AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene040267

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040267.t1 MTR_7g445710 84.167 120 18 1 1 120 425 543 9.50e-69 215
MS.gene040267.t1 MTR_7g450730 82.203 118 20 1 3 120 389 505 4.85e-64 202
MS.gene040267.t1 MTR_7g445530 86.667 90 11 1 1 90 425 513 2.06e-49 164
MS.gene040267.t1 MTR_5g013420 66.667 90 29 1 31 120 1001 1089 8.23e-39 138
MS.gene040267.t1 MTR_5g013420 65.556 90 30 1 31 120 1001 1089 1.22e-37 134
MS.gene040267.t1 MTR_4g010550 64.444 90 31 1 31 120 376 464 1.39e-37 132
MS.gene040267.t1 MTR_4g010830 64.444 90 31 1 31 120 892 980 1.80e-37 134
MS.gene040267.t1 MTR_7g445600 78.947 76 10 2 20 90 282 356 6.76e-34 120
MS.gene040267.t1 MTR_7g084090 46.610 118 60 2 5 120 641 757 3.61e-27 104
MS.gene040267.t1 MTR_6g061200 45.763 118 61 2 5 120 549 665 7.22e-27 103
MS.gene040267.t1 MTR_6g061270 52.222 90 42 1 31 120 606 694 4.86e-26 101
MS.gene040267.t1 MTR_7g052480 47.778 90 46 1 31 120 468 556 5.29e-24 95.9
MS.gene040267.t1 MTR_1g048950 46.237 93 44 2 28 120 447 533 3.45e-22 90.5
MS.gene040267.t1 MTR_8g078490 45.652 92 42 3 29 120 1170 1253 3.13e-17 76.6
MS.gene040267.t1 MTR_3g011440 38.182 110 64 3 9 115 551 659 9.02e-17 75.1
MS.gene040267.t1 MTR_8g042750 38.739 111 60 4 10 115 576 683 8.12e-16 72.4
MS.gene040267.t1 MTR_4g132610 40.860 93 47 2 28 120 963 1047 6.01e-14 67.0
MS.gene040267.t1 MTR_5g018850 40.426 94 48 2 27 120 1422 1507 6.43e-14 67.0
MS.gene040267.t1 MTR_8g070075 48.333 60 30 1 31 90 691 749 4.12e-13 64.7
MS.gene040267.t1 MTR_7g088370 42.169 83 43 3 33 115 623 700 4.42e-13 64.7
MS.gene040267.t1 MTR_8g070070 46.667 60 31 1 31 90 698 756 1.89e-12 62.8
MS.gene040267.t1 MTR_1g035420 41.791 67 38 1 31 97 587 652 2.31e-12 62.4
MS.gene040267.t1 MTR_8g071030 48.333 60 30 1 31 90 678 736 2.34e-12 62.4
MS.gene040267.t1 MTR_8g078505 41.860 86 41 3 30 115 457 533 2.48e-12 62.4
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene040267.t1 AT2G35160 63.333 90 32 1 31 120 706 794 3.86e-37 133
MS.gene040267.t1 AT2G35160 63.333 90 32 1 31 120 706 794 3.86e-37 133
MS.gene040267.t1 AT2G35160 63.333 90 32 1 31 120 706 794 3.86e-37 133
MS.gene040267.t1 AT2G35160 63.333 90 32 1 31 120 706 794 3.86e-37 133
MS.gene040267.t1 AT2G35160 63.333 90 32 1 31 120 670 758 4.14e-37 133
MS.gene040267.t1 AT2G22740 61.702 94 35 1 27 120 698 790 1.92e-36 131
MS.gene040267.t1 AT2G22740 61.702 94 35 1 27 120 698 790 1.92e-36 131
MS.gene040267.t1 AT5G13960 50.000 90 44 1 31 120 402 490 3.47e-24 96.3
MS.gene040267.t1 AT5G13960 50.000 90 44 1 31 120 536 624 3.57e-24 96.3
MS.gene040267.t1 AT5G04940 42.045 88 45 4 31 115 581 665 1.67e-15 71.6
MS.gene040267.t1 AT5G04940 42.045 88 45 4 31 115 581 665 1.67e-15 71.6
MS.gene040267.t1 AT1G73100 39.535 86 46 3 33 115 582 664 1.42e-13 66.2
MS.gene040267.t1 AT2G24740 37.647 85 51 1 33 115 666 750 2.37e-13 65.5
MS.gene040267.t1 AT1G17770 39.773 88 45 3 33 115 604 688 6.35e-12 61.2
MS.gene040267.t1 AT4G13460 48.333 60 30 1 31 90 579 637 1.36e-11 60.5
MS.gene040267.t1 AT4G13460 48.333 60 30 1 31 90 579 637 1.36e-11 60.5
MS.gene040267.t1 AT3G61740 38.636 88 46 2 28 115 934 1013 8.91e-11 58.2

Find 22 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTACCACTTGAAGCTTCTA+AGG 0.221245 7.1:-65636958 None:intergenic
AACATTTCGAGCAAACAAAT+TGG 0.261209 7.1:-65637075 None:intergenic
ACCATTGATGCTGCTAAGTA+TGG 0.290913 7.1:+65637017 MS.gene040267:CDS
TTCATATATGGTTGATAGTA+AGG 0.403159 7.1:+65636917 None:intergenic
ACAAATTGGGAGAACAACTA+TGG 0.427505 7.1:-65637061 None:intergenic
ACATTTCGAGCAAACAAATT+GGG 0.449844 7.1:-65637074 None:intergenic
AATCAAGTGACTGATTCAAA+TGG 0.475671 7.1:+65637203 MS.gene040267:CDS
ACCATACTTAGCAGCATCAA+TGG 0.496537 7.1:-65637018 None:intergenic
CTGATTCAAATGGAAATGTA+AGG 0.504655 7.1:+65637213 MS.gene040267:CDS
AGGAAGAAAGTGTGTTATTG+TGG 0.526623 7.1:+65637233 MS.gene040267:CDS
AGAAGCTTCAAGTGGTAAAG+AGG 0.540440 7.1:+65636962 MS.gene040267:CDS
TTACCACTTGAAGCTTCTAA+GGG 0.542917 7.1:-65636957 None:intergenic
CTAAGTATGGTAACGTGGCA+AGG 0.558339 7.1:+65637030 MS.gene040267:CDS
ATTGATGATCGATGTGATAG+TGG 0.558469 7.1:+65636987 MS.gene040267:CDS
AAAGTCAGCTCATTCATGCT+CGG 0.562361 7.1:-65637161 None:intergenic
ACTATCACATCGATCATCAA+TGG 0.565161 7.1:-65636985 None:intergenic
ATGATCGATGTGATAGTGGT+AGG 0.614728 7.1:+65636991 MS.gene040267:CDS
GTTCTCAGCTGCATATAGCA+TGG 0.637418 7.1:-65637135 None:intergenic
CAACCCTTAGAAGCTTCAAG+TGG 0.647600 7.1:+65636954 MS.gene040267:CDS
CTTGTCAATACAGTCTACGA+AGG 0.678324 7.1:-65637268 None:intergenic
GCTGCATATAGCATGGTGTG+TGG 0.707345 7.1:-65637128 None:intergenic
TGCTGCTAAGTATGGTAACG+TGG 0.728265 7.1:+65637025 MS.gene040267:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AACATTTCGAGCAAACAAAT+TGG - chr7.1:65637078-65637097 None:intergenic 30.0%
ACATTTCGAGCAAACAAATT+GGG - chr7.1:65637077-65637096 None:intergenic 30.0%
CTGATTCAAATGGAAATGTA+AGG + chr7.1:65637213-65637232 MS.gene040267:CDS 30.0%
! AATCAAGTGACTGATTCAAA+TGG + chr7.1:65637203-65637222 MS.gene040267:CDS 30.0%
ACAAATTGGGAGAACAACTA+TGG - chr7.1:65637064-65637083 None:intergenic 35.0%
ACTATCACATCGATCATCAA+TGG - chr7.1:65636988-65637007 None:intergenic 35.0%
TTACCACTTGAAGCTTCTAA+GGG - chr7.1:65636960-65636979 None:intergenic 35.0%
TTTACCACTTGAAGCTTCTA+AGG - chr7.1:65636961-65636980 None:intergenic 35.0%
! AGGAAGAAAGTGTGTTATTG+TGG + chr7.1:65637233-65637252 MS.gene040267:CDS 35.0%
! ATTGATGATCGATGTGATAG+TGG + chr7.1:65636987-65637006 MS.gene040267:CDS 35.0%
AAAGTCAGCTCATTCATGCT+CGG - chr7.1:65637164-65637183 None:intergenic 40.0%
ACCATACTTAGCAGCATCAA+TGG - chr7.1:65637021-65637040 None:intergenic 40.0%
ACCATTGATGCTGCTAAGTA+TGG + chr7.1:65637017-65637036 MS.gene040267:CDS 40.0%
AGAAGCTTCAAGTGGTAAAG+AGG + chr7.1:65636962-65636981 MS.gene040267:CDS 40.0%
! ACGATGATGATGATGATCTG+AGG + chr7.1:65637102-65637121 MS.gene040267:CDS 40.0%
!! ATGATCGATGTGATAGTGGT+AGG + chr7.1:65636991-65637010 MS.gene040267:CDS 40.0%
CAACCCTTAGAAGCTTCAAG+TGG + chr7.1:65636954-65636973 MS.gene040267:CDS 45.0%
GTTCTCAGCTGCATATAGCA+TGG - chr7.1:65637138-65637157 None:intergenic 45.0%
! CTAAGTATGGTAACGTGGCA+AGG + chr7.1:65637030-65637049 MS.gene040267:CDS 45.0%
! TGCTGCTAAGTATGGTAACG+TGG + chr7.1:65637025-65637044 MS.gene040267:CDS 45.0%
GCTGCATATAGCATGGTGTG+TGG - chr7.1:65637131-65637150 None:intergenic 50.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 65636924 65637286 65636924 ID=MS.gene040267
chr7.1 mRNA 65636924 65637286 65636924 ID=MS.gene040267.t1;Parent=MS.gene040267
chr7.1 exon 65636924 65637286 65636924 ID=MS.gene040267.t1.exon1;Parent=MS.gene040267.t1
chr7.1 CDS 65636924 65637286 65636924 ID=cds.MS.gene040267.t1;Parent=MS.gene040267.t1
Gene Sequence

>MS.gene040267

ATGGTTGATAGTAAGGAGATGAGTTCATATCAACCCTTAGAAGCTTCAAGTGGTAAAGAGGCCATTGATGATCGATGTGATAGTGGTAGGTTTACCATTGATGCTGCTAAGTATGGTAACGTGGCAAGGTTTATCAACCATAGTTGTTCTCCCAATTTGTTTGCTCGAAATGTTCTTTACGATGATGATGATGATCTGAGGATTCCACACACCATGCTATATGCAGCTGAGAACATTCCGAGCATGAATGAGCTGACTTTAAATTACAATTACAAGATAAATCAAGTGACTGATTCAAATGGAAATGTAAGGAAGAAAGTGTGTTATTGTGGAGCTTCTGAATGCCTTCGTAGACTGTATTGA
Protein sequence

>MS.gene040267.t1

MVDSKEMSSYQPLEASSGKEAIDDRCDSGRFTIDAAKYGNVARFINHSCSPNLFARNVLYDDDDDLRIPHTMLYAAENIPSMNELTLNYNYKINQVTDSNGNVRKKVCYCGASECLRRLY