AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene45139

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene45139.t1 MTR_5g035910 96.154 52 2 0 73 124 511 562 4.12e-27 104
MS.gene45139.t1 MTR_5g035910 83.333 60 9 1 1 60 613 671 1.01e-25 100
MS.gene45139.t1 MTR_7g063030 92.308 52 4 0 73 124 508 559 9.06e-27 103
MS.gene45139.t1 MTR_7g063030 92.308 52 4 0 73 124 502 553 3.59e-26 102
MS.gene45139.t1 MTR_7g063010 88.462 52 6 0 73 124 504 555 7.72e-25 98.2
MS.gene45139.t1 MTR_7g063010 54.098 61 27 1 1 60 606 666 2.40e-11 59.7
MS.gene45139.t1 MTR_3g068025 84.615 52 8 0 73 124 514 565 1.48e-23 94.7
MS.gene45139.t1 MTR_7g062950 65.385 52 18 0 73 124 506 557 9.57e-16 72.4
MS.gene45139.t1 MTR_1g052275 63.462 52 19 0 73 124 508 559 1.86e-15 71.6
MS.gene45139.t1 MTR_7g062990 61.111 54 19 1 73 124 512 565 2.34e-15 71.2
MS.gene45139.t1 MTR_7g062680 61.538 52 20 0 73 124 516 567 9.26e-15 69.7
MS.gene45139.t1 MTR_7g062940 61.538 52 20 0 73 124 505 556 9.53e-15 69.7
MS.gene45139.t1 MTR_7g062700 59.615 52 21 0 73 124 508 559 2.44e-14 68.6
MS.gene45139.t1 MTR_7g062750 59.615 52 21 0 73 124 508 559 2.77e-14 68.2
MS.gene45139.t1 MTR_7g062890 61.538 52 20 0 73 124 504 555 3.96e-14 67.8
MS.gene45139.t1 MTR_2g090410 59.615 52 17 1 73 124 1216 1263 7.65e-14 67.0
MS.gene45139.t1 MTR_2g090410 64.865 37 13 0 73 109 513 549 1.76e-11 60.5
MS.gene45139.t1 MTR_7g062660 61.538 52 20 0 73 124 499 550 1.08e-13 66.6
MS.gene45139.t1 MTR_2g090250 76.316 38 9 0 73 110 511 548 1.35e-13 66.2
MS.gene45139.t1 MTR_7g062770 59.615 52 21 0 73 124 510 561 3.44e-13 65.1
MS.gene45139.t1 MTR_7g062920 59.615 52 21 0 73 124 506 557 4.10e-13 64.7
MS.gene45139.t1 MTR_4g093070 54.717 53 23 1 73 124 513 565 9.35e-13 63.9
MS.gene45139.t1 MTR_3g460810 55.769 52 22 1 73 124 492 542 1.30e-12 63.5
MS.gene45139.t1 MTR_4g093110 50.980 51 25 0 74 124 508 558 2.97e-12 62.4
MS.gene45139.t1 MTR_4g093140 50.980 51 25 0 74 124 508 558 3.36e-12 62.4
MS.gene45139.t1 MTR_4g105070 55.769 52 23 0 73 124 520 571 3.53e-12 62.4
MS.gene45139.t1 MTR_8g068050 50.000 52 26 0 73 124 410 461 4.13e-12 62.0
MS.gene45139.t1 MTR_4g093080 51.923 52 24 1 73 124 515 565 4.24e-12 62.0
MS.gene45139.t1 MTR_8g068050 50.000 52 26 0 73 124 520 571 4.78e-12 62.0
MS.gene45139.t1 MTR_2g013720 65.789 38 13 0 73 110 519 556 4.97e-12 61.6
MS.gene45139.t1 MTR_3g007870 51.923 52 24 1 73 124 512 562 9.22e-12 60.8
MS.gene45139.t1 MTR_5g095970 51.923 52 24 1 73 124 525 575 9.60e-12 60.8
MS.gene45139.t1 MTR_4g093050 49.020 51 26 0 74 124 513 563 1.68e-11 60.1
MS.gene45139.t1 MTR_7g062900 55.769 52 23 0 73 124 464 515 2.98e-11 59.7
MS.gene45139.t1 MTR_7g116130 42.308 52 30 0 73 124 521 572 6.84e-11 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene45139.t1 AT3G55550 73.077 52 14 0 73 124 512 563 3.86e-20 85.1
MS.gene45139.t1 AT1G70110 65.385 52 18 0 73 124 509 560 9.28e-19 80.9
MS.gene45139.t1 AT3G59740 65.385 52 18 0 73 124 502 553 3.24e-18 79.3
MS.gene45139.t1 AT2G37710 67.925 53 16 1 73 124 512 564 2.37e-17 77.0
MS.gene45139.t1 AT1G70130 59.615 52 21 0 73 124 499 550 4.49e-17 76.3
MS.gene45139.t1 AT3G59750 63.462 52 19 0 73 124 469 520 6.64e-17 75.9
MS.gene45139.t1 AT4G02420 69.231 52 15 1 74 124 516 567 1.21e-16 75.1
MS.gene45139.t1 AT4G29050 62.264 53 19 1 73 124 509 561 3.19e-16 73.9
MS.gene45139.t1 AT4G29050 62.264 53 19 1 73 124 523 575 3.26e-16 73.9
MS.gene45139.t1 AT3G59700 59.615 52 21 0 73 124 504 555 5.76e-16 73.2
MS.gene45139.t1 AT3G53810 62.264 53 19 1 73 124 512 564 1.47e-14 68.9
MS.gene45139.t1 AT5G59260 51.923 52 25 0 73 124 520 571 1.82e-14 68.9
MS.gene45139.t1 AT4G02410 66.667 48 16 0 74 121 521 568 2.28e-14 68.6
MS.gene45139.t1 AT2G43700 54.000 50 23 0 75 124 502 551 9.83e-14 66.6
MS.gene45139.t1 AT2G43700 54.000 50 23 0 75 124 478 527 1.10e-13 66.6
MS.gene45139.t1 AT2G43700 54.000 50 23 0 75 124 478 527 1.10e-13 66.6
MS.gene45139.t1 AT2G43700 54.000 50 23 0 75 124 478 527 1.10e-13 66.6
MS.gene45139.t1 AT2G43700 54.000 50 23 0 75 124 478 527 1.10e-13 66.6
MS.gene45139.t1 AT4G04960 60.784 51 16 1 74 124 516 562 1.26e-13 66.2
MS.gene45139.t1 AT3G08870 55.769 52 19 1 73 124 556 603 2.44e-13 65.5
MS.gene45139.t1 AT4G04960 60.784 51 16 1 74 124 516 562 2.60e-13 65.5
MS.gene45139.t1 AT3G08870 55.769 52 19 1 73 124 535 582 2.71e-13 65.5
MS.gene45139.t1 AT5G01540 55.769 52 19 1 73 124 534 581 6.47e-13 64.3
MS.gene45139.t1 AT5G59270 48.077 52 27 0 73 124 533 584 1.08e-12 63.5
MS.gene45139.t1 AT2G29220 49.020 51 26 0 74 124 506 556 1.86e-12 63.2
MS.gene45139.t1 AT5G59270 48.077 52 27 0 73 124 514 565 2.53e-12 62.8
MS.gene45139.t1 AT5G59270 48.077 52 27 0 73 124 517 568 2.53e-12 62.8
MS.gene45139.t1 AT3G45420 40.217 92 48 2 39 124 474 564 2.90e-12 62.4
MS.gene45139.t1 AT5G60280 55.769 52 22 1 73 124 502 552 4.27e-12 62.0
MS.gene45139.t1 AT5G01550 53.846 52 20 1 73 124 548 595 4.79e-12 62.0
MS.gene45139.t1 AT4G28350 67.568 37 12 0 74 110 517 553 5.36e-12 61.6
MS.gene45139.t1 AT2G43690 47.059 51 27 0 73 123 465 515 8.29e-12 61.2
MS.gene45139.t1 AT2G29250 49.020 51 26 0 74 124 505 555 9.67e-12 60.8
MS.gene45139.t1 AT2G43690 47.059 51 27 0 73 123 501 551 1.57e-11 60.5
MS.gene45139.t1 AT2G43690 47.059 51 27 0 73 123 501 551 1.57e-11 60.5
MS.gene45139.t1 AT5G60320 51.923 52 24 1 73 124 512 562 2.10e-11 60.1
MS.gene45139.t1 AT5G01560 51.923 52 21 1 73 124 531 578 2.34e-11 60.1
MS.gene45139.t1 AT5G60310 48.077 52 26 1 73 124 507 557 3.03e-11 59.7
MS.gene45139.t1 AT3G45440 53.846 52 23 1 73 124 506 556 3.18e-11 59.7
MS.gene45139.t1 AT3G45440 53.846 52 23 1 73 124 506 556 3.18e-11 59.7
MS.gene45139.t1 AT3G45440 53.846 52 23 1 73 124 506 556 3.18e-11 59.7
MS.gene45139.t1 AT3G45440 53.846 52 23 1 73 124 559 609 3.21e-11 59.7
MS.gene45139.t1 AT3G45430 53.846 52 23 1 73 124 508 558 3.44e-11 59.3
MS.gene45139.t1 AT3G45430 53.846 52 23 1 73 124 508 558 3.44e-11 59.3
MS.gene45139.t1 AT3G45430 53.846 52 23 1 73 124 508 558 3.44e-11 59.3
MS.gene45139.t1 AT5G55830 49.057 53 26 1 73 124 533 585 4.22e-11 59.3
MS.gene45139.t1 AT5G60270 51.923 52 24 1 73 124 508 558 4.73e-11 58.9
MS.gene45139.t1 AT1G15530 55.769 52 22 1 73 124 525 575 5.00e-11 58.9
MS.gene45139.t1 AT5G60300 51.923 52 24 1 73 124 508 558 5.62e-11 58.9
MS.gene45139.t1 AT5G60300 51.923 52 24 1 73 124 508 558 5.62e-11 58.9
MS.gene45139.t1 AT5G60300 51.923 52 24 1 73 124 508 558 5.77e-11 58.9
MS.gene45139.t1 AT3G46760 53.846 52 24 0 73 124 205 256 6.24e-11 58.5

Find 31 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTGATGATTTGAGTAATTC+AGG 0.222813 5.1:-26633814 MS.gene45139:CDS
ACAAGTGATGATGAGGATTT+TGG 0.230179 5.1:-26633854 None:intergenic
GTGGGAACCTTTAGGCTATT+TGG 0.232555 5.1:-26633056 MS.gene45139:CDS
GTAGATGCTCTTCCTGTTCT+AGG 0.275295 5.1:+26633022 None:intergenic
CCCACCACTCTTGTGGTCCC+TGG 0.357271 5.1:+26633074 None:intergenic
TTCTGCTTGAGGTTGCTTGT+GGG 0.368531 5.1:-26632970 MS.gene45139:CDS
ACAAGAAGAGTTAGTGTTTG+TGG 0.392340 5.1:-26632921 MS.gene45139:CDS
TGTAATGCCTTAGACTCAAT+AGG 0.409339 5.1:+26632941 None:intergenic
GAGAAGGCCTATTGAGTCTA+AGG 0.417516 5.1:-26632948 MS.gene45139:CDS
GCACCGGAGTTGCCTAGAAC+AGG 0.425900 5.1:-26633034 MS.gene45139:CDS
CAAGAGTGGTGGGAACCTTT+AGG 0.440507 5.1:-26633064 MS.gene45139:CDS
AGAGTTAGTGTTTGTGGACT+GGG 0.448490 5.1:-26632915 MS.gene45139:CDS
TATGAACATGGTGCTAATCC+AGG 0.453333 5.1:-26633092 MS.gene45139:CDS
CTTCTGCTTGAGGTTGCTTG+TGG 0.454996 5.1:-26632971 MS.gene45139:CDS
CCTGAATTACTCAAATCATC+AGG 0.472864 5.1:+26633814 None:intergenic
TTGAGGTTGCTTGTGGGAGA+AGG 0.474358 5.1:-26632964 MS.gene45139:CDS
ATTTGGTGCACTTCTGCTTG+AGG 0.507190 5.1:-26632981 MS.gene45139:CDS
ACCTTTAGGCTATTTGGCAC+CGG 0.525213 5.1:-26633050 MS.gene45139:CDS
TGAACTCATGATATCAATTG+AGG 0.526355 5.1:+26633738 None:intergenic
AAGAGTTAGTGTTTGTGGAC+TGG 0.531353 5.1:-26632916 MS.gene45139:CDS
AATTCATCAAACACATGTTG+TGG 0.538666 5.1:+26633781 None:intergenic
AAAGGTTCCCACCACTCTTG+TGG 0.545636 5.1:+26633067 None:intergenic
AGTGTTTGTGGACTGGGTGT+AGG 0.546562 5.1:-26632909 None:intergenic
TCCGGTGCCAAATAGCCTAA+AGG 0.552067 5.1:+26633049 None:intergenic
CTTGAAAATAGATATACTGA+TGG 0.553273 5.1:-26633706 MS.gene45139:CDS
TCCAGGGACCACAAGAGTGG+TGG 0.564859 5.1:-26633075 MS.gene45139:CDS
CTTCCTGTTCTAGGCAACTC+CGG 0.587316 5.1:+26633031 None:intergenic
ATGAACATGGTGCTAATCCA+GGG 0.605499 5.1:-26633091 MS.gene45139:CDS
CCAGGGACCACAAGAGTGGT+GGG 0.611319 5.1:-26633074 MS.gene45139:CDS
TAATCCAGGGACCACAAGAG+TGG 0.669305 5.1:-26633078 MS.gene45139:CDS
TTGGCAAGGTTATATGAACA+TGG 0.685229 5.1:-26633104 MS.gene45139:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAATCATAAATGAAAAAT+TGG + chr5.1:26633577-26633596 None:intergenic 15.0%
!! ATACATGAATATAAACTTAT+TGG + chr5.1:26633466-26633485 None:intergenic 15.0%
!! ATGTAAAATGTAAAATGTAT+AGG + chr5.1:26633141-26633160 None:intergenic 15.0%
!! TACATGAATATAAACTTATT+GGG + chr5.1:26633465-26633484 None:intergenic 15.0%
!!! TTTGTTTTCTTACATATTTT+TGG + chr5.1:26633404-26633423 None:intergenic 15.0%
!! CCTTGTATAGAATAAAAAAA+TGG - chr5.1:26633184-26633203 MS.gene45139:intron 20.0%
!!! AAAATGGATATACTTTTTCT+AGG - chr5.1:26633200-26633219 MS.gene45139:intron 20.0%
!!! CCATTTTTTTATTCTATACA+AGG + chr5.1:26633187-26633206 None:intergenic 20.0%
! CTTGAAAATAGATATACTGA+TGG - chr5.1:26633048-26633067 MS.gene45139:CDS 25.0%
!! ACATGTGTTTGATGAATTTT+TGG - chr5.1:26632978-26632997 MS.gene45139:CDS 25.0%
!!! AAACTTAGTTGATTTTGGTT+TGG - chr5.1:26633631-26633650 MS.gene45139:intron 25.0%
!!! ACTTCAAACTTAGTTGATTT+TGG - chr5.1:26633626-26633645 MS.gene45139:intron 25.0%
AATTCATCAAACACATGTTG+TGG + chr5.1:26632976-26632995 None:intergenic 30.0%
GAATGCATTCAATCAAATCA+TGG - chr5.1:26633222-26633241 MS.gene45139:intron 30.0%
GGAAAAGAAACTTGAGATAA+CGG + chr5.1:26633444-26633463 None:intergenic 30.0%
TGAACTCATGATATCAATTG+AGG + chr5.1:26633019-26633038 None:intergenic 30.0%
! TTTTACATTTTACATGCCCA+TGG - chr5.1:26633146-26633165 MS.gene45139:intron 30.0%
!! ATGAACATTGACTTGAGATT+AGG + chr5.1:26633498-26633517 None:intergenic 30.0%
ACAAGAAGAGTTAGTGTTTG+TGG - chr5.1:26633833-26633852 MS.gene45139:CDS 35.0%
CCTGAATTACTCAAATCATC+AGG + chr5.1:26632943-26632962 None:intergenic 35.0%
CCTGATGATTTGAGTAATTC+AGG - chr5.1:26632940-26632959 MS.gene45139:CDS 35.0%
CTAGGATTAAGAAGTGATAG+AGG + chr5.1:26633102-26633121 None:intergenic 35.0%
CTTGTCATCCTTTCTTAGTT+GGG - chr5.1:26633595-26633614 MS.gene45139:intron 35.0%
TCTTGTCATCCTTTCTTAGT+TGG - chr5.1:26633594-26633613 MS.gene45139:intron 35.0%
TGTAATGCCTTAGACTCAAT+AGG + chr5.1:26633816-26633835 None:intergenic 35.0%
TTAATCCTAGAGAAGAAGCA+AGG - chr5.1:26633112-26633131 MS.gene45139:intron 35.0%
TTGGCAAGGTTATATGAACA+TGG - chr5.1:26633650-26633669 MS.gene45139:intron 35.0%
TTGTATGTCCCAACTAAGAA+AGG + chr5.1:26633606-26633625 None:intergenic 35.0%
! AAAAAACAGTTTTGCGACGT+CGG - chr5.1:26633316-26633335 MS.gene45139:intron 35.0%
! AGATAACGGTCTTTGTAAAG+CGG + chr5.1:26633430-26633449 None:intergenic 35.0%
! AGTTCAGACGTTTTTGCATT+TGG - chr5.1:26633756-26633775 MS.gene45139:CDS 35.0%
! TAGCAGCAAATCACATCTTT+TGG - chr5.1:26633545-26633564 MS.gene45139:intron 35.0%
!!! CGCAAAACTGTTTTTTGACT+TGG + chr5.1:26633312-26633331 None:intergenic 35.0%
!!! TAGTTGATTTTGGTTTGGCA+AGG - chr5.1:26633636-26633655 MS.gene45139:intron 35.0%
AAGAGTTAGTGTTTGTGGAC+TGG - chr5.1:26633838-26633857 MS.gene45139:CDS 40.0%
AAGTAACACTACGATGCGAT+TGG - chr5.1:26633284-26633303 MS.gene45139:intron 40.0%
AGAGTTAGTGTTTGTGGACT+GGG - chr5.1:26633839-26633858 MS.gene45139:CDS 40.0%
! ATGAACATGGTGCTAATCCA+GGG - chr5.1:26633663-26633682 MS.gene45139:intron 40.0%
! TATGAACATGGTGCTAATCC+AGG - chr5.1:26633662-26633681 MS.gene45139:intron 40.0%
ACCTTTAGGCTATTTGGCAC+CGG - chr5.1:26633704-26633723 MS.gene45139:CDS 45.0%
GAGAAGGCCTATTGAGTCTA+AGG - chr5.1:26633806-26633825 MS.gene45139:CDS 45.0%
GTAGATGCTCTTCCTGTTCT+AGG + chr5.1:26633735-26633754 None:intergenic 45.0%
GTGGGAACCTTTAGGCTATT+TGG - chr5.1:26633698-26633717 MS.gene45139:intron 45.0%
TTCTGCTTGAGGTTGCTTGT+GGG - chr5.1:26633784-26633803 MS.gene45139:CDS 45.0%
!! ATTTGGTGCACTTCTGCTTG+AGG - chr5.1:26633773-26633792 MS.gene45139:CDS 45.0%
AAAGGTTCCCACCACTCTTG+TGG + chr5.1:26633690-26633709 None:intergenic 50.0%
CTTCTGCTTGAGGTTGCTTG+TGG - chr5.1:26633783-26633802 MS.gene45139:CDS 50.0%
GGTCACCTTGCTTCTTCTCT+AGG + chr5.1:26633120-26633139 None:intergenic 50.0%
TAATCCAGGGACCACAAGAG+TGG - chr5.1:26633676-26633695 MS.gene45139:intron 50.0%
TTGAGGTTGCTTGTGGGAGA+AGG - chr5.1:26633790-26633809 MS.gene45139:CDS 50.0%
! CAAGAGTGGTGGGAACCTTT+AGG - chr5.1:26633690-26633709 MS.gene45139:intron 50.0%
! CTTCCTGTTCTAGGCAACTC+CGG + chr5.1:26633726-26633745 None:intergenic 50.0%
! TCCGGTGCCAAATAGCCTAA+AGG + chr5.1:26633708-26633727 None:intergenic 50.0%
GAGCGAAGTCAGCGAACCAT+GGG + chr5.1:26633165-26633184 None:intergenic 55.0%
CCAGGGACCACAAGAGTGGT+GGG - chr5.1:26633680-26633699 MS.gene45139:intron 60.0%
GCACCGGAGTTGCCTAGAAC+AGG - chr5.1:26633720-26633739 MS.gene45139:CDS 60.0%
GGAGCGAAGTCAGCGAACCA+TGG + chr5.1:26633166-26633185 None:intergenic 60.0%
TCCAGGGACCACAAGAGTGG+TGG - chr5.1:26633679-26633698 MS.gene45139:intron 60.0%
CCCACCACTCTTGTGGTCCC+TGG + chr5.1:26633683-26633702 None:intergenic 65.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 26632910 26633866 26632910 ID=MS.gene45139
chr5.1 mRNA 26632910 26633866 26632910 ID=MS.gene45139.t1;Parent=MS.gene45139
chr5.1 exon 26633701 26633866 26633701 ID=MS.gene45139.t1.exon1;Parent=MS.gene45139.t1
chr5.1 CDS 26633701 26633866 26633701 ID=cds.MS.gene45139.t1;Parent=MS.gene45139.t1
chr5.1 exon 26632910 26633118 26632910 ID=MS.gene45139.t1.exon2;Parent=MS.gene45139.t1
chr5.1 CDS 26632910 26633118 26632910 ID=cds.MS.gene45139.t1;Parent=MS.gene45139.t1
Gene Sequence

>MS.gene45139

ATGAGGATTTTGGATGGAGAAGTTGAGTTGCCTGATGATTTGAGTAATTCAGGAGTTATTGATCCACAACATGTGTTTGATGAATTTTTGGACTCTCTTGCATATTCCTCAATTGATATCATGAGTTCAAGCTCTTATCTTGAAAATAGATATACTGATGGAACTTGTAATATATCTTTTGAGAATTCACCTCTATCACTTCTTAATCCTAGAGAAGAAGCAAGGTGACCTATACATTTTACATTTTACATGCCCATGGTTCGCTGACTTCGCTCCTTGTATAGAATAAAAAAATGGATATACTTTTTCTAGGAATGCATTCAATCAAATCATGGTATGTAGATAGTGAAGATACTTTAGTAACAAACTTATTAAAGTAACACTACGATGCGATTGGATCCAAGTCAAAAAACAGTTTTGCGACGTCGGTGTATATCAATTAATCTCATCAAAATATGTAAATATGTAATGTAACAAAAAAAAAAAAAAAACCAAAAATATGTAAGAAAACAAAATTCCGCTTTACAAAGACCGTTATCTCAAGTTTCTTTTCCCAATAAGTTTATATTCATGTATGTATATTGACCTAATCTCAAGTCAATGTTCATTAGTCTAAGAAAGAAAGAAAAAAAGACTAGCAGCAAATCACATCTTTTGGATTTTTCCAATTTTTCATTTATGATTTCTTGTCATCCTTTCTTAGTTGGGACATACAAACTTCAAACTTAGTTGATTTTGGTTTGGCAAGGTTATATGAACATGGTGCTAATCCAGGGACCACAAGAGTGGTGGGAACCTTTAGGCTATTTGGCACCGGAGTTGCCTAGAACAGGAAGAGCATCTACGAGTTCAGACGTTTTTGCATTTGGTGCACTTCTGCTTGAGGTTGCTTGTGGGAGAAGGCCTATTGAGTCTAAGGCATTACAAGAAGAGTTAGTGTTTGTGGACTGGGTGTAG
Protein sequence

>MS.gene45139.t1

MRILDGEVELPDDLSNSGVIDPQHVFDEFLDSLAYSSIDIMSSSSYLENRYTDGTCYMNMVLIQGPQEWWEPLGYLAPELPRTGRASTSSDVFAFGALLLEVACGRRPIESKALQEELVFVDWV