AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene64883


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64883.t1 MTR_5g024180 99.286 140 1 0 1 140 1 140 1.66e-95 271
MS.gene64883.t1 MTR_8g073345 68.421 133 39 2 1 132 1 131 1.97e-56 172
MS.gene64883.t1 MTR_8g073345 67.969 128 38 2 1 127 1 126 4.25e-53 164
MS.gene64883.t1 MTR_5g024180 94.624 93 2 1 43 132 3 95 1.09e-50 157
MS.gene64883.t1 MTR_3g115580 60.952 105 33 2 6 105 13 114 2.10e-34 117
MS.gene64883.t1 MTR_7g068280 60.000 100 39 1 32 131 47 145 2.76e-30 107
MS.gene64883.t1 MTR_7g082820 53.211 109 45 3 28 131 4 111 6.07e-28 100
MS.gene64883.t1 MTR_1g115220 48.485 99 49 1 32 130 98 194 6.08e-25 95.1
MS.gene64883.t1 MTR_0405s0060 94.118 34 2 0 82 115 74 107 2.46e-14 67.8
MS.gene64883.t1 MTR_4g094622 38.272 81 50 0 25 105 53 133 3.81e-14 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene64883.t1 AT1G20693 62.903 124 40 3 18 139 23 142 5.09e-42 136
MS.gene64883.t1 AT1G20693 64.545 110 35 2 18 127 23 128 3.74e-38 126
MS.gene64883.t1 AT1G20693 64.545 110 35 2 18 127 23 128 3.85e-38 126
MS.gene64883.t1 AT2G17560 50.769 130 61 1 6 135 8 134 1.06e-37 125
MS.gene64883.t1 AT1G20696 66.327 98 32 1 30 127 29 125 5.88e-37 123
MS.gene64883.t1 AT2G17560 52.033 123 56 1 6 128 8 127 7.88e-37 123
MS.gene64883.t1 AT2G17560 52.033 123 56 1 6 128 8 127 7.88e-37 123
MS.gene64883.t1 AT3G51880 61.468 109 37 3 24 131 40 144 1.98e-35 120
MS.gene64883.t1 AT3G51880 61.468 109 37 3 24 131 40 144 1.98e-35 120
MS.gene64883.t1 AT3G51880 61.468 109 37 3 24 131 40 144 1.98e-35 120
MS.gene64883.t1 AT3G51880 61.468 109 37 3 24 131 40 144 2.38e-35 120
MS.gene64883.t1 AT1G20696 72.368 76 21 0 30 105 29 104 6.91e-34 116
MS.gene64883.t1 AT1G20696 72.368 76 21 0 30 105 29 104 8.14e-34 115
MS.gene64883.t1 AT3G51880 60.952 105 36 3 24 127 40 140 4.71e-33 114
MS.gene64883.t1 AT4G35570 47.222 108 53 1 7 114 9 112 9.20e-30 104
MS.gene64883.t1 AT4G35570 47.222 108 53 1 7 114 9 112 9.20e-30 104
MS.gene64883.t1 AT1G20696 56.842 95 38 2 44 136 1 94 1.30e-26 95.9
MS.gene64883.t1 AT1G20696 57.143 84 35 1 44 127 1 83 8.54e-24 89.0
MS.gene64883.t1 AT5G23420 46.667 75 37 2 28 101 107 179 7.66e-14 66.2
MS.gene64883.t1 AT4G23800 49.315 73 34 1 32 104 251 320 1.06e-12 64.3
MS.gene64883.t1 AT4G23800 41.892 74 42 1 32 105 369 441 8.83e-12 61.6
MS.gene64883.t1 AT4G23800 49.315 73 34 1 32 104 251 320 1.14e-12 64.3
MS.gene64883.t1 AT4G23800 41.892 74 42 1 32 105 375 447 9.29e-12 61.6
MS.gene64883.t1 AT2G34450 35.714 70 45 0 36 105 63 132 2.79e-12 60.8
MS.gene64883.t1 AT2G34450 35.714 70 45 0 36 105 63 132 2.79e-12 60.8
MS.gene64883.t1 AT2G34450 35.714 70 45 0 36 105 63 132 2.79e-12 60.8
MS.gene64883.t1 AT2G34450 36.620 71 44 1 36 105 63 133 8.07e-12 59.3
MS.gene64883.t1 AT4G11080 42.553 94 45 2 32 125 242 326 8.07e-12 61.6

Find 35 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GACAATGCGTGCTTACAATA+TGG 0.281097 5.3:+14003238 MS.gene64883:CDS
GGAGGCCTCTTAGGCTTGTT+AGG 0.297257 5.3:-14002647 None:intergenic
AAAGCACTTGGAGGCCTCTT+AGG 0.299005 5.3:-14002656 None:intergenic
TTGAATTAGGTTGGGAAAGC+TGG 0.350890 5.3:+14003034 MS.gene64883:intron
AAGCGCAAGGGCGCTGGTAC+TGG 0.369054 5.3:+14002596 MS.gene64883:CDS
TTATCAGCCTTAGCATTGAA+TGG 0.428927 5.3:-14003194 None:intergenic
ACAGCAACGGACTTGTTGCT+TGG 0.433440 5.3:-14002924 None:intergenic
TTAGCATCGGAAACAGCTTT+CGG 0.437399 5.3:-14002457 None:intergenic
ATGCTAAACCTGCTGATAAC+CGG 0.456641 5.3:+14002473 MS.gene64883:CDS
ACAATGCGTGCTTACAATAT+GGG 0.459061 5.3:+14003239 MS.gene64883:CDS
ATCATCATTCACTTCAGACT+TGG 0.478350 5.3:-14003409 None:intergenic
TGCTAAGGCTGATAAGTTGA+AGG 0.485540 5.3:+14003202 MS.gene64883:CDS
GAATCTCACCGGTTATCAGC+AGG 0.496399 5.3:-14002481 None:intergenic
GTTCAGAGAGAGGTTTAAGA+AGG 0.508587 5.3:+14002896 MS.gene64883:CDS
GGAAAGCTGGTGGAAAGGAA+TGG 0.519414 5.3:+14003047 MS.gene64883:CDS
AGGTTGAAGCGCAAGGGCGC+TGG 0.524589 5.3:+14002590 MS.gene64883:intron
GTTTGTTAGGTTGAAGCGCA+AGG 0.526395 5.3:+14002583 MS.gene64883:intron
AAGAATGCTTCTGAGGAAGA+AGG 0.530721 5.3:+14003375 MS.gene64883:CDS
AATTAGGTTGGGAAAGCTGG+TGG 0.535794 5.3:+14003037 MS.gene64883:intron
GGTTGGGAAAGCTGGTGGAA+AGG 0.549667 5.3:+14003042 MS.gene64883:intron
AGGATCCTAACAAGCCTAAG+AGG 0.555088 5.3:+14002642 MS.gene64883:CDS
AAAACGAAGAAAGCACTTGG+AGG 0.557236 5.3:-14002665 None:intergenic
TTTGTTAGGTTGAAGCGCAA+GGG 0.561375 5.3:+14002584 MS.gene64883:intron
TAAGGCTCCATTCAATGCTA+AGG 0.574542 5.3:+14003187 MS.gene64883:CDS
GACTGAGAAGAATGCTTCTG+AGG 0.577758 5.3:+14003368 MS.gene64883:intron
ATGAAAACGAAGAAAGCACT+TGG 0.589018 5.3:-14002668 None:intergenic
GTGAATGATGATGATGAGGA+TGG 0.602793 5.3:+14003420 MS.gene64883:CDS
AAGCAACAAGTCCGTTGCTG+TGG 0.608709 5.3:+14002926 MS.gene64883:CDS
GTTATCAGCAGGTTTAGCAT+CGG 0.618036 5.3:-14002470 None:intergenic
TTAGGTCTGAGTTCAGAGAG+AGG 0.622758 5.3:+14002886 MS.gene64883:intron
CAGAAATCTCACCACAGCAA+CGG 0.627421 5.3:-14002937 None:intergenic
ATCGGAAACAGCTTTCGGCA+TGG 0.634546 5.3:-14002452 None:intergenic
TGAAGTGAATGATGATGATG+AGG 0.653732 5.3:+14003416 MS.gene64883:CDS
TAAGCAATCGAAGAAAGCGA+AGG 0.658279 5.3:+14002622 MS.gene64883:CDS
TAAGGCTGATAAGTTGAAGG+AGG 0.688265 5.3:+14003205 MS.gene64883:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTATTATTCTATAATTTTTT+AGG + chr5.3:14003471-14003490 MS.gene64883:intron 10.0%
!! TTCATAAAAATCAAATTCAA+CGG - chr5.3:14002980-14002999 None:intergenic 15.0%
!!! TTTTTGATTTTTTGTTTGTT+AGG + chr5.3:14002570-14002589 MS.gene64883:intron 15.0%
!!! ATTTTTGTTTTGCGTTTTTT+AGG + chr5.3:14002868-14002887 MS.gene64883:intron 20.0%
!!! GATCATTATTTTATGTTTTC+AGG + chr5.3:14003513-14003532 MS.gene64883:intron 20.0%
!!! TTGTGATTTATGTGTATTTT+AGG + chr5.3:14003163-14003182 MS.gene64883:intron 20.0%
!!! TTTATGTGTATTTTAGGATA+AGG + chr5.3:14003169-14003188 MS.gene64883:intron 20.0%
! AGAATCAAATCAAACTTCAA+CGG - chr5.3:14002844-14002863 None:intergenic 25.0%
!! CTAAATCTTAATTAGCGTTT+TGG + chr5.3:14003126-14003145 MS.gene64883:intron 25.0%
!! TCTAACGTGATTTTTGAATT+AGG + chr5.3:14003021-14003040 MS.gene64883:intron 25.0%
!!! CATTATTTTATGTTTTCAGG+AGG + chr5.3:14003516-14003535 MS.gene64883:intron 25.0%
!!! TTGCTGATTTGAACTAATTT+TGG + chr5.3:14003338-14003357 MS.gene64883:intron 25.0%
CCAAAACTCAATAAACGAAA+AGG - chr5.3:14002794-14002813 None:intergenic 30.0%
! ACGTGATTTTTGAATTAGGT+TGG + chr5.3:14003025-14003044 MS.gene64883:intron 30.0%
! CCTTTTCGTTTATTGAGTTT+TGG + chr5.3:14002791-14002810 MS.gene64883:intron 30.0%
! CGTGATTTTTGAATTAGGTT+GGG + chr5.3:14003026-14003045 MS.gene64883:intron 30.0%
! CTTCGTTTTCATGTAAGATT+CGG + chr5.3:14002679-14002698 MS.gene64883:intron 30.0%
! TTCACTGTTCTGATTTTACT+CGG + chr5.3:14003303-14003322 MS.gene64883:intron 30.0%
!! TATTTTATGTTTTCAGGAGG+AGG + chr5.3:14003519-14003538 MS.gene64883:intron 30.0%
ACAATGCGTGCTTACAATAT+GGG + chr5.3:14003239-14003258 MS.gene64883:CDS 35.0%
ATCATCATTCACTTCAGACT+TGG - chr5.3:14003412-14003431 None:intergenic 35.0%
GTGCTAAAAGTTGTTCGAAT+CGG + chr5.3:14002701-14002720 MS.gene64883:intron 35.0%
! TGAAGTGAATGATGATGATG+AGG + chr5.3:14003416-14003435 MS.gene64883:CDS 35.0%
! TTATCAGCCTTAGCATTGAA+TGG - chr5.3:14003197-14003216 None:intergenic 35.0%
!! ATGAAAACGAAGAAAGCACT+TGG - chr5.3:14002671-14002690 None:intergenic 35.0%
AGAATCACGAATCTCGAAGT+CGG - chr5.3:14002512-14002531 None:intergenic 40.0%
ATGCTAAACCTGCTGATAAC+CGG + chr5.3:14002473-14002492 MS.gene64883:CDS 40.0%
GACAATGCGTGCTTACAATA+TGG + chr5.3:14003238-14003257 MS.gene64883:CDS 40.0%
GTTATCAGCAGGTTTAGCAT+CGG - chr5.3:14002473-14002492 None:intergenic 40.0%
GTTCAGAGAGAGGTTTAAGA+AGG + chr5.3:14002896-14002915 MS.gene64883:CDS 40.0%
TAAGCAATCGAAGAAAGCGA+AGG + chr5.3:14002622-14002641 MS.gene64883:CDS 40.0%
TAAGGCTCCATTCAATGCTA+AGG + chr5.3:14003187-14003206 MS.gene64883:CDS 40.0%
TCGAGATTCGTGATTCTCAT+CGG + chr5.3:14002515-14002534 MS.gene64883:intron 40.0%
! AAGAATGCTTCTGAGGAAGA+AGG + chr5.3:14003375-14003394 MS.gene64883:CDS 40.0%
! GTGAATGATGATGATGAGGA+TGG + chr5.3:14003420-14003439 MS.gene64883:CDS 40.0%
! TAAGGCTGATAAGTTGAAGG+AGG + chr5.3:14003205-14003224 MS.gene64883:CDS 40.0%
! TGCTAAGGCTGATAAGTTGA+AGG + chr5.3:14003202-14003221 MS.gene64883:CDS 40.0%
! TTAGCATCGGAAACAGCTTT+CGG - chr5.3:14002460-14002479 None:intergenic 40.0%
!! AAAACGAAGAAAGCACTTGG+AGG - chr5.3:14002668-14002687 None:intergenic 40.0%
!! TTGAATTAGGTTGGGAAAGC+TGG + chr5.3:14003034-14003053 MS.gene64883:intron 40.0%
!! TTTGTTAGGTTGAAGCGCAA+GGG + chr5.3:14002584-14002603 MS.gene64883:intron 40.0%
AAGCTCTGTCTGATGCTGTT+AGG + chr5.3:14003071-14003090 MS.gene64883:intron 45.0%
AGGATCCTAACAAGCCTAAG+AGG + chr5.3:14002642-14002661 MS.gene64883:CDS 45.0%
AGTCGGAAGAAGAATCTCAC+CGG - chr5.3:14002495-14002514 None:intergenic 45.0%
CAGAAATCTCACCACAGCAA+CGG - chr5.3:14002940-14002959 None:intergenic 45.0%
GACTGAGAAGAATGCTTCTG+AGG + chr5.3:14003368-14003387 MS.gene64883:intron 45.0%
TTAGGTCTGAGTTCAGAGAG+AGG + chr5.3:14002886-14002905 MS.gene64883:intron 45.0%
!! AATTAGGTTGGGAAAGCTGG+TGG + chr5.3:14003037-14003056 MS.gene64883:intron 45.0%
!! ATGTTTTCAGGAGGAGGATG+AGG + chr5.3:14003525-14003544 MS.gene64883:intron 45.0%
!! GTTTGTTAGGTTGAAGCGCA+AGG + chr5.3:14002583-14002602 MS.gene64883:intron 45.0%
AAGCAACAAGTCCGTTGCTG+TGG + chr5.3:14002926-14002945 MS.gene64883:CDS 50.0%
GGAAAGCTGGTGGAAAGGAA+TGG + chr5.3:14003047-14003066 MS.gene64883:CDS 50.0%
! AAAGCACTTGGAGGCCTCTT+AGG - chr5.3:14002659-14002678 None:intergenic 50.0%
! GAATCTCACCGGTTATCAGC+AGG - chr5.3:14002484-14002503 None:intergenic 50.0%
!! ACAGCAACGGACTTGTTGCT+TGG - chr5.3:14002927-14002946 None:intergenic 50.0%
GGTTGGGAAAGCTGGTGGAA+AGG + chr5.3:14003042-14003061 MS.gene64883:intron 55.0%
! GGAGGCCTCTTAGGCTTGTT+AGG - chr5.3:14002650-14002669 None:intergenic 55.0%
! AGGTTGAAGCGCAAGGGCGC+TGG + chr5.3:14002590-14002609 MS.gene64883:intron 65.0%
!! AAGCGCAAGGGCGCTGGTAC+TGG + chr5.3:14002596-14002615 MS.gene64883:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 14002454 14003552 14002454 ID=MS.gene64883
chr5.3 mRNA 14002454 14003552 14002454 ID=MS.gene64883.t1;Parent=MS.gene64883
chr5.3 exon 14002454 14002494 14002454 ID=MS.gene64883.t1.exon1;Parent=MS.gene64883.t1
chr5.3 CDS 14002454 14002494 14002454 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14002592 14002690 14002592 ID=MS.gene64883.t1.exon2;Parent=MS.gene64883.t1
chr5.3 CDS 14002592 14002690 14002592 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14002890 14002947 14002890 ID=MS.gene64883.t1.exon3;Parent=MS.gene64883.t1
chr5.3 CDS 14002890 14002947 14002890 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14003043 14003087 14003043 ID=MS.gene64883.t1.exon4;Parent=MS.gene64883.t1
chr5.3 CDS 14003043 14003087 14003043 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14003185 14003265 14003185 ID=MS.gene64883.t1.exon5;Parent=MS.gene64883.t1
chr5.3 CDS 14003185 14003265 14003185 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14003369 14003449 14003369 ID=MS.gene64883.t1.exon6;Parent=MS.gene64883.t1
chr5.3 CDS 14003369 14003449 14003369 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
chr5.3 exon 14003535 14003552 14003535 ID=MS.gene64883.t1.exon7;Parent=MS.gene64883.t1
chr5.3 CDS 14003535 14003552 14003535 ID=cds.MS.gene64883.t1;Parent=MS.gene64883.t1
Gene Sequence

>MS.gene64883

ATGCCGAAAGCTGTTTCCGATGCTAAACCTGCTGATAACCGGTGAGATTCTTCTTCCGACTTCGAGATTCGTGATTCTCATCGGTTAATTTGTTAGATCTGAATTTTTTGTTAACGTTTTTGATTTTTTGTTTGTTAGGTTGAAGCGCAAGGGCGCTGGTACTGGAACTAAGCAATCGAAGAAAGCGAAGGATCCTAACAAGCCTAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATGTAAGATTCGGTGCTAAAAGTTGTTCGAATCGGTGCTAATTGTTCACGAATTTGTTGCAGTGAAGTTTCATTTAATTCTGACGAGTTTCGTTTTTTTTTTCCTTTTCGTTTATTGAGTTTTGGTGAAGTTCGAAACGTTACGAATGTGTTCCGTTGAAGTTTGATTTGATTCTAATGATTTTTGTTTTGCGTTTTTTAGGTCTGAGTTCAGAGAGAGGTTTAAGAAGGAGAATCCAAGCAACAAGTCCGTTGCTGTGGTGAGATTTCTGACACGATCTAGTTTTTACCGTTGAATTTGATTTTTATGAAATTTTGAATGTTATTGAGTTTTCTAACGTGATTTTTGAATTAGGTTGGGAAAGCTGGTGGAAAGGAATGGAAAGCTCTGTCTGATGCTGTTAGGATTTCGCTTCTGTTTAACTGAAGAAAAATAATCTAAATCTTAATTAGCGTTTTGGTTTTAAAATCGTTTTTGTGATTTATGTGTATTTTAGGATAAGGCTCCATTCAATGCTAAGGCTGATAAGTTGAAGGAGGAGTATGAGAAGACAATGCGTGCTTACAATATGGGAATTGTAATTACTTTTATAACTTTTCTGTTACTTTGATTTTTTCACTGTTCTGATTTTACTCGGATTTTTTTTTTGTTGCTGATTTGAACTAATTTTGGTGTATTAGACTGAGAAGAATGCTTCTGAGGAAGAAGGATCTGAGAAGTCCAAGTCTGAAGTGAATGATGATGATGAGGATGGTGATGATGTAAGATTTTTCTCATCGTTTGTATTATTCTATAATTTTTTAGGTTTTTATATATTGAAATTTGATCATTATTTTATGTTTTCAGGAGGAGGATGAGGAGTAA

Protein sequence

>MS.gene64883.t1

MPKAVSDAKPADNRLKRKGAGTGTKQSKKAKDPNKPKRPPSAFFVFMSEFRERFKKENPSNKSVAVVGKAGGKEWKALSDADKAPFNAKADKLKEEYEKTMRAYNMGITEKNASEEEGSEKSKSEVNDDDEDGDDEEDEE