AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene05656

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05656.t1 MTR_5g095740 44.681 94 51 1 47 139 18 111 3.91e-22 90.1
MS.gene05656.t1 MTR_3g058980 45.000 100 52 1 56 155 32 128 9.58e-22 89.4
MS.gene05656.t1 MTR_1g083070 42.529 87 50 0 55 141 8 94 2.33e-21 86.7
MS.gene05656.t1 MTR_2g026710 41.000 100 58 1 41 139 6 105 3.06e-21 87.4
MS.gene05656.t1 MTR_7g100650 41.053 95 55 1 46 139 20 114 4.25e-21 87.0
MS.gene05656.t1 MTR_7g061270 41.053 95 55 1 46 139 20 114 4.67e-21 87.0
MS.gene05656.t1 MTR_1g039040 35.433 127 79 3 49 172 3 129 1.11e-20 86.7
MS.gene05656.t1 MTR_8g093920 46.429 84 45 0 56 139 45 128 1.37e-20 86.7
MS.gene05656.t1 MTR_8g091720 38.095 105 64 1 36 139 12 116 1.91e-20 86.3
MS.gene05656.t1 MTR_1g088860 42.857 84 48 0 56 139 41 124 3.56e-20 85.1
MS.gene05656.t1 MTR_4g133952 45.238 84 46 0 56 139 63 146 4.70e-20 85.9
MS.gene05656.t1 MTR_1g072790 41.667 84 49 0 56 139 34 117 1.01e-19 83.6
MS.gene05656.t1 MTR_4g119500 35.185 108 66 2 32 139 7 110 1.19e-18 79.3
MS.gene05656.t1 MTR_0392s0020 40.476 84 50 0 56 139 23 106 1.32e-18 79.7
MS.gene05656.t1 MTR_4g133938 42.857 84 48 0 56 139 24 107 1.46e-18 79.3
MS.gene05656.t1 MTR_5g095900 34.066 91 60 0 55 145 20 110 2.36e-16 74.7
MS.gene05656.t1 MTR_1g029070 36.905 84 53 0 56 139 57 140 3.24e-15 71.6
MS.gene05656.t1 MTR_1g029100 35.802 81 52 0 56 136 7 87 3.32e-12 61.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene05656.t1 AT2G38880 36.607 112 70 1 38 148 7 118 1.04e-22 90.5
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 2.96e-22 89.4
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 2.96e-22 89.4
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 2.96e-22 89.4
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 3.52e-22 89.0
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 6.21e-22 89.0
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 6.21e-22 89.0
MS.gene05656.t1 AT4G14540 46.429 84 45 0 56 139 26 109 8.43e-22 88.6
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 9.60e-22 87.0
MS.gene05656.t1 AT2G37060 41.935 93 53 1 48 139 26 118 7.26e-21 86.7
MS.gene05656.t1 AT2G37060 41.935 93 53 1 48 139 26 118 7.26e-21 86.7
MS.gene05656.t1 AT2G37060 41.935 93 53 1 48 139 26 118 7.26e-21 86.7
MS.gene05656.t1 AT5G47640 46.429 84 45 0 56 139 32 115 9.65e-21 86.7
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 1.85e-20 85.1
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 1.85e-20 85.1
MS.gene05656.t1 AT2G38880 37.864 103 63 1 38 139 7 109 1.85e-20 85.1
MS.gene05656.t1 AT1G21970 36.957 138 81 2 46 177 54 191 3.78e-20 86.3
MS.gene05656.t1 AT2G13570 46.429 84 45 0 56 139 41 124 6.20e-20 85.1
MS.gene05656.t1 AT1G09030 40.476 84 50 0 56 139 8 91 2.08e-19 81.6
MS.gene05656.t1 AT3G53340 39.785 93 55 1 48 139 25 117 5.40e-19 81.6
MS.gene05656.t1 AT3G53340 39.785 93 55 1 48 139 25 117 5.40e-19 81.6
MS.gene05656.t1 AT2G47810 40.476 84 50 0 56 139 56 139 8.11e-19 80.9
MS.gene05656.t1 AT3G53340 39.785 93 55 1 48 139 25 117 1.25e-18 79.3
MS.gene05656.t1 AT5G47670 38.298 94 57 1 47 139 24 117 2.28e-18 80.9
MS.gene05656.t1 AT5G47670 38.298 94 57 1 47 139 53 146 3.27e-18 80.9
MS.gene05656.t1 AT5G47670 38.298 94 57 1 47 139 53 146 3.27e-18 80.9
MS.gene05656.t1 AT3G53340 39.785 93 55 1 48 139 25 117 6.02e-18 78.2
MS.gene05656.t1 AT3G53340 39.785 93 55 1 48 139 25 117 6.02e-18 78.2

Find 53 sgRNAs with CRISPR-Local

Find 72 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGGAATGAATTGGATAATT+TGG 0.149282 3.2:+51329350 MS.gene05656:CDS
CAGGGAATGCAGGAAAATTT+TGG 0.155460 3.2:+51329062 MS.gene05656:CDS
CTCAAACTCATTTATTGATT+TGG 0.201982 3.2:+51329302 MS.gene05656:CDS
ATTAAGGGTCATAAAGTCTA+TGG 0.242488 3.2:+51329098 MS.gene05656:CDS
TTTCGTTATAGTAATGAAAT+TGG 0.264459 3.2:+51329165 MS.gene05656:CDS
CCACCGCCACCCATTGCAAT+TGG 0.296308 3.2:+51329261 MS.gene05656:CDS
CTTGGATTCATTATACTTGT+TGG 0.316399 3.2:-51328850 None:intergenic
GGTACAAGGGCATCATTTCT+TGG 0.339623 3.2:-51328868 None:intergenic
GGGTGGCGGTGGTGGTAAGG+TGG 0.341905 3.2:-51329250 None:intergenic
TAGACTTTATGACCCTTAAT+AGG 0.346002 3.2:-51329095 None:intergenic
TGGAATGAATTGGATAATTT+GGG 0.348468 3.2:+51329351 MS.gene05656:CDS
TTTGTCTCGAATTGCTAGTT+GGG 0.369014 3.2:-51328890 None:intergenic
GATGATAAAATGAATGATTA+AGG 0.370091 3.2:+51329453 MS.gene05656:CDS
GAATGAGGTTTGGAATGAAT+TGG 0.382994 3.2:+51329341 MS.gene05656:CDS
TGGGTGCAGATGACCTATTA+AGG 0.383571 3.2:+51329082 MS.gene05656:CDS
AAGTTTGTTAAAGCAGTCTC+TGG 0.385163 3.2:-51329384 None:intergenic
CCACCCATTGCAATTGGGTC+AGG 0.408457 3.2:+51329267 MS.gene05656:CDS
TACATATCTTATAAACTTTG+AGG 0.420260 3.2:-51329013 None:intergenic
GGGTGCAGATGACCTATTAA+GGG 0.425849 3.2:+51329083 MS.gene05656:CDS
TTCCCTGTGACAACGTTCAA+TGG 0.434461 3.2:-51329046 None:intergenic
ATTGGATATTTGAAACTTGT+TGG 0.437848 3.2:+51329183 MS.gene05656:CDS
CAGCGGGCATGAATGAGGTT+TGG 0.446236 3.2:+51329331 MS.gene05656:CDS
GGTGGCGGTGGTGGTAAGGT+GGG 0.449680 3.2:-51329249 None:intergenic
CACCGCCACCCATTGCAATT+GGG 0.468956 3.2:+51329262 MS.gene05656:CDS
CCAATTGCAATGGGTGGCGG+TGG 0.473098 3.2:-51329261 None:intergenic
AATGGGTGGCGGTGGTGGTA+AGG 0.484109 3.2:-51329253 None:intergenic
ATTGCAATGGGTGGCGGTGG+TGG 0.491572 3.2:-51329258 None:intergenic
GAATTGCTAGTTGGGGTACA+AGG 0.493363 3.2:-51328882 None:intergenic
GAATTGGATAATTTGGGTGC+TGG 0.493441 3.2:+51329357 MS.gene05656:CDS
AAGCCATTGAACGTTGTCAC+AGG 0.498720 3.2:+51329043 MS.gene05656:CDS
TGACGATATCTTTCAAGAGA+TGG 0.505210 3.2:+51329431 MS.gene05656:CDS
AACGTTGTCACAGGGAATGC+AGG 0.505564 3.2:+51329052 MS.gene05656:CDS
GACCCAATTGCAATGGGTGG+CGG 0.506575 3.2:-51329264 None:intergenic
AGTTTGTTAAAGCAGTCTCT+GGG 0.515893 3.2:-51329383 None:intergenic
TCAAAATCCAACTCAAGCTC+TGG 0.519412 3.2:+51328546 MS.gene05656:CDS
ATCTGAAGAGCTGGTAAGGT+GGG 0.524201 3.2:-51329219 None:intergenic
AGAGCTGGTAAGGTGGGCTT+AGG 0.525041 3.2:-51329213 None:intergenic
AGCGATCTGAAGAGCTGGTA+AGG 0.528940 3.2:-51329223 None:intergenic
CTCTCGTGGAGCAAAGGAGA+TGG 0.534626 3.2:+51328978 MS.gene05656:CDS
AAGCCTGACCCAATTGCAAT+GGG 0.536639 3.2:-51329270 None:intergenic
TGAAGCAGCGGGCATGAATG+AGG 0.557960 3.2:+51329326 MS.gene05656:CDS
ATTGATTTGGATGAAGCAGC+GGG 0.566122 3.2:+51329315 MS.gene05656:CDS
TTGTCTCGAATTGCTAGTTG+GGG 0.568122 3.2:-51328889 None:intergenic
TAAGCCTGACCCAATTGCAA+TGG 0.575839 3.2:-51329271 None:intergenic
TTAAGGGTCATAAAGTCTAT+GGG 0.580731 3.2:+51329099 MS.gene05656:CDS
GGAGAAGCGATCTGAAGAGC+TGG 0.588114 3.2:-51329228 None:intergenic
AAATATTCCCTCGTTAACAA+TGG 0.602859 3.2:+51328523 MS.gene05656:CDS
AGCCATTGAACGTTGTCACA+GGG 0.613629 3.2:+51329044 MS.gene05656:CDS
GATCTGAAGAGCTGGTAAGG+TGG 0.631761 3.2:-51329220 None:intergenic
TATTGATTTGGATGAAGCAG+CGG 0.641197 3.2:+51329314 MS.gene05656:CDS
AATTGCTAGTTGGGGTACAA+GGG 0.641551 3.2:-51328881 None:intergenic
CCTGACCCAATTGCAATGGG+TGG 0.641990 3.2:-51329267 None:intergenic
GTTTGTTAAAGCAGTCTCTG+GGG 0.684155 3.2:-51329382 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATAATGAAAGTATTTATT+AGG + chr3.2:51328772-51328791 MS.gene05656:intron 10.0%
!! TAAAATAACAATTTGATCTA+TGG - chr3.2:51328683-51328702 None:intergenic 15.0%
!! TACATATCTTATAAACTTTG+AGG - chr3.2:51329016-51329035 None:intergenic 20.0%
!! TTTCGTTATAGTAATGAAAT+TGG + chr3.2:51329165-51329184 MS.gene05656:CDS 20.0%
! TGGAATGAATTGGATAATTT+GGG + chr3.2:51329351-51329370 MS.gene05656:CDS 25.0%
! TTGGAATGAATTGGATAATT+TGG + chr3.2:51329350-51329369 MS.gene05656:CDS 25.0%
!! ATTGGATATTTGAAACTTGT+TGG + chr3.2:51329183-51329202 MS.gene05656:CDS 25.0%
!! CTCAAACTCATTTATTGATT+TGG + chr3.2:51329302-51329321 MS.gene05656:CDS 25.0%
!!! ATTGTAGCCACATTTTTTAT+TGG - chr3.2:51328925-51328944 None:intergenic 25.0%
AAATATTCCCTCGTTAACAA+TGG + chr3.2:51328523-51328542 MS.gene05656:CDS 30.0%
AAGTATTTATTAGGATGTGC+AGG + chr3.2:51328781-51328800 MS.gene05656:intron 30.0%
ATTAAGGGTCATAAAGTCTA+TGG + chr3.2:51329098-51329117 MS.gene05656:CDS 30.0%
CTTGGATTCATTATACTTGT+TGG - chr3.2:51328853-51328872 None:intergenic 30.0%
TACCTTGCCAATAAAAAATG+TGG + chr3.2:51328915-51328934 MS.gene05656:CDS 30.0%
TAGACTTTATGACCCTTAAT+AGG - chr3.2:51329098-51329117 None:intergenic 30.0%
TCATCTATGTTGCATCAAAT+TGG + chr3.2:51328805-51328824 MS.gene05656:intron 30.0%
TGTCTCTAGATTTCAATACT+AGG + chr3.2:51328624-51328643 MS.gene05656:intron 30.0%
TTAAGGGTCATAAAGTCTAT+GGG + chr3.2:51329099-51329118 MS.gene05656:CDS 30.0%
!! ATTTTGACCATTGTTAACGA+GGG - chr3.2:51328533-51328552 None:intergenic 30.0%
TGACGATATCTTTCAAGAGA+TGG + chr3.2:51329431-51329450 MS.gene05656:CDS 35.0%
TTTGTCTCGAATTGCTAGTT+GGG - chr3.2:51328893-51328912 None:intergenic 35.0%
! AGGGAATGCAGGAAAATTTT+GGG + chr3.2:51329063-51329082 MS.gene05656:CDS 35.0%
! GAATGAGGTTTGGAATGAAT+TGG + chr3.2:51329341-51329360 MS.gene05656:CDS 35.0%
! TTTTGTCTCGAATTGCTAGT+TGG - chr3.2:51328894-51328913 None:intergenic 35.0%
!! AAGTTTGTTAAAGCAGTCTC+TGG - chr3.2:51329387-51329406 None:intergenic 35.0%
!! AGTTTGTTAAAGCAGTCTCT+GGG - chr3.2:51329386-51329405 None:intergenic 35.0%
!! GATTTTGACCATTGTTAACG+AGG - chr3.2:51328534-51328553 None:intergenic 35.0%
!! TACTAGGTTGATAGATGAGT+TGG + chr3.2:51328640-51328659 MS.gene05656:intron 35.0%
!! TATTGATTTGGATGAAGCAG+CGG + chr3.2:51329314-51329333 MS.gene05656:CDS 35.0%
!!! ACAACGTTCAATGGCTTTTT+TGG - chr3.2:51329040-51329059 None:intergenic 35.0%
!!! AGCCACATTTTTTATTGGCA+AGG - chr3.2:51328920-51328939 None:intergenic 35.0%
AAAAATCTCTCGTGGAGCAA+AGG + chr3.2:51328972-51328991 MS.gene05656:CDS 40.0%
AATTGCTAGTTGGGGTACAA+GGG - chr3.2:51328884-51328903 None:intergenic 40.0%
CCAAACACAAAAATCTCTCG+TGG + chr3.2:51328964-51328983 MS.gene05656:CDS 40.0%
GAATTGGATAATTTGGGTGC+TGG + chr3.2:51329357-51329376 MS.gene05656:CDS 40.0%
TCAAAATCCAACTCAAGCTC+TGG + chr3.2:51328546-51328565 MS.gene05656:CDS 40.0%
TTGTCTCGAATTGCTAGTTG+GGG - chr3.2:51328892-51328911 None:intergenic 40.0%
! CAGGGAATGCAGGAAAATTT+TGG + chr3.2:51329062-51329081 MS.gene05656:CDS 40.0%
! CCACGAGAGATTTTTGTGTT+TGG - chr3.2:51328967-51328986 None:intergenic 40.0%
! CGAGAGATTTTTGTGTTTGG+TGG - chr3.2:51328964-51328983 None:intergenic 40.0%
! GTTTGTTAAAGCAGTCTCTG+GGG - chr3.2:51329385-51329404 None:intergenic 40.0%
! TGTTTTACCAGAGCTTGAGT+TGG - chr3.2:51328556-51328575 None:intergenic 40.0%
!! ATTGATTTGGATGAAGCAGC+GGG + chr3.2:51329315-51329334 MS.gene05656:CDS 40.0%
AAGCCATTGAACGTTGTCAC+AGG + chr3.2:51329043-51329062 MS.gene05656:CDS 45.0%
AAGCCTGACCCAATTGCAAT+GGG - chr3.2:51329273-51329292 None:intergenic 45.0%
AGCCATTGAACGTTGTCACA+GGG + chr3.2:51329044-51329063 MS.gene05656:CDS 45.0%
ATCTGAAGAGCTGGTAAGGT+GGG - chr3.2:51329222-51329241 None:intergenic 45.0%
GAATTGCTAGTTGGGGTACA+AGG - chr3.2:51328885-51328904 None:intergenic 45.0%
GGGTGCAGATGACCTATTAA+GGG + chr3.2:51329083-51329102 MS.gene05656:CDS 45.0%
TAAGCCTGACCCAATTGCAA+TGG - chr3.2:51329274-51329293 None:intergenic 45.0%
TGGGTGCAGATGACCTATTA+AGG + chr3.2:51329082-51329101 MS.gene05656:CDS 45.0%
TTCCCTGTGACAACGTTCAA+TGG - chr3.2:51329049-51329068 None:intergenic 45.0%
!! GGTACAAGGGCATCATTTCT+TGG - chr3.2:51328871-51328890 None:intergenic 45.0%
AACGTTGTCACAGGGAATGC+AGG + chr3.2:51329052-51329071 MS.gene05656:CDS 50.0%
AGCGATCTGAAGAGCTGGTA+AGG - chr3.2:51329226-51329245 None:intergenic 50.0%
GATCTGAAGAGCTGGTAAGG+TGG - chr3.2:51329223-51329242 None:intergenic 50.0%
TGGAGCTCTTGTATCTGCAG+AGG - chr3.2:51328833-51328852 None:intergenic 50.0%
CACCGCCACCCATTGCAATT+GGG + chr3.2:51329262-51329281 MS.gene05656:CDS 55.0%
CAGCGGGCATGAATGAGGTT+TGG + chr3.2:51329331-51329350 MS.gene05656:CDS 55.0%
CCACCCATTGCAATTGGGTC+AGG + chr3.2:51329267-51329286 MS.gene05656:CDS 55.0%
CCTGACCCAATTGCAATGGG+TGG - chr3.2:51329270-51329289 None:intergenic 55.0%
CTCTCGTGGAGCAAAGGAGA+TGG + chr3.2:51328978-51328997 MS.gene05656:CDS 55.0%
GACCCAATTGCAATGGGTGG+CGG - chr3.2:51329267-51329286 None:intergenic 55.0%
GGAGAAGCGATCTGAAGAGC+TGG - chr3.2:51329231-51329250 None:intergenic 55.0%
TGAAGCAGCGGGCATGAATG+AGG + chr3.2:51329326-51329345 MS.gene05656:CDS 55.0%
! AGAGCTGGTAAGGTGGGCTT+AGG - chr3.2:51329216-51329235 None:intergenic 55.0%
CCACCGCCACCCATTGCAAT+TGG + chr3.2:51329261-51329280 MS.gene05656:CDS 60.0%
! AATGGGTGGCGGTGGTGGTA+AGG - chr3.2:51329256-51329275 None:intergenic 60.0%
! ATTGCAATGGGTGGCGGTGG+TGG - chr3.2:51329261-51329280 None:intergenic 60.0%
! CCAATTGCAATGGGTGGCGG+TGG - chr3.2:51329264-51329283 None:intergenic 60.0%
! GGTGGCGGTGGTGGTAAGGT+GGG - chr3.2:51329252-51329271 None:intergenic 65.0%
! GGGTGGCGGTGGTGGTAAGG+TGG - chr3.2:51329253-51329272 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 51328514 51329473 51328514 ID=MS.gene05656
chr3.2 mRNA 51328514 51329473 51328514 ID=MS.gene05656.t1;Parent=MS.gene05656
chr3.2 exon 51328514 51328598 51328514 ID=MS.gene05656.t1.exon1;Parent=MS.gene05656.t1
chr3.2 CDS 51328514 51328598 51328514 ID=cds.MS.gene05656.t1;Parent=MS.gene05656.t1
chr3.2 exon 51328839 51329473 51328839 ID=MS.gene05656.t1.exon2;Parent=MS.gene05656.t1
chr3.2 CDS 51328839 51329473 51328839 ID=cds.MS.gene05656.t1;Parent=MS.gene05656.t1
Gene Sequence

>MS.gene05656

ATGGAGAATAAATATTCCCTCGTTAACAATGGTCAAAATCCAACTCAAGCTCTGGTAAAACACAAAATCAGAATAACTTACACACGTATATGAATTTTATTTAATAAAATTGTCTCTAGATTTCAATACTAGGTTGATAGATGAGTTGGTTTTGAGTCATTTCAAACCATAGATCAAATTGTTATTTTATTTTTAACTATTTGATTCATTTTGCTTTCTATCAGTGTTTTGCATACAATGTGTTATTTTTAAATGTTAAAATAATGAAAGTATTTATTAGGATGTGCAGGTTCATCTATGTTGCATCAAATTGGTGCCTCTGCAGATACAAGAGCTCCAACAAGTATAATGAATCCAAGAAATGATGCCCTTGTACCCCAACTAGCAATTCGAGACAAAAATACCTTGCCAATAAAAAATGTGGCTACAATCATGAGAAAAGTTCTTCCACCAAACACAAAAATCTCTCGTGGAGCAAAGGAGATGGTTGAACAAATCACCTCAAAGTTTATAAGATATGTAACCAAAAAAGCCATTGAACGTTGTCACAGGGAATGCAGGAAAATTTTGGGTGCAGATGACCTATTAAGGGTCATAAAGTCTATGGGTTATAATAACTATTATGAGTATCTCAATTTTTATCTCAAATGCTTTCGTTATAGTAATGAAATTGGATATTTGAAACTTGTTGGTGAGCTTCCTAAGCCCACCTTACCAGCTCTTCAGATCGCTTCTCCCACCTTACCACCACCGCCACCCATTGCAATTGGGTCAGGCTTATCTTTGAACTCAAACTCATTTATTGATTTGGATGAAGCAGCGGGCATGAATGAGGTTTGGAATGAATTGGATAATTTGGGTGCTGGTTCCCCAGAGACTGCTTTAACAAACTTTGATCATTCAATTCAATTCAACTTTGACGATATCTTTCAAGAGATGGATGATAAAATGAATGATTAA
Protein sequence

>MS.gene05656.t1

MENKYSLVNNGQNPTQALVKHKIRITYTHTRAPTSIMNPRNDALVPQLAIRDKNTLPIKNVATIMRKVLPPNTKISRGAKEMVEQITSKFIRYVTKKAIERCHRECRKILGADDLLRVIKSMGYNNYYEYLNFYLKCFRYSNEIGYLKLVGELPKPTLPALQIASPTLPPPPPIAIGSGLSLNSNSFIDLDEAAGMNEVWNELDNLGAGSPETALTNFDHSIQFNFDDIFQEMDDKMND