AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40420

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40420.t1 MTR_4g051538 80.000 240 38 4 1 236 1 234 2.78e-127 360
MS.gene40420.t1 MTR_3g104630 48.201 139 47 5 106 228 16 145 6.31e-31 112
MS.gene40420.t1 MTR_1g108510 30.247 162 100 3 5 156 5 163 4.76e-17 77.4
MS.gene40420.t1 MTR_3g030770 30.120 166 103 3 1 156 1 163 1.39e-16 76.3
MS.gene40420.t1 MTR_1g108580 32.847 137 82 2 1 127 1 137 2.22e-16 75.9
MS.gene40420.t1 MTR_1g106070 32.374 139 78 3 1 126 1 136 3.00e-16 74.3
MS.gene40420.t1 MTR_3g052920 34.586 133 77 3 5 127 5 137 4.69e-16 75.1
MS.gene40420.t1 MTR_8g043650 33.577 137 81 3 1 127 1 137 8.16e-16 74.3
MS.gene40420.t1 MTR_1g012570 33.333 132 77 3 5 126 5 135 8.49e-16 74.3
MS.gene40420.t1 MTR_3g052870 42.308 78 45 0 5 82 5 82 1.59e-15 73.2
MS.gene40420.t1 MTR_1g105910 34.586 133 77 3 5 127 5 137 1.76e-15 73.6
MS.gene40420.t1 MTR_3g080940 42.683 82 47 0 1 82 1 82 1.83e-15 72.8
MS.gene40420.t1 MTR_1g077360 40.244 82 49 0 1 82 1 82 2.07e-15 73.2
MS.gene40420.t1 MTR_1g105920 42.308 78 45 0 5 82 5 82 2.29e-15 73.2
MS.gene40420.t1 MTR_2g085250 40.260 77 46 0 1 77 1 77 2.92e-15 72.8
MS.gene40420.t1 MTR_5g053390 27.317 205 107 6 5 191 5 185 3.13e-15 72.8
MS.gene40420.t1 MTR_2g085280 40.260 77 46 0 1 77 1 77 3.20e-15 72.8
MS.gene40420.t1 MTR_2g030740 42.308 78 45 0 5 82 5 82 3.20e-15 72.8
MS.gene40420.t1 MTR_5g055100 27.723 202 112 7 1 187 1 183 3.72e-15 72.4
MS.gene40420.t1 MTR_4g094632 35.294 102 62 1 9 106 2 103 1.51e-14 69.3
MS.gene40420.t1 MTR_5g045560 41.667 72 42 0 1 72 1 72 4.65e-14 69.7
MS.gene40420.t1 MTR_2g093190 29.747 158 98 4 1 148 1 155 4.96e-14 69.3
MS.gene40420.t1 MTR_8g086290 36.000 75 48 0 4 78 7 81 7.04e-14 67.8
MS.gene40420.t1 MTR_0121s0100 36.364 77 49 0 1 77 1 77 7.12e-14 66.6
MS.gene40420.t1 MTR_4g094638 38.571 70 43 0 9 78 2 71 1.28e-13 67.4
MS.gene40420.t1 MTR_1g075600 37.179 78 49 0 5 82 5 82 1.58e-13 68.2
MS.gene40420.t1 MTR_2g105290 27.160 162 107 4 4 158 7 164 1.82e-13 66.6
MS.gene40420.t1 MTR_3g030780 38.889 72 44 0 1 72 1 72 4.41e-13 64.7
MS.gene40420.t1 MTR_0121s0080 28.205 117 71 1 5 121 5 108 4.48e-12 63.9
MS.gene40420.t1 MTR_8g079502 33.735 83 47 1 9 83 2 84 2.13e-11 61.2
MS.gene40420.t1 MTR_1g047550 33.333 72 48 0 9 80 2 73 5.91e-11 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40420.t1 AT4G36590 45.679 81 43 1 5 84 3 83 4.08e-17 78.2
MS.gene40420.t1 AT1G29962 43.750 80 44 1 1 80 1 79 3.55e-16 74.3
MS.gene40420.t1 AT2G34440 31.013 158 100 5 9 159 2 157 1.01e-15 72.8
MS.gene40420.t1 AT5G60440 42.308 78 44 1 5 82 3 79 1.68e-14 71.6
MS.gene40420.t1 AT2G24840 40.000 80 48 0 7 86 61 140 2.63e-14 70.9
MS.gene40420.t1 AT1G28460 42.308 78 44 1 1 78 1 77 1.54e-13 67.0
MS.gene40420.t1 AT1G01530 33.645 107 67 1 5 107 3 109 6.16e-13 66.6
MS.gene40420.t1 AT3G04100 35.714 84 51 1 5 88 10 90 4.54e-12 63.5
MS.gene40420.t1 AT1G28450 38.750 80 48 1 1 80 1 79 1.69e-11 61.6
MS.gene40420.t1 AT3G66656 40.000 65 39 0 9 73 2 66 1.79e-11 61.2
MS.gene40420.t1 AT1G65360 39.683 63 38 0 5 67 3 65 7.66e-11 60.5

Find 33 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGAAGATGTTGGAAAGTTC+TGG 0.270990 6.3:+71018650 MS.gene40420:CDS
TCTGAGTTAACAACACTTTC+AGG 0.273550 6.3:+71018419 MS.gene40420:CDS
ACACAAGGAGTCAACCTTAT+TGG 0.323352 6.3:+71019309 MS.gene40420:CDS
TTTCCTCTTGAAGACCTCTT+TGG 0.325481 6.3:-71018308 None:intergenic
ATCATTTCCTCTTCTATTGA+AGG 0.331143 6.3:-71018545 None:intergenic
AACAGCAAAGATCATGAAAT+TGG 0.350136 6.3:+71018991 MS.gene40420:CDS
ATCCTCCGCTTGCACCAATA+AGG 0.357163 6.3:-71019323 None:intergenic
TGTTGGAAAGTTCTGGATAT+TGG 0.391346 6.3:+71018657 MS.gene40420:CDS
TTTATTTGTGACAGCAACTA+AGG 0.402905 6.3:-71018741 None:intergenic
ATTCTCATGCTTTCTCCAAC+GGG 0.403336 6.3:+71018455 MS.gene40420:CDS
TTTCTTTCACTTGATCATAC+TGG 0.408170 6.3:-71018709 None:intergenic
TTTGTTATAGATTCAGAAGA+TGG 0.410640 6.3:-71018500 None:intergenic
CCTCTTGAAGACCTCTTTGG+CGG 0.454706 6.3:-71018305 None:intergenic
GCATTTACAACGAGAAAGTC+TGG 0.455029 6.3:+71018380 MS.gene40420:CDS
TATTCTCATGCTTTCTCCAA+CGG 0.502164 6.3:+71018454 MS.gene40420:CDS
TGATCCAAAAGGTAAAGGTA+TGG 0.511773 6.3:+71019260 MS.gene40420:intron
TGAAAATCCTTCAATAGAAG+AGG 0.547647 6.3:+71018538 MS.gene40420:CDS
GACTCCATTCAGTTCCTCGA+TGG 0.554069 6.3:-71018938 None:intergenic
TCTACCATCGAGGAACTGAA+TGG 0.572587 6.3:+71018934 MS.gene40420:CDS
TGGATATTGGTCAATTCAAG+AGG 0.585196 6.3:+71018670 MS.gene40420:CDS
GTCAACCTTATTGGTGCAAG+CGG 0.586884 6.3:+71019318 MS.gene40420:CDS
AACCTTATTGGTGCAAGCGG+AGG 0.596051 6.3:+71019321 MS.gene40420:CDS
GAGTAAGAATGCCGCCAAAG+AGG 0.604888 6.3:+71018294 None:intergenic
TTTGGATGAAAAGCATGTTG+CGG 0.642474 6.3:+71018610 MS.gene40420:CDS
TGTAGTAATTTCTACCATCG+AGG 0.654680 6.3:+71018924 MS.gene40420:intron
CCGCCAAAGAGGTCTTCAAG+AGG 0.664394 6.3:+71018305 MS.gene40420:CDS
TGAAAGTGTTGTTAACTCAG+AGG 0.669188 6.3:-71018417 None:intergenic
GGAGGAGATCTTAACCCTCG+TGG 0.672202 6.3:+71018788 MS.gene40420:CDS
GCAAGCGGAGGATATGAAAG+TGG 0.676676 6.3:+71019333 MS.gene40420:CDS
AAGCATGAGAATATCAACTG+AGG 0.702546 6.3:-71018444 None:intergenic
TCTCGTGATATAGAAACACA+AGG 0.706006 6.3:+71019294 MS.gene40420:CDS
AAGATGTACACATACCACGA+GGG 0.757349 6.3:-71018802 None:intergenic
AAAGTCTGGAATTTACAACA+AGG 0.757794 6.3:+71018394 MS.gene40420:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTAAAATAATTAGACAAAA+AGG - chr6.3:71018885-71018904 None:intergenic 10.0%
!! AAAAACAAAAAATTAAACAC+AGG - chr6.3:71019037-71019056 None:intergenic 15.0%
!! ATAAATAAAGTCTTGAAAAA+TGG + chr6.3:71018767-71018786 MS.gene40420:CDS 15.0%
!!! CTAATTATTTTAAATGAATC+TGG + chr6.3:71018891-71018910 MS.gene40420:intron 15.0%
!! AAAAAATTAAACACAGGAAT+GGG - chr6.3:71019031-71019050 None:intergenic 20.0%
!! ACCATTTAATATTCACTTAT+GGG + chr6.3:71019112-71019131 MS.gene40420:intron 20.0%
!! TACCATTTAATATTCACTTA+TGG + chr6.3:71019111-71019130 MS.gene40420:intron 20.0%
!! TCTTCTTAATTTCTATTACT+AGG + chr6.3:71019153-71019172 MS.gene40420:intron 20.0%
!!! TCATTTTGCTGTATAATATT+CGG - chr6.3:71018575-71018594 None:intergenic 20.0%
!!! TGAAAAAAATGATGATCTTT+TGG + chr6.3:71018592-71018611 MS.gene40420:CDS 20.0%
! AAAAAGATTGAATCCATGAA+AGG - chr6.3:71019241-71019260 None:intergenic 25.0%
! AATAAAGTCTTGAAAAATGG+AGG + chr6.3:71018770-71018789 MS.gene40420:CDS 25.0%
! ACGTAAAAATTTGAAGATGT+TGG + chr6.3:71018640-71018659 MS.gene40420:CDS 25.0%
! CAAAAAATTAAACACAGGAA+TGG - chr6.3:71019032-71019051 None:intergenic 25.0%
! GAATATTAAATGGTAAAAGC+TGG - chr6.3:71019106-71019125 None:intergenic 25.0%
! TCCCATAAGTGAATATTAAA+TGG - chr6.3:71019116-71019135 None:intergenic 25.0%
!! TTCAATCTTTTTGATCCAAA+AGG + chr6.3:71019249-71019268 MS.gene40420:intron 25.0%
!! TTTGTTATAGATTCAGAAGA+TGG - chr6.3:71018503-71018522 None:intergenic 25.0%
!! TTTTGCTTGAAATATTCTAG+CGG + chr6.3:71019053-71019072 MS.gene40420:intron 25.0%
AACAGCAAAGATCATGAAAT+TGG + chr6.3:71018991-71019010 MS.gene40420:CDS 30.0%
ATCATTTCCTCTTCTATTGA+AGG - chr6.3:71018548-71018567 None:intergenic 30.0%
TATGTATTGTCTTCCTTTCA+TGG + chr6.3:71019225-71019244 MS.gene40420:intron 30.0%
TGAAAATCCTTCAATAGAAG+AGG + chr6.3:71018538-71018557 MS.gene40420:CDS 30.0%
TTCAAGAGGAAAACAAAAAG+TGG + chr6.3:71018319-71018338 MS.gene40420:CDS 30.0%
TTTATTTGTGACAGCAACTA+AGG - chr6.3:71018744-71018763 None:intergenic 30.0%
TTTCTTTCACTTGATCATAC+TGG - chr6.3:71018712-71018731 None:intergenic 30.0%
! AAAGTCTGGAATTTACAACA+AGG + chr6.3:71018394-71018413 MS.gene40420:CDS 30.0%
! CTTTTTGATCCAAAAGGTAA+AGG + chr6.3:71019255-71019274 MS.gene40420:intron 30.0%
! GATGGTTTTCCATAACAAAA+TGG - chr6.3:71018485-71018504 None:intergenic 30.0%
!! AAATCCTGCTTATGTTTTTG+AGG + chr6.3:71018966-71018985 MS.gene40420:CDS 30.0%
AAGCATGAGAATATCAACTG+AGG - chr6.3:71018447-71018466 None:intergenic 35.0%
TATTCTCATGCTTTCTCCAA+CGG + chr6.3:71018454-71018473 MS.gene40420:CDS 35.0%
TCTCGTGATATAGAAACACA+AGG + chr6.3:71019294-71019313 MS.gene40420:CDS 35.0%
TCTGAGTTAACAACACTTTC+AGG + chr6.3:71018419-71018438 MS.gene40420:CDS 35.0%
TGATCCAAAAGGTAAAGGTA+TGG + chr6.3:71019260-71019279 MS.gene40420:intron 35.0%
TGGATATTGGTCAATTCAAG+AGG + chr6.3:71018670-71018689 MS.gene40420:CDS 35.0%
TGTAGTAATTTCTACCATCG+AGG + chr6.3:71018924-71018943 MS.gene40420:intron 35.0%
TTGAAGATGTTGGAAAGTTC+TGG + chr6.3:71018650-71018669 MS.gene40420:CDS 35.0%
TTGTCCTCAAAAACATAAGC+AGG - chr6.3:71018973-71018992 None:intergenic 35.0%
! ACGGGAAAACCATTTTGTTA+TGG + chr6.3:71018473-71018492 MS.gene40420:CDS 35.0%
! TAACAAAATGGTTTTCCCGT+TGG - chr6.3:71018473-71018492 None:intergenic 35.0%
! TTTGGATGAAAAGCATGTTG+CGG + chr6.3:71018610-71018629 MS.gene40420:CDS 35.0%
!! TGAAAGTGTTGTTAACTCAG+AGG - chr6.3:71018420-71018439 None:intergenic 35.0%
!! TGTTGGAAAGTTCTGGATAT+TGG + chr6.3:71018657-71018676 MS.gene40420:CDS 35.0%
AAGATGTACACATACCACGA+GGG - chr6.3:71018805-71018824 None:intergenic 40.0%
ACACAAGGAGTCAACCTTAT+TGG + chr6.3:71019309-71019328 MS.gene40420:CDS 40.0%
ATTCTCATGCTTTCTCCAAC+GGG + chr6.3:71018455-71018474 MS.gene40420:CDS 40.0%
GCATTTACAACGAGAAAGTC+TGG + chr6.3:71018380-71018399 MS.gene40420:CDS 40.0%
GGTGACACTCACACATTAAA+TGG + chr6.3:71019074-71019093 MS.gene40420:intron 40.0%
TTTCCTCTTGAAGACCTCTT+TGG - chr6.3:71018311-71018330 None:intergenic 40.0%
! GCAACCATACCTTTACCTTT+TGG - chr6.3:71019267-71019286 None:intergenic 40.0%
GAAGATGTACACATACCACG+AGG - chr6.3:71018806-71018825 None:intergenic 45.0%
GTCAACCTTATTGGTGCAAG+CGG + chr6.3:71019318-71019337 MS.gene40420:CDS 45.0%
TCTACCATCGAGGAACTGAA+TGG + chr6.3:71018934-71018953 MS.gene40420:CDS 45.0%
AACCTTATTGGTGCAAGCGG+AGG + chr6.3:71019321-71019340 MS.gene40420:CDS 50.0%
ATCCTCCGCTTGCACCAATA+AGG - chr6.3:71019326-71019345 None:intergenic 50.0%
CCTCTTGAAGACCTCTTTGG+CGG - chr6.3:71018308-71018327 None:intergenic 50.0%
GACTCCATTCAGTTCCTCGA+TGG - chr6.3:71018941-71018960 None:intergenic 50.0%
GCAAGCGGAGGATATGAAAG+TGG + chr6.3:71019333-71019352 MS.gene40420:CDS 50.0%
CCGCCAAAGAGGTCTTCAAG+AGG + chr6.3:71018305-71018324 MS.gene40420:CDS 55.0%
GGAGGAGATCTTAACCCTCG+TGG + chr6.3:71018788-71018807 MS.gene40420:CDS 55.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 71018302 71019383 71018302 ID=MS.gene40420
chr6.3 mRNA 71018302 71019383 71018302 ID=MS.gene40420.t1;Parent=MS.gene40420
chr6.3 exon 71018302 71018809 71018302 ID=MS.gene40420.t1.exon1;Parent=MS.gene40420.t1
chr6.3 CDS 71018302 71018809 71018302 ID=cds.MS.gene40420.t1;Parent=MS.gene40420.t1
chr6.3 exon 71018929 71019018 71018929 ID=MS.gene40420.t1.exon2;Parent=MS.gene40420.t1
chr6.3 CDS 71018929 71019018 71018929 ID=cds.MS.gene40420.t1;Parent=MS.gene40420.t1
chr6.3 exon 71019271 71019383 71019271 ID=MS.gene40420.t1.exon3;Parent=MS.gene40420.t1
chr6.3 CDS 71019271 71019383 71019271 ID=cds.MS.gene40420.t1;Parent=MS.gene40420.t1
Gene Sequence

>MS.gene40420

ATGCCGCCAAAGAGGTCTTCAAGAGGAAAACAAAAAGTGGAGCTAAAAAAAATTGAGAGTAAGAATGATCTCTTTGTTGCATTTACAACGAGAAAGTCTGGAATTTACAACAAGGCCTCTGAGTTAACAACACTTTCAGGAGCCTCAGTTGATATTCTCATGCTTTCTCCAACGGGAAAACCATTTTGTTATGGAAAACCATCTTCTGAATCTATAACAAAAACTAGTTTGAATGATGAAAATCCTTCAATAGAAGAGGAAATGATGAAACCGAATATTATACAGCAAAATGAAAAAAATGATGATCTTTTGGATGAAAAGCATGTTGCGGATGCACAACGTAAAAATTTGAAGATGTTGGAAAGTTCTGGATATTGGTCAATTCAAGAGGAAGATGATAAAAGCTACCAGTATGATCAAGTGAAAGAAATTGACAAATCCTTAGTTGCTGTCACAAATAAATTGATAAATAAAGTCTTGAAAAATGGAGGAGATCTTAACCCTCGTGGTATGTGTACATCTTCTAATTAACTATGTGTTATATTTGATCTATTAATGACGTCAAATGATTTCATGTCATCCTTTTTGTCTAATTATTTTAAATGAATCTGGTTATAATTTTTGTAGTAATTTCTACCATCGAGGAACTGAATGGAGTCAAAACAAATCCTGCTTATGTTTTTGAGGACAACAGCAAAGATCATGAAATTGGTGCAAGTAAGAATTCCCATTCCTGTGTTTAATTTTTTGTTTTTGCTTGAAATATTCTAGCGGTGACACTCACACATTAAATGGTGAAATCCAGCTTTTACCATTTAATATTCACTTATGGGAAAAATCTCAATTACTTTTCTTCTTAATTTCTATTACTAGGCATGCAAACATTTACTTATAATATTTCATGCGACAAATCTAACATATGTTATGTATTGTCTTCCTTTCATGGATTCAATCTTTTTGATCCAAAAGGTAAAGGTATGGTTGCTAATGCTTCTCGTGATATAGAAACACAAGGAGTCAACCTTATTGGTGCAAGCGGAGGATATGAAAGTGGTGTTGATCATGCTTCTCGAGATATATGA
Protein sequence

>MS.gene40420.t1

MPPKRSSRGKQKVELKKIESKNDLFVAFTTRKSGIYNKASELTTLSGASVDILMLSPTGKPFCYGKPSSESITKTSLNDENPSIEEEMMKPNIIQQNEKNDDLLDEKHVADAQRKNLKMLESSGYWSIQEEDDKSYQYDQVKEIDKSLVAVTNKLINKVLKNGGDLNPRVISTIEELNGVKTNPAYVFEDNSKDHEIGASKGMVANASRDIETQGVNLIGASGGYESGVDHASRDI