:78735062-78735081 Msa0428010:CDS 35.0%
!! TCCCAAAATGGAGTTCTAAA+TGG + chr3_2:78735089-78735108 Msa0428010:CDS 35.0%
CTTTAGGTCCTCTATAATAC+TGG - chr3_2:78735182-78735201 None:intergenic 35.0%
! TGAATGGCTTGTAATGCTTT+AGG - chr3_2:78735198-78735217 None:intergenic 35.0%
TGCAAGATATACATCTCCAC+TGG - chr3_2:78735061-78735080 None:intergenic 40.0%
TGCAAAGGAAGATCCCAAAA+TGG + chr3_2:78735077-78735096 Msa0428010:CDS 40.0%
TAGGTCCTCTATAATACTGG+CGG - chr3_2:78735179-78735198 None:intergenic 40.0%
! TTCTTGGAGCAGTGGGATTT+TGG + chr3_2:78735017-78735036 Msa0428010:CDS 45.0%
CTCAACCGCCAGTATTATAG+AGG + chr3_2:78735171-78735190 Msa0428010:CDS 45.0%
! TCTGGGATTTCTTGGAGCAG+TGG + chr3_2:78735009-78735028 Msa0428010:CDS 50.0%
CTGGGATTTCTTGGAGCAGT+GGG + chr3_2:78735010-78735029 Msa0428010:CDS 50.0%
GTATCAGTTGTGGCTGCTCT+TGG + chr3_2:78735148-78735167 Msa0428010:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 78734959 78735231 78734959 ID=Msa0428010;Name=Msa0428010
chr3_2 mRNA 78734959 78735231 78734959 ID=Msa0428010-mRNA-1;Parent=Msa0428010;Name=Msa0428010-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|90
chr3_2 exon 78734959 78735231 78734959 ID=Msa0428010-mRNA-1:exon:20964;Parent=Msa0428010-mRNA-1
chr3_2 CDS 78734959 78735231 78734959 ID=Msa0428010-mRNA-1:cds;Parent=Msa0428010-mRNA-1
Gene Sequence

>Msa0428010

ATGATCCTAACTACTTTTGTTGCAATGTTGATTCCTTTCTTTAATGATGTTCTGGGATTTCTTGGAGCAGTGGGATTTTGGCCTTTAACAGTTTATTATCCAGTGGAGATGTATATCTTGCAAAGGAAGATCCCAAAATGGAGTTCTAAATGGATTTTGTTGGAAATCATAAGTGTTATATGCTTTATTGTATCAGTTGTGGCTGCTCTTGGCTCAACCGCCAGTATTATAGAGGACCTAAAGCATTACAAGCCATTCAGCTCAGAGTATTGA

Protein sequence

>Msa0428010

MILTTFVAMLIPFFNDVLGFLGAVGFWPLTVYYPVEMYILQRKIPKWSSKWILLEIISVICFIVSVVAALGSTASIIEDLKHYKPFSSEY*