AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40595


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40595.t1 MTR_3g109925 100.000 158 0 0 1 158 318 475 1.92e-111 325
MS.gene40595.t1 MTR_3g109925 100.000 158 0 0 1 158 375 532 6.98e-111 325
MS.gene40595.t1 MTR_8g105970 92.437 119 9 0 3 121 235 353 3.30e-77 234
MS.gene40595.t1 MTR_7g113470 37.821 156 97 0 1 156 362 517 1.49e-32 120
MS.gene40595.t1 MTR_3g086330 38.710 155 94 1 3 156 377 531 2.20e-32 120
MS.gene40595.t1 MTR_7g067470 37.179 156 98 0 1 156 362 517 6.43e-32 119
MS.gene40595.t1 MTR_5g087560 36.943 157 96 2 2 155 370 526 2.92e-27 106
MS.gene40595.t1 MTR_2g013540 37.419 155 96 1 3 156 221 375 3.56e-24 97.1
MS.gene40595.t1 MTR_2g013540 37.419 155 96 1 3 156 370 524 6.89e-24 97.1
MS.gene40595.t1 MTR_8g088270 35.443 158 94 1 6 155 377 534 1.39e-23 96.3
MS.gene40595.t1 MTR_1g030650 30.719 153 106 0 6 158 374 526 1.49e-22 93.2
MS.gene40595.t1 MTR_6g032870 31.373 153 105 0 6 158 371 523 2.66e-22 92.4
MS.gene40595.t1 MTR_4g057020 96.667 30 1 0 1 30 101 130 1.43e-12 62.0
MS.gene40595.t1 MTR_7g406870 26.144 153 111 2 4 155 374 525 4.67e-11 60.1
MS.gene40595.t1 MTR_7g406870 26.144 153 111 2 4 155 262 413 6.09e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40595.t1 AT3G18190 93.038 158 11 0 1 158 379 536 4.98e-105 310
MS.gene40595.t1 AT1G24510 42.949 156 88 1 2 156 300 455 1.16e-35 128
MS.gene40595.t1 AT1G24510 42.949 156 88 1 2 156 323 478 1.22e-35 129
MS.gene40595.t1 AT1G24510 43.226 155 87 1 3 156 377 531 1.99e-35 129
MS.gene40595.t1 AT5G20890 37.821 156 97 0 1 156 362 517 4.15e-31 117
MS.gene40595.t1 AT3G11830 36.306 157 97 2 2 155 370 526 3.18e-27 106
MS.gene40595.t1 AT3G11830 36.306 157 95 3 2 155 370 524 1.38e-25 102
MS.gene40595.t1 AT3G20050 36.709 158 92 1 6 155 377 534 1.65e-24 99.0
MS.gene40595.t1 AT3G03960 31.169 154 106 0 5 158 376 529 1.99e-23 95.9
MS.gene40595.t1 AT5G26360 37.419 155 96 1 3 156 370 524 1.66e-21 90.1
MS.gene40595.t1 AT5G16070 30.323 155 94 5 4 146 373 525 3.65e-12 63.5
MS.gene40595.t1 AT3G02530 29.221 154 97 4 4 146 374 526 1.84e-11 61.6

Find 36 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTCTCAGCAAGGGTATA+TGG 0.307049 3.3:+90259661 None:intergenic
TGTCAAGGCAATTGGGTGCT+TGG 0.354279 3.3:-90259750 MS.gene40595:CDS
GATAGAGCTGTCAAGGCAAT+TGG 0.370145 3.3:-90259758 MS.gene40595:CDS
ATGATGCTTTGTGTGTTGTT+AGG 0.372583 3.3:-90259828 MS.gene40595:CDS
GTCAAGGCAATTGGGTGCTT+GGG 0.415529 3.3:-90259749 MS.gene40595:CDS
AGCTCAGTAACAATTGCAAT+CGG 0.423035 3.3:+90259628 None:intergenic
TTTGTGTGTTGTTAGGTGTT+TGG 0.427682 3.3:-90259821 MS.gene40595:CDS
ACCACAACTGTGCTTGTTCG+TGG 0.463002 3.3:-90259892 MS.gene40595:CDS
GAATGTGGTGCAGCCATTGC+TGG 0.481414 3.3:-90259527 MS.gene40595:CDS
GCAATTGGGTGCTTGGGCTA+AGG 0.488468 3.3:-90259743 MS.gene40595:CDS
TATACCCTTGCTGAGAATGC+AGG 0.493053 3.3:-90259658 MS.gene40595:CDS
CTGAGGAATCGTCATGCTAA+AGG 0.500255 3.3:-90259607 MS.gene40595:CDS
TCAACACTGGAATCAATGTC+AGG 0.507995 3.3:-90259579 MS.gene40595:CDS
ATAGAGCTGTCAAGGCAATT+GGG 0.513984 3.3:-90259757 MS.gene40595:CDS
GATTGCAGGTGGTGGTGCTC+CGG 0.514051 3.3:-90259782 MS.gene40595:CDS
TGCCTTGACAGCTCTATCTC+CGG 0.516484 3.3:+90259763 None:intergenic
CTCCGGAGATAGAGCTGTCA+AGG 0.563162 3.3:-90259765 MS.gene40595:CDS
CCTCACACACTCTGTTGCCA+AGG 0.573445 3.3:+90259486 None:intergenic
TGGAACAACTTCAAGTGCCT+CGG 0.574575 3.3:+90259681 None:intergenic
GCTCAGTAACAATTGCAATC+GGG 0.575791 3.3:+90259629 None:intergenic
GCACTTGTGCTAACCAGCAA+TGG 0.592202 3.3:+90259514 None:intergenic
TCAAACCTGCATTCTCAGCA+AGG 0.593910 3.3:+90259653 None:intergenic
CTGTATTCGTGCATTTGCCG+AGG 0.594695 3.3:-90259698 MS.gene40595:CDS
ACACTCTGTTGCCAAGGTGA+TGG 0.598855 3.3:+90259492 None:intergenic
GCTAAAGGTGAGATCAACAC+TGG 0.604820 3.3:-90259592 MS.gene40595:CDS
TTGCAATTGTTACTGAGCTG+AGG 0.612866 3.3:-90259624 MS.gene40595:CDS
TCCACGAACAAGCACAGTTG+TGG 0.612984 3.3:+90259891 None:intergenic
GCTGCACCACATTCTCCTCA+AGG 0.613760 3.3:+90259536 None:intergenic
TAGCACAAGTGCCATCACCT+TGG 0.618089 3.3:-90259503 MS.gene40595:CDS
TCAAATTACAAACATCCTTG+AGG 0.621720 3.3:-90259551 MS.gene40595:CDS
ACTGGAATCAATGTCAGGAA+AGG 0.625427 3.3:-90259574 MS.gene40595:CDS
AAACATCCTTGAGGAGAATG+TGG 0.628033 3.3:-90259542 MS.gene40595:CDS
TTAGGTGTTTGGTTGCCAAG+AGG 0.631658 3.3:-90259810 MS.gene40595:CDS
CCTTGGCAACAGAGTGTGTG+AGG 0.652881 3.3:-90259486 MS.gene40595:CDS
CAAACCTGCATTCTCAGCAA+GGG 0.653006 3.3:+90259654 None:intergenic
TTGATGATATTGTAACTGTG+AGG 0.759737 3.3:-90259450 MS.gene40595:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TCAAATTACAAACATCCTTG+AGG - chr3.3:90259797-90259816 MS.gene40595:CDS 30.0%
! TTGATGATATTGTAACTGTG+AGG - chr3.3:90259898-90259917 MS.gene40595:CDS 30.0%
AGCTCAGTAACAATTGCAAT+CGG + chr3.3:90259723-90259742 None:intergenic 35.0%
! ATGATGCTTTGTGTGTTGTT+AGG - chr3.3:90259520-90259539 MS.gene40595:CDS 35.0%
! TTTGTGTGTTGTTAGGTGTT+TGG - chr3.3:90259527-90259546 MS.gene40595:CDS 35.0%
AAACATCCTTGAGGAGAATG+TGG - chr3.3:90259806-90259825 MS.gene40595:CDS 40.0%
ACCTGCAATCAAAAACCTCT+TGG + chr3.3:90259556-90259575 None:intergenic 40.0%
ACTGGAATCAATGTCAGGAA+AGG - chr3.3:90259774-90259793 MS.gene40595:CDS 40.0%
ATAGAGCTGTCAAGGCAATT+GGG - chr3.3:90259591-90259610 MS.gene40595:CDS 40.0%
GCTCAGTAACAATTGCAATC+GGG + chr3.3:90259722-90259741 None:intergenic 40.0%
TCAACACTGGAATCAATGTC+AGG - chr3.3:90259769-90259788 MS.gene40595:CDS 40.0%
TTGCAATTGTTACTGAGCTG+AGG - chr3.3:90259724-90259743 MS.gene40595:CDS 40.0%
!! AAGAGGTTTTTGATTGCAGG+TGG - chr3.3:90259555-90259574 MS.gene40595:CDS 40.0%
CAAACCTGCATTCTCAGCAA+GGG + chr3.3:90259697-90259716 None:intergenic 45.0%
CTGAGGAATCGTCATGCTAA+AGG - chr3.3:90259741-90259760 MS.gene40595:CDS 45.0%
GATAGAGCTGTCAAGGCAAT+TGG - chr3.3:90259590-90259609 MS.gene40595:CDS 45.0%
GCTAAAGGTGAGATCAACAC+TGG - chr3.3:90259756-90259775 MS.gene40595:CDS 45.0%
TATACCCTTGCTGAGAATGC+AGG - chr3.3:90259690-90259709 MS.gene40595:CDS 45.0%
TCAAACCTGCATTCTCAGCA+AGG + chr3.3:90259698-90259717 None:intergenic 45.0%
TGGAACAACTTCAAGTGCCT+CGG + chr3.3:90259670-90259689 None:intergenic 45.0%
TTAGGTGTTTGGTTGCCAAG+AGG - chr3.3:90259538-90259557 MS.gene40595:CDS 45.0%
! AAGGTTTTGCATGGGATGGA+GGG - chr3.3:90259624-90259643 MS.gene40595:CDS 45.0%
! CTTGGGCTAAGGTTTTGCAT+GGG - chr3.3:90259616-90259635 MS.gene40595:CDS 45.0%
! GCATTCTCAGCAAGGGTATA+TGG + chr3.3:90259690-90259709 None:intergenic 45.0%
! TAAGGTTTTGCATGGGATGG+AGG - chr3.3:90259623-90259642 MS.gene40595:CDS 45.0%
!! AGGTTTTTGATTGCAGGTGG+TGG - chr3.3:90259558-90259577 MS.gene40595:CDS 45.0%
!! GCCAAGAGGTTTTTGATTGC+AGG - chr3.3:90259552-90259571 MS.gene40595:CDS 45.0%
ACACTCTGTTGCCAAGGTGA+TGG + chr3.3:90259859-90259878 None:intergenic 50.0%
ACCACAACTGTGCTTGTTCG+TGG - chr3.3:90259456-90259475 MS.gene40595:CDS 50.0%
CTGTATTCGTGCATTTGCCG+AGG - chr3.3:90259650-90259669 MS.gene40595:CDS 50.0%
GCACTTGTGCTAACCAGCAA+TGG + chr3.3:90259837-90259856 None:intergenic 50.0%
GTCAAGGCAATTGGGTGCTT+GGG - chr3.3:90259599-90259618 MS.gene40595:CDS 50.0%
TAGCACAAGTGCCATCACCT+TGG - chr3.3:90259845-90259864 MS.gene40595:CDS 50.0%
TCCACGAACAAGCACAGTTG+TGG + chr3.3:90259460-90259479 None:intergenic 50.0%
TGCCTTGACAGCTCTATCTC+CGG + chr3.3:90259588-90259607 None:intergenic 50.0%
TGTCAAGGCAATTGGGTGCT+TGG - chr3.3:90259598-90259617 MS.gene40595:CDS 50.0%
! GCTTGGGCTAAGGTTTTGCA+TGG - chr3.3:90259615-90259634 MS.gene40595:CDS 50.0%
! GGCTAAGGTTTTGCATGGGA+TGG - chr3.3:90259620-90259639 MS.gene40595:CDS 50.0%
CCTCACACACTCTGTTGCCA+AGG + chr3.3:90259865-90259884 None:intergenic 55.0%
CCTTGGCAACAGAGTGTGTG+AGG - chr3.3:90259862-90259881 MS.gene40595:CDS 55.0%
CTCCGGAGATAGAGCTGTCA+AGG - chr3.3:90259583-90259602 MS.gene40595:CDS 55.0%
GAATGTGGTGCAGCCATTGC+TGG - chr3.3:90259821-90259840 MS.gene40595:CDS 55.0%
GCAATTGGGTGCTTGGGCTA+AGG - chr3.3:90259605-90259624 MS.gene40595:CDS 55.0%
GCTGCACCACATTCTCCTCA+AGG + chr3.3:90259815-90259834 None:intergenic 55.0%
! GATTGCAGGTGGTGGTGCTC+CGG - chr3.3:90259566-90259585 MS.gene40595:CDS 60.0%


Chromosome Type Strat End Strand Name
chr3.3 gene 90259447 90259923 90259447 ID=MS.gene40595
chr3.3 mRNA 90259447 90259923 90259447 ID=MS.gene40595.t1;Parent=MS.gene40595
chr3.3 exon 90259447 90259923 90259447 ID=MS.gene40595.t1.exon1;Parent=MS.gene40595.t1
chr3.3 CDS 90259447 90259923 90259447 ID=cds.MS.gene40595.t1;Parent=MS.gene40595.t1
Gene Sequence

>MS.gene40595

ATGGGAAAGACCACAACTGTGCTTGTTCGTGGATCTAATTTGCTTGTGCTCGATGAAGCTGAGCGAAGTCTGCATGATGCTTTGTGTGTTGTTAGGTGTTTGGTTGCCAAGAGGTTTTTGATTGCAGGTGGTGGTGCTCCGGAGATAGAGCTGTCAAGGCAATTGGGTGCTTGGGCTAAGGTTTTGCATGGGATGGAGGGTTACTGTATTCGTGCATTTGCCGAGGCACTTGAAGTTGTTCCATATACCCTTGCTGAGAATGCAGGTTTGAACCCGATTGCAATTGTTACTGAGCTGAGGAATCGTCATGCTAAAGGTGAGATCAACACTGGAATCAATGTCAGGAAAGGTCAAATTACAAACATCCTTGAGGAGAATGTGGTGCAGCCATTGCTGGTTAGCACAAGTGCCATCACCTTGGCAACAGAGTGTGTGAGGATGATTTTGAAGATTGATGATATTGTAACTGTGAGGTAG

Protein sequence

>MS.gene40595.t1

MGKTTTVLVRGSNLLVLDEAERSLHDALCVVRCLVAKRFLIAGGGAPEIELSRQLGAWAKVLHGMEGYCIRAFAEALEVVPYTLAENAGLNPIAIVTELRNRHAKGEINTGINVRKGQITNILEENVVQPLLVSTSAITLATECVRMILKIDDIVTVR