AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0003280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0003280 MtrunA17_Chr1g0155721 95.506 89 2 1 1 87 31 119 4.03e-55 166
Msa0003280 MtrunA17_Chr3g0142051 82.927 82 12 1 1 80 31 112 3.49e-44 138
Msa0003280 MtrunA17_Chr5g0404831 69.512 82 23 1 1 80 33 114 6.75e-37 120
Msa0003280 MtrunA17_Chr7g0216481 57.831 83 33 1 1 81 51 133 6.29e-32 108
Msa0003280 MtrunA17_Chr8g0393201 56.098 82 34 1 1 80 252 333 2.43e-26 98.6
Msa0003280 MtrunA17_Chr8g0334481 45.570 79 41 1 1 77 51 129 8.89e-25 90.1
Msa0003280 MtrunA17_Chr7g0245141 43.529 85 46 1 1 83 49 133 2.51e-23 86.7
Msa0003280 MtrunA17_Chr5g0415761 53.571 84 37 1 1 82 45 128 1.84e-22 84.0
Msa0003280 MtrunA17_Chr5g0415771 53.012 83 37 1 1 81 44 126 6.49e-21 80.1
Msa0003280 MtrunA17_Chr2g0280411 46.067 89 46 1 1 87 34 122 7.50e-20 77.4
Msa0003280 MtrunA17_Chr5g0415741 50.000 84 40 1 1 82 43 126 3.00e-19 75.9
Msa0003280 MtrunA17_Chr4g0052481 43.662 71 36 1 2 68 85 155 5.13e-19 76.3
Msa0003280 MtrunA17_Chr1g0201781 40.845 71 39 2 1 68 81 151 1.87e-16 69.7
Msa0003280 MtrunA17_Chr2g0319291 40.506 79 45 1 1 77 35 113 2.46e-16 68.2
Msa0003280 MtrunA17_Chr3g0125821 40.230 87 48 2 1 83 89 175 4.39e-16 68.9
Msa0003280 MtrunA17_Chr7g0249461 41.250 80 44 1 1 77 101 180 8.96e-16 68.2
Msa0003280 MtrunA17_Chr4g0042051 40.506 79 45 1 1 77 35 113 2.57e-15 65.9
Msa0003280 MtrunA17_Chr7g0264661 34.177 79 52 0 2 80 49 127 5.67e-15 65.1
Msa0003280 MtrunA17_Chr3g0142031 70.732 41 10 1 32 70 5 45 6.42e-14 60.1
Msa0003280 MtrunA17_Chr2g0317731 42.254 71 38 2 1 68 89 159 1.00e-13 62.8
Msa0003280 MtrunA17_Chr8g0360031 38.554 83 47 3 1 79 92 174 7.67e-13 60.5
Msa0003280 MtrunA17_Chr1g0211871 37.363 91 43 4 1 83 89 173 7.88e-13 60.5
Msa0003280 MtrunA17_Chr4g0044731 35.526 76 46 1 1 73 84 159 8.50e-13 60.1
Msa0003280 MtrunA17_Chr6g0488561 34.066 91 55 3 1 86 98 188 1.13e-11 57.8
Msa0003280 MtrunA17_Chr4g0047431 36.250 80 49 1 2 79 25 104 2.52e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0003280 AT3G51030.1 69.512 82 23 1 1 80 31 112 2.71e-39 126
Msa0003280 AT1G45145.1 60.976 82 30 1 1 80 30 111 1.10e-32 110
Msa0003280 AT1G19730.1 60.674 89 32 2 1 86 31 119 6.77e-31 105
Msa0003280 AT5G42980.1 57.955 88 35 1 1 86 30 117 1.65e-30 104
Msa0003280 AT5G39950.1 51.852 81 37 1 1 79 50 130 1.58e-26 94.7
Msa0003280 AT3G17880.2 48.235 85 42 1 1 83 288 372 4.43e-24 93.6
Msa0003280 AT3G17880.1 48.235 85 42 1 1 83 295 379 5.17e-24 93.6
Msa0003280 AT3G08710.2 43.750 80 43 1 1 78 48 127 2.54e-23 87.0
Msa0003280 AT3G08710.3 43.750 80 43 1 1 78 48 127 2.54e-23 87.0
Msa0003280 AT3G08710.1 43.750 80 43 1 1 78 48 127 2.54e-23 87.0
Msa0003280 AT1G59730.1 44.578 83 44 1 1 81 46 128 4.39e-22 83.6
Msa0003280 AT3G56420.1 46.053 76 39 1 1 74 65 140 2.64e-21 82.0
Msa0003280 AT3G56420.2 46.053 76 39 1 1 74 65 140 2.64e-21 82.0
Msa0003280 AT3G56420.3 46.053 76 39 1 1 74 65 140 2.64e-21 82.0
Msa0003280 AT1G69880.1 42.353 85 47 1 1 83 62 146 3.63e-20 79.0
Msa0003280 AT2G35010.2 43.750 80 41 1 2 77 110 189 2.22e-18 75.5
Msa0003280 AT2G35010.1 43.750 80 41 1 2 77 110 189 2.22e-18 75.5
Msa0003280 AT2G40790.2 43.421 76 41 1 1 74 65 140 5.12e-18 73.6
Msa0003280 AT2G40790.1 43.421 76 41 1 1 74 65 140 5.12e-18 73.6
Msa0003280 AT1G11530.1 45.570 79 41 1 1 77 27 105 1.56e-17 71.6
Msa0003280 AT5G16400.1 40.000 80 45 1 1 77 100 179 1.06e-15 68.6
Msa0003280 AT1G43560.1 37.647 85 45 3 1 77 79 163 1.25e-15 67.8
Msa0003280 AT1G76760.1 39.437 71 40 2 1 68 84 154 3.52e-15 67.0
Msa0003280 AT1G31020.1 44.286 70 35 1 2 67 75 144 5.26e-15 66.2
Msa0003280 AT3G02730.1 37.209 86 51 1 1 83 90 175 1.07e-14 65.9
Msa0003280 AT1G03680.1 38.554 83 47 3 1 79 95 177 2.55e-13 62.0
Msa0003280 AT3G15360.1 37.349 83 48 3 1 79 107 189 6.10e-13 61.2
Msa0003280 AT4G26160.1 36.047 86 50 3 1 81 116 201 1.01e-12 61.2
Msa0003280 AT3G53220.1 31.646 79 54 0 2 80 47 125 1.67e-12 58.9
Msa0003280 AT4G03520.1 36.620 71 42 2 1 68 101 171 8.32e-12 58.2
Msa0003280 AT2G15570.2 35.526 76 46 1 1 73 88 163 1.67e-11 57.4
Msa0003280 AT2G15570.1 35.526 76 46 1 1 73 87 162 1.77e-11 57.0
Msa0003280 AT4G32580.1 33.333 81 52 1 1 79 24 104 7.85e-11 55.1

Find 23 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGCAATCTCAGCTAGAAT+TGG 0.355652 1_1:-5785834 None:intergenic
AGAAGGTAAGGAAGTGGATA+AGG 0.412033 1_1:+5786291 Msa0003280:CDS
CTTATTCTTGAAAGAAGGTA+AGG 0.442943 1_1:+5786279 Msa0003280:CDS
ACCTTCTTATTCTTGAAAGA+AGG 0.451509 1_1:+5786274 Msa0003280:CDS
ACCTTGAGGAAGATGACTTC+AGG 0.453976 1_1:-5785864 None:intergenic
AAATGCAATCACCAAGCATA+AGG 0.465102 1_1:+5786342 Msa0003280:CDS
TAAGGTAGTTGGTGCTAGGA+AGG 0.479587 1_1:+5786309 Msa0003280:CDS
TGGATAAGGTAGTTGGTGCT+AGG 0.488936 1_1:+5786305 Msa0003280:CDS
AAGGAAGTGGATAAGGTAGT+TGG 0.491604 1_1:+5786298 Msa0003280:CDS
AACAGTTGCATCCTTATGCT+TGG 0.492616 1_1:-5786353 None:intergenic
ACCTTCTTTCAAGAATAAGA+AGG 0.495256 1_1:-5786275 None:intergenic
TTCAGAGTGTTGCTGAGGAA+TGG 0.506641 1_1:+5786233 Msa0003280:intron
CTAGAATTGGAGCAATAAAA+CGG 0.524722 1_1:-5785821 None:intergenic
CTTGAAAGAAGGTAAGGAAG+TGG 0.537499 1_1:+5786285 Msa0003280:CDS
TGGTGCTAGGAAGGAAGAGC+TGG 0.539272 1_1:+5786318 Msa0003280:CDS
TCTTTCAAGAATAAGAAGGT+TGG 0.555397 1_1:-5786271 None:intergenic
TCCTGAAGTCATCTTCCTCA+AGG 0.561588 1_1:+5785863 Msa0003280:CDS
GAATAATAAATAGATTGTGG+TGG 0.594177 1_1:+5785770 None:intergenic
TGCTGAGGAATGGTCTGTTG+AGG 0.618156 1_1:+5786243 Msa0003280:CDS
CTTCATCAATATCCACCTTG+AGG 0.619089 1_1:-5785878 None:intergenic
ATTGGAGCAATAAAACGGCA+TGG 0.627618 1_1:-5785816 None:intergenic
CCTATTTCAGAGTGTTGCTG+AGG 0.630806 1_1:+5786228 Msa0003280:intron
TGAAGTCATCTTCCTCAAGG+TGG 0.658466 1_1:+5785866 Msa0003280:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTTCTAATATTTTAAGA+TGG + chr1_1:5786140-5786159 Msa0003280:intron 15.0%
!! ATTAAACTTGAGAAAGAATA+AGG - chr1_1:5785935-5785954 None:intergenic 20.0%
CTAGAATTGGAGCAATAAAA+CGG - chr1_1:5785824-5785843 None:intergenic 30.0%
! TGTAGTTTTTGTCAAAATCG+TGG + chr1_1:5786015-5786034 Msa0003280:intron 30.0%
GATCATAAGATGACATAACA+TGG - chr1_1:5786095-5786114 None:intergenic 30.0%
TCTTTCAAGAATAAGAAGGT+TGG - chr1_1:5786274-5786293 None:intergenic 30.0%
ACCTTCTTATTCTTGAAAGA+AGG + chr1_1:5786274-5786293 Msa0003280:CDS 30.0%
ACCTTCTTTCAAGAATAAGA+AGG - chr1_1:5786278-5786297 None:intergenic 30.0%
CTTATTCTTGAAAGAAGGTA+AGG + chr1_1:5786279-5786298 Msa0003280:CDS 30.0%
TTAGCAATCTCAGCTAGAAT+TGG - chr1_1:5785837-5785856 None:intergenic 35.0%
GGTGGATATTGATGAAGTAA+AGG + chr1_1:5785884-5785903 Msa0003280:intron 35.0%
!! AACTAGTCTTAAAGCCGATT+CGG + chr1_1:5786205-5786224 Msa0003280:intron 35.0%
AAATGCAATCACCAAGCATA+AGG + chr1_1:5786342-5786361 Msa0003280:CDS 35.0%
!!! TGGTGGATTTTACTGCTTCA+TGG + chr1_1:5785787-5785806 Msa0003280:CDS 40.0%
! GATTTTACTGCTTCATGGTG+TGG + chr1_1:5785792-5785811 Msa0003280:CDS 40.0%
ATTGGAGCAATAAAACGGCA+TGG - chr1_1:5785819-5785838 None:intergenic 40.0%
CTTCATCAATATCCACCTTG+AGG - chr1_1:5785881-5785900 None:intergenic 40.0%
CTTGAAAGAAGGTAAGGAAG+TGG + chr1_1:5786285-5786304 Msa0003280:CDS 40.0%
AGAAGGTAAGGAAGTGGATA+AGG + chr1_1:5786291-5786310 Msa0003280:CDS 40.0%
AAGGAAGTGGATAAGGTAGT+TGG + chr1_1:5786298-5786317 Msa0003280:CDS 40.0%
AACAGTTGCATCCTTATGCT+TGG - chr1_1:5786356-5786375 None:intergenic 40.0%
TCCTGAAGTCATCTTCCTCA+AGG + chr1_1:5785863-5785882 Msa0003280:CDS 45.0%
ACCTTGAGGAAGATGACTTC+AGG - chr1_1:5785867-5785886 None:intergenic 45.0%
TGAAGTCATCTTCCTCAAGG+TGG + chr1_1:5785866-5785885 Msa0003280:CDS 45.0%
!! CACTCTGAAATAGGCCGAAT+CGG - chr1_1:5786222-5786241 None:intergenic 45.0%
!! CCTCAGCAACACTCTGAAAT+AGG - chr1_1:5786231-5786250 None:intergenic 45.0%
!! CCTATTTCAGAGTGTTGCTG+AGG + chr1_1:5786228-5786247 Msa0003280:intron 45.0%
!! TTCAGAGTGTTGCTGAGGAA+TGG + chr1_1:5786233-5786252 Msa0003280:intron 45.0%
! TGGATAAGGTAGTTGGTGCT+AGG + chr1_1:5786305-5786324 Msa0003280:CDS 45.0%
!! TAAGGTAGTTGGTGCTAGGA+AGG + chr1_1:5786309-5786328 Msa0003280:CDS 45.0%
TGCTGAGGAATGGTCTGTTG+AGG + chr1_1:5786243-5786262 Msa0003280:CDS 50.0%
! TGGTGCTAGGAAGGAAGAGC+TGG + chr1_1:5786318-5786337 Msa0003280:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 5785783 5786387 5785783 ID=Msa0003280;Name=Msa0003280
chr1_1 mRNA 5785783 5786387 5785783 ID=Msa0003280-mRNA-1;Parent=Msa0003280;Name=Msa0003280-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|0|0|1|1|1|2|0|88
chr1_1 exon 5785783 5785899 5785783 ID=Msa0003280-mRNA-1:exon:1779;Parent=Msa0003280-mRNA-1
chr1_1 exon 5786238 5786387 5786238 ID=Msa0003280-mRNA-1:exon:1780;Parent=Msa0003280-mRNA-1
chr1_1 CDS 5785783 5785899 5785783 ID=Msa0003280-mRNA-1:cds;Parent=Msa0003280-mRNA-1
chr1_1 CDS 5786238 5786387 5786238 ID=Msa0003280-mRNA-1:cds;Parent=Msa0003280-mRNA-1
Gene Sequence

>Msa0003280

ATTGTGGTGGATTTTACTGCTTCATGGTGTGGTCCATGCCGTTTTATTGCTCCAATTCTAGCTGAGATTGCTAAGAAGACTCCTGAAGTCATCTTCCTCAAGGTGGATATTGATGAAAGTGTTGCTGAGGAATGGTCTGTTGAGGCTATGCCAACCTTCTTATTCTTGAAAGAAGGTAAGGAAGTGGATAAGGTAGTTGGTGCTAGGAAGGAAGAGCTGGAAAATGCAATCACCAAGCATAAGGATGCAACTGTTGCTACTACTTGA

Protein sequence

>Msa0003280

IVVDFTASWCGPCRFIAPILAEIAKKTPEVIFLKVDIDESVAEEWSVEAMPTFLFLKEGKEVDKVVGARKEELENAITKHKDATVATT*