AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1435040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1435040 MtrunA17_Chr3g0136561 100.000 129 0 0 11 139 776 904 6.08e-88 274
Msa1435040 MtrunA17_Chr4g0035081 65.000 120 41 1 19 138 384 502 8.18e-57 184
Msa1435040 MtrunA17_Chr1g0188051 66.957 115 38 0 22 136 390 504 6.34e-56 182
Msa1435040 MtrunA17_Chr7g0250661 63.248 117 43 0 22 138 173 289 6.34e-56 176
Msa1435040 MtrunA17_Chr2g0306781 64.103 117 42 0 22 138 283 399 1.08e-55 179
Msa1435040 MtrunA17_Chr5g0423521 66.667 117 38 1 22 138 375 490 1.23e-55 181
Msa1435040 MtrunA17_Chr1g0166191 58.824 136 54 1 5 138 377 512 1.32e-55 181
Msa1435040 MtrunA17_Chr1g0209881 65.812 117 39 1 22 138 375 490 1.71e-55 180
Msa1435040 MtrunA17_Chr7g0276251 65.574 122 40 1 19 138 407 528 2.58e-54 178
Msa1435040 MtrunA17_Chr4g0063011 63.248 117 43 0 22 138 378 494 2.63e-54 177
Msa1435040 MtrunA17_Chr4g0026871 57.627 118 50 0 22 139 111 228 1.84e-50 160
Msa1435040 MtrunA17_Chr7g0276241 62.281 114 41 1 24 135 170 283 5.13e-50 161
Msa1435040 MtrunA17_Chr6g0461631 57.265 117 50 0 22 138 140 256 5.90e-50 160
Msa1435040 MtrunA17_Chr4g0026721 55.085 118 53 0 22 139 43 160 5.51e-48 152
Msa1435040 MtrunA17_Chr2g0282281 64.220 109 38 1 21 129 395 502 6.61e-46 155
Msa1435040 MtrunA17_Chr2g0277841 57.391 115 48 1 24 138 338 451 2.68e-45 153
Msa1435040 MtrunA17_Chr6g0480561 54.545 121 55 0 19 139 349 469 3.24e-45 153
Msa1435040 MtrunA17_Chr2g0295781 55.652 115 50 1 24 138 338 451 1.12e-43 149
Msa1435040 MtrunA17_Chr4g0030601 48.387 124 59 2 12 135 315 433 1.79e-39 137
Msa1435040 MtrunA17_Chr4g0030591 52.294 109 49 1 27 135 337 442 3.55e-39 137
Msa1435040 MtrunA17_Chr4g0030581 52.294 109 49 1 27 135 336 441 5.42e-39 136
Msa1435040 MtrunA17_Chr1g0204301 51.786 112 54 0 24 135 372 483 8.52e-39 136
Msa1435040 MtrunA17_Chr6g0469631 49.123 114 58 0 24 137 370 483 6.72e-37 131
Msa1435040 MtrunA17_Chr2g0327721 47.656 128 58 3 9 135 325 444 2.35e-36 129
Msa1435040 MtrunA17_Chr3g0115041 49.123 114 58 0 24 137 371 484 5.85e-36 129
Msa1435040 MtrunA17_Chr3g0115021 49.123 114 58 0 24 137 371 484 6.16e-36 128
Msa1435040 MtrunA17_Chr1g0212951 46.789 109 55 1 27 135 346 451 6.62e-34 123
Msa1435040 MtrunA17_Chr4g0026791 64.179 67 24 0 24 90 113 179 3.37e-27 99.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1435040 AT2G26250.1 77.966 118 26 0 21 138 433 550 7.67e-67 211
Msa1435040 AT1G19440.1 69.492 118 35 1 22 139 399 515 1.41e-59 192
Msa1435040 AT2G16280.1 67.797 118 37 1 22 139 395 511 7.99e-57 184
Msa1435040 AT1G68530.1 67.826 115 36 1 22 136 376 489 2.01e-56 183
Msa1435040 AT4G34510.1 65.254 118 40 1 22 139 370 486 1.04e-54 178
Msa1435040 AT2G26640.1 64.103 117 42 0 22 138 387 503 1.06e-54 179
Msa1435040 AT2G15090.1 65.517 116 39 1 24 139 366 480 4.54e-54 177
Msa1435040 AT1G01120.1 66.102 118 39 1 22 138 409 526 5.17e-54 177
Msa1435040 AT5G43760.1 64.407 118 41 1 22 138 403 520 8.10e-54 177
Msa1435040 AT1G04220.1 64.706 119 38 1 22 136 395 513 2.21e-53 176
Msa1435040 AT4G34250.1 62.712 118 43 1 22 139 372 488 2.24e-53 175
Msa1435040 AT1G25450.1 65.217 115 39 1 22 136 371 484 3.02e-53 175
Msa1435040 AT3G10280.1 61.345 119 44 1 23 139 341 459 1.26e-50 167
Msa1435040 AT2G46720.1 61.345 119 44 1 23 139 348 466 1.38e-50 167
Msa1435040 AT5G49070.1 58.824 119 48 1 20 138 338 455 2.97e-50 166
Msa1435040 AT4G34520.1 61.207 116 44 1 24 139 377 491 7.86e-50 166
Msa1435040 AT3G52160.2 56.637 113 49 0 15 127 224 336 3.94e-44 147
Msa1435040 AT3G52160.1 64.948 97 34 0 31 127 353 449 3.41e-43 147
Msa1435040 AT1G71160.1 54.867 113 50 1 24 136 335 446 4.14e-41 142
Msa1435040 AT2G28630.2 54.545 110 49 1 27 135 337 446 1.32e-40 141
Msa1435040 AT2G28630.1 54.545 110 49 1 27 135 337 446 1.32e-40 141
Msa1435040 AT1G07720.1 50.000 110 54 1 27 135 338 447 2.20e-37 132
Msa1435040 AT1G07720.2 50.000 110 54 1 27 135 381 490 3.51e-37 132
Msa1435040 AT5G04530.1 39.024 123 71 2 13 135 319 437 1.72e-29 111

Find 23 sgRNAs with CRISPR-Local

Find 108 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGGTATGAACTTGCTTATA+TGG 0.315118 tig0027613:-7327 Msa1435040:CDS
GTGTCACAAAACCTTCTTCT+AGG 0.319740 tig0027613:-7208 Msa1435040:CDS
CGTGTTTGGCAACTCGCTTT+TGG 0.347268 tig0027613:-7275 Msa1435040:CDS
TCAAAAGCTAGTTTGTAGTT+AGG 0.354642 tig0027613:+7482 None:intergenic
TTAGTGTGGAGGAACTTCTT+TGG 0.395590 tig0027613:-7553 Msa1435040:intron
TTAAAAGAGGAGACCGTGTT+TGG 0.419933 tig0027613:-7289 Msa1435040:CDS
AGTTTGTAGTTAGGAATGTA+TGG 0.424543 tig0027613:+7491 None:intergenic
TACTAGAAGTGTTGCCGAAT+CGG 0.436153 tig0027613:+7357 None:intergenic
AACCTTCTTCTAGGAACCCT+TGG 0.447884 tig0027613:-7199 Msa1435040:CDS
AGAATGACGCTGCACCGATT+CGG 0.461090 tig0027613:-7371 Msa1435040:CDS
TTAAGTGTAACAGTGCTGTT+TGG 0.462133 tig0027613:-7244 Msa1435040:CDS
GCTTGTTAATTGAGAGAAGC+AGG 0.477899 tig0027613:+7155 None:intergenic
AGCCAAGGGTTCCTAGAAGA+AGG 0.494068 tig0027613:+7197 None:intergenic
ACACTTCTAGTAGCAGCATC+TGG 0.506481 tig0027613:-7346 Msa1435040:CDS
ACTTGCTTATATGGAAGCTA+AGG 0.533019 tig0027613:-7318 Msa1435040:CDS
ATGTATGGCTTGTTTGATGA+TGG 0.542182 tig0027613:+7506 None:intergenic
GCATCAATGCAGTCAAGCCA+AGG 0.562088 tig0027613:+7182 None:intergenic
TGAATTGAGTGACAAGAACA+TGG 0.579983 tig0027613:-7402 Msa1435040:CDS
TCGGTGCAGCGTCATTCTAG+AGG 0.593076 tig0027613:+7376 None:intergenic
GTGGAGGAACTTCTTTGGTG+TGG 0.609109 tig0027613:-7548 Msa1435040:CDS
TCTTTGCTACATTAGTGTGG+AGG 0.612338 tig0027613:-7564 Msa1435040:intron
CATCAATGCAGTCAAGCCAA+GGG 0.623256 tig0027613:+7183 None:intergenic
CAAAAGCGAGTTGCCAAACA+CGG 0.635869 tig0027613:+7276 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAATCAAAATAACTACTAA+TGG - tig0027613:7181-7200 Msa1435040:CDS 15.0%
!! ATAATCAAAATAACTACTAA+TGG - tig0027613:7181-7200 Msa1435040:CDS 15.0%
!! GAAAAAAAAAGAGATTAAAG+AGG - tig0027613:7258-7277 Msa1435040:CDS 20.0%
!! GAAAAAAAAAGAGATTAAAG+AGG - tig0027613:7258-7277 Msa1435040:CDS 20.0%
! AAGATAATGTGAAAGAAAAG+TGG - tig0027613:7302-7321 Msa1435040:CDS 25.0%
!!! TGTGGTTACCAATATTTTTT+TGG - tig0027613:7458-7477 Msa1435040:CDS 25.0%
! AGGTTAAGCCAAAAAAATAT+TGG + tig0027613:7469-7488 None:intergenic 25.0%
! AGCAAAGACTTAATTGAAAT+TGG - tig0027613:7622-7641 Msa1435040:intron 25.0%
! AAAGACTTAATTGAAATTGG+TGG - tig0027613:7625-7644 Msa1435040:intron 25.0%
!!! AAAATAAGCTGTTCTGAAAA+GGG + tig0027613:7697-7716 None:intergenic 25.0%
! AAGATAATGTGAAAGAAAAG+TGG - tig0027613:7302-7321 Msa1435040:CDS 25.0%
!!! TGTGGTTACCAATATTTTTT+TGG - tig0027613:7458-7477 Msa1435040:CDS 25.0%
! AGGTTAAGCCAAAAAAATAT+TGG + tig0027613:7469-7488 None:intergenic 25.0%
! AGCAAAGACTTAATTGAAAT+TGG - tig0027613:7622-7641 Msa1435040:intron 25.0%
! AAAGACTTAATTGAAATTGG+TGG - tig0027613:7625-7644 Msa1435040:intron 25.0%
!!! AAAATAAGCTGTTCTGAAAA+GGG + tig0027613:7697-7716 None:intergenic 25.0%
TAAATGACCTAACTTTCATG+TGG - tig0027613:7394-7413 Msa1435040:CDS 30.0%
AAATGACCTAACTTTCATGT+GGG - tig0027613:7395-7414 Msa1435040:CDS 30.0%
! TTTGTTGGTGTTTATTCACA+AGG + tig0027613:7421-7440 None:intergenic 30.0%
TGTGAATAAACACCAACAAA+AGG - tig0027613:7421-7440 Msa1435040:CDS 30.0%
GTCGAACTTCATATTATCAA+AGG + tig0027613:7489-7508 None:intergenic 30.0%
AAAACAAACATCACAACACT+AGG - tig0027613:7658-7677 Msa1435040:intron 30.0%
!! GAAAATAAGCTGTTCTGAAA+AGG + tig0027613:7698-7717 None:intergenic 30.0%
! TTTTCTTTGCTACATTAGTG+TGG - tig0027613:7713-7732 Msa1435040:intron 30.0%
AGTTTGTAGTTAGGAATGTA+TGG + tig0027613:7792-7811 None:intergenic 30.0%
! TCAAAAGCTAGTTTGTAGTT+AGG + tig0027613:7801-7820 None:intergenic 30.0%
GCTAAGGAAAAAGTTAAAAG+AGG - tig0027613:7978-7997 Msa1435040:intron 30.0%
TAAATGACCTAACTTTCATG+TGG - tig0027613:7394-7413 Msa1435040:CDS 30.0%
AAATGACCTAACTTTCATGT+GGG - tig0027613:7395-7414 Msa1435040:CDS 30.0%
! TTTGTTGGTGTTTATTCACA+AGG + tig0027613:7421-7440 None:intergenic 30.0%
TGTGAATAAACACCAACAAA+AGG - tig0027613:7421-7440 Msa1435040:CDS 30.0%
GTCGAACTTCATATTATCAA+AGG + tig0027613:7489-7508 None:intergenic 30.0%
AAAACAAACATCACAACACT+AGG - tig0027613:7658-7677 Msa1435040:intron 30.0%
!! GAAAATAAGCTGTTCTGAAA+AGG + tig0027613:7698-7717 None:intergenic 30.0%
! TTTTCTTTGCTACATTAGTG+TGG - tig0027613:7713-7732 Msa1435040:intron 30.0%
AGTTTGTAGTTAGGAATGTA+TGG + tig0027613:7792-7811 None:intergenic 30.0%
! TCAAAAGCTAGTTTGTAGTT+AGG + tig0027613:7801-7820 None:intergenic 30.0%
GCTAAGGAAAAAGTTAAAAG+AGG - tig0027613:7978-7997 Msa1435040:intron 30.0%
!! ACCAACAAAAGGTATGCTTT+TGG - tig0027613:7432-7451 Msa1435040:CDS 35.0%
!! TCCAAAAGCATACCTTTTGT+TGG + tig0027613:7436-7455 None:intergenic 35.0%
! AAGGTATGCTTTTGGATATG+TGG - tig0027613:7440-7459 Msa1435040:CDS 35.0%
ATCTTACTGTAACACAATGC+AGG - tig0027613:7551-7570 Msa1435040:CDS 35.0%
GAAGACGATCAGAAATTCAA+GGG - tig0027613:7589-7608 Msa1435040:intron 35.0%
!! ATGTATGGCTTGTTTGATGA+TGG + tig0027613:7777-7796 None:intergenic 35.0%
!!! CTTTTGAAGCTCATCAAGAA+TGG + tig0027613:7853-7872 None:intergenic 35.0%
TGAATTGAGTGACAAGAACA+TGG - tig0027613:7878-7897 Msa1435040:intron 35.0%
! CTGGTATGAACTTGCTTATA+TGG - tig0027613:7953-7972 Msa1435040:intron 35.0%
ACTTGCTTATATGGAAGCTA+AGG - tig0027613:7962-7981 Msa1435040:intron 35.0%
! TTAAGTGTAACAGTGCTGTT+TGG - tig0027613:8036-8055 Msa1435040:intron 35.0%
!! ACCAACAAAAGGTATGCTTT+TGG - tig0027613:7432-7451 Msa1435040:CDS 35.0%
!! TCCAAAAGCATACCTTTTGT+TGG + tig0027613:7436-7455 None:intergenic 35.0%
! AAGGTATGCTTTTGGATATG+TGG - tig0027613:7440-7459 Msa1435040:CDS 35.0%
ATCTTACTGTAACACAATGC+AGG - tig0027613:7551-7570 Msa1435040:CDS 35.0%
GAAGACGATCAGAAATTCAA+GGG - tig0027613:7589-7608 Msa1435040:intron 35.0%
!! ATGTATGGCTTGTTTGATGA+TGG + tig0027613:7777-7796 None:intergenic 35.0%
!!! CTTTTGAAGCTCATCAAGAA+TGG + tig0027613:7853-7872 None:intergenic 35.0%
TGAATTGAGTGACAAGAACA+TGG - tig0027613:7878-7897 Msa1435040:intron 35.0%
! CTGGTATGAACTTGCTTATA+TGG - tig0027613:7953-7972 Msa1435040:intron 35.0%
ACTTGCTTATATGGAAGCTA+AGG - tig0027613:7962-7981 Msa1435040:intron 35.0%
! TTAAGTGTAACAGTGCTGTT+TGG - tig0027613:8036-8055 Msa1435040:intron 35.0%
ATTTCTGATCGTCTTCCTCT+TGG + tig0027613:7585-7604 None:intergenic 40.0%
GGAAGACGATCAGAAATTCA+AGG - tig0027613:7588-7607 Msa1435040:intron 40.0%
!! TAAGCTGTTCTGAAAAGGGT+AGG + tig0027613:7693-7712 None:intergenic 40.0%
TCTTTGCTACATTAGTGTGG+AGG - tig0027613:7716-7735 Msa1435040:intron 40.0%
TTAGTGTGGAGGAACTTCTT+TGG - tig0027613:7727-7746 Msa1435040:intron 40.0%
!! TACTAGAAGTGTTGCCGAAT+CGG + tig0027613:7926-7945 None:intergenic 40.0%
TTAAAAGAGGAGACCGTGTT+TGG - tig0027613:7991-8010 Msa1435040:intron 40.0%
GTGTCACAAAACCTTCTTCT+AGG - tig0027613:8072-8091 Msa1435040:intron 40.0%
ATTTCTGATCGTCTTCCTCT+TGG + tig0027613:7585-7604 None:intergenic 40.0%
GGAAGACGATCAGAAATTCA+AGG - tig0027613:7588-7607 Msa1435040:intron 40.0%
!! TAAGCTGTTCTGAAAAGGGT+AGG + tig0027613:7693-7712 None:intergenic 40.0%
TCTTTGCTACATTAGTGTGG+AGG - tig0027613:7716-7735 Msa1435040:intron 40.0%
TTAGTGTGGAGGAACTTCTT+TGG - tig0027613:7727-7746 Msa1435040:intron 40.0%
!! TACTAGAAGTGTTGCCGAAT+CGG + tig0027613:7926-7945 None:intergenic 40.0%
TTAAAAGAGGAGACCGTGTT+TGG - tig0027613:7991-8010 Msa1435040:intron 40.0%
GTGTCACAAAACCTTCTTCT+AGG - tig0027613:8072-8091 Msa1435040:intron 40.0%
ACAAGGCCCACATGAAAGTT+AGG + tig0027613:7404-7423 None:intergenic 45.0%
CATCACAACACTAGGACCAT+TGG - tig0027613:7666-7685 Msa1435040:intron 45.0%
TCTGAAAAGGGTAGGACCAA+TGG + tig0027613:7685-7704 None:intergenic 45.0%
ACACTTCTAGTAGCAGCATC+TGG - tig0027613:7934-7953 Msa1435040:intron 45.0%
CAAAAGCGAGTTGCCAAACA+CGG + tig0027613:8007-8026 None:intergenic 45.0%
! AACCTTCTTCTAGGAACCCT+TGG - tig0027613:8081-8100 Msa1435040:intron 45.0%
CATCAATGCAGTCAAGCCAA+GGG + tig0027613:8100-8119 None:intergenic 45.0%
ACAAGGCCCACATGAAAGTT+AGG + tig0027613:7404-7423 None:intergenic 45.0%
CATCACAACACTAGGACCAT+TGG - tig0027613:7666-7685 Msa1435040:intron 45.0%
TCTGAAAAGGGTAGGACCAA+TGG + tig0027613:7685-7704 None:intergenic 45.0%
ACACTTCTAGTAGCAGCATC+TGG - tig0027613:7934-7953 Msa1435040:intron 45.0%
CAAAAGCGAGTTGCCAAACA+CGG + tig0027613:8007-8026 None:intergenic 45.0%
! AACCTTCTTCTAGGAACCCT+TGG - tig0027613:8081-8100 Msa1435040:intron 45.0%
CATCAATGCAGTCAAGCCAA+GGG + tig0027613:8100-8119 None:intergenic 45.0%
!!! TTTATTTTTTTAAACTTTAA+AGG + tig0027613:7360-7379 None:intergenic 5.0%
!!! TTTATTTTTTTAAACTTTAA+AGG + tig0027613:7360-7379 None:intergenic 5.0%
ATGCAGGTGTGTGTACCAAG+AGG - tig0027613:7567-7586 Msa1435040:intron 50.0%
GTGGAGGAACTTCTTTGGTG+TGG - tig0027613:7732-7751 Msa1435040:intron 50.0%
!! AGAATGACGCTGCACCGATT+CGG - tig0027613:7909-7928 Msa1435040:intron 50.0%
! CGTGTTTGGCAACTCGCTTT+TGG - tig0027613:8005-8024 Msa1435040:intron 50.0%
!!! TGGCAACTCGCTTTTGGTTC+TGG - tig0027613:8011-8030 Msa1435040:intron 50.0%
AGCCAAGGGTTCCTAGAAGA+AGG + tig0027613:8086-8105 None:intergenic 50.0%
GCATCAATGCAGTCAAGCCA+AGG + tig0027613:8101-8120 None:intergenic 50.0%
ATGCAGGTGTGTGTACCAAG+AGG - tig0027613:7567-7586 Msa1435040:intron 50.0%
GTGGAGGAACTTCTTTGGTG+TGG - tig0027613:7732-7751 Msa1435040:intron 50.0%
!! AGAATGACGCTGCACCGATT+CGG - tig0027613:7909-7928 Msa1435040:intron 50.0%
! CGTGTTTGGCAACTCGCTTT+TGG - tig0027613:8005-8024 Msa1435040:intron 50.0%
!!! TGGCAACTCGCTTTTGGTTC+TGG - tig0027613:8011-8030 Msa1435040:intron 50.0%
AGCCAAGGGTTCCTAGAAGA+AGG + tig0027613:8086-8105 None:intergenic 50.0%
GCATCAATGCAGTCAAGCCA+AGG + tig0027613:8101-8120 None:intergenic 50.0%
TCGGTGCAGCGTCATTCTAG+AGG + tig0027613:7907-7926 None:intergenic 55.0%
TCGGTGCAGCGTCATTCTAG+AGG + tig0027613:7907-7926 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
tig0027613 gene 7160 8142 7160 ID=Msa1435040;Name=Msa1435040
tig0027613 mRNA 7160 8142 7160 ID=Msa1435040-mRNA-1;Parent=Msa1435040;Name=Msa1435040-mRNA-1;_AED=0.44;_eAED=0.44;_QI=0|0|0|0.5|1|1|2|0|139
tig0027613 exon 8135 8142 8135 ID=Msa1435040-mRNA-1:exon:9502;Parent=Msa1435040-mRNA-1
tig0027613 exon 7160 7571 7160 ID=Msa1435040-mRNA-1:exon:9501;Parent=Msa1435040-mRNA-1
tig0027613 CDS 8135 8142 8135 ID=Msa1435040-mRNA-1:cds;Parent=Msa1435040-mRNA-1
tig0027613 CDS 7160 7571 7160 ID=Msa1435040-mRNA-1:cds;Parent=Msa1435040-mRNA-1
Gene Sequence

>Msa1435040

ATGGAAAATGTGGAGGAACTTCTTTGGTGTGGAAAATCTGATAAAAATTCACCATCATCAAACAAGCCATACATTCCTAACTACAAACTAGCTTTTGAGCATTTTTGTGTGCATGCTGCTAGCAAAACCATTCTTGATGAGCTTCAAAAGAATCTTGAATTGAGTGACAAGAACATGGAAGCCTCTAGAATGACGCTGCACCGATTCGGCAACACTTCTAGTAGCAGCATCTGGTATGAACTTGCTTATATGGAAGCTAAGGAAAAAGTTAAAAGAGGAGACCGTGTTTGGCAACTCGCTTTTGGTTCTGGTTTTAAGTGTAACAGTGCTGTTTGGCGTTCTATGCGTCGTGTCACAAAACCTTCTTCTAGGAACCCTTGGCTTGACTGCATTGATGCATATCCTGCTTCTCTCAATTAA

Protein sequence

>Msa1435040

MENVEELLWCGKSDKNSPSSNKPYIPNYKLAFEHFCVHAASKTILDELQKNLELSDKNMEASRMTLHRFGNTSSSSIWYELAYMEAKEKVKRGDRVWQLAFGSGFKCNSAVWRSMRRVTKPSSRNPWLDCIDAYPASLN*