AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1412130


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1412130 MtrunA17_Chr3g0144941 97.419 155 3 1 1 154 1 155 1.34e-106 300
Msa1412130 MtrunA17_Chr4g0035414 71.895 153 39 1 1 149 1 153 8.97e-65 194
Msa1412130 MtrunA17_Chr1g0155551 61.491 161 50 4 1 151 1 159 3.75e-57 176
Msa1412130 MtrunA17_Chr8g0378901 53.416 161 67 5 1 154 1 160 1.73e-46 148
Msa1412130 MtrunA17_Chr3g0141881 59.341 91 34 1 17 107 53 140 3.91e-30 107
Msa1412130 MtrunA17_Chr1g0194681 44.545 110 58 1 1 110 1 107 4.33e-25 94.0
Msa1412130 MtrunA17_Chr6g0456061 44.118 102 47 2 26 124 86 180 3.21e-18 77.4
Msa1412130 MtrunA17_Chr8g0341311 50.685 73 36 0 26 98 70 142 2.54e-17 74.7
Msa1412130 MtrunA17_Chr7g0225661 44.444 99 51 2 1 98 57 152 2.61e-17 74.7
Msa1412130 MtrunA17_Chr7g0220571 51.250 80 39 0 19 98 76 155 4.44e-17 74.3
Msa1412130 MtrunA17_Chr4g0054291 39.091 110 60 1 7 109 45 154 6.39e-16 70.9
Msa1412130 MtrunA17_Chr5g0400901 41.053 95 48 1 27 121 58 144 2.04e-14 66.6
Msa1412130 MtrunA17_Chr7g0269951 45.000 120 60 2 27 146 19 132 4.51e-13 62.4
Msa1412130 MtrunA17_Chr3g0139301 34.259 108 67 1 6 109 98 205 1.14e-12 63.9
Msa1412130 MtrunA17_Chr8g0369161 36.735 98 58 2 24 118 300 396 2.90e-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
Msa1412130 AT1G75390.1 53.459 159 58 4 2 147 9 164 2.83e-48 154
Msa1412130 AT4G34590.1 57.143 133 47 2 26 148 23 155 5.19e-44 142
Msa1412130 AT2G18160.1 47.020 151 56 5 22 151 23 170 7.83e-37 125
Msa1412130 AT1G75390.2 60.825 97 34 2 2 94 9 105 1.21e-32 112
Msa1412130 AT3G62420.1 44.526 137 75 1 13 149 8 143 1.29e-30 108
Msa1412130 AT2G04038.1 48.837 86 41 1 16 98 57 142 4.39e-18 76.6
Msa1412130 AT5G15830.1 34.932 146 79 3 9 154 55 184 8.82e-18 76.3
Msa1412130 AT1G13600.1 45.361 97 48 2 16 107 70 166 1.16e-16 73.6
Msa1412130 AT3G30530.1 52.055 73 35 0 26 98 77 149 2.79e-16 72.0
Msa1412130 AT5G38800.1 47.500 80 42 0 19 98 61 140 1.48e-15 70.1
Msa1412130 AT5G49450.1 36.190 105 64 1 27 128 13 117 1.96e-12 61.2
Msa1412130 AT4G37730.1 45.000 80 37 1 26 98 193 272 4.52e-12 62.8
Msa1412130 AT2G22850.1 37.079 89 56 0 23 111 122 210 2.78e-11 59.7
Msa1412130 AT2G22850.2 37.079 89 56 0 23 111 122 210 2.78e-11 59.7
Msa1412130 AT3G49760.1 55.814 43 19 0 28 70 70 112 4.41e-11 58.2
Msa1412130 AT1G68880.1 38.554 83 51 0 12 94 29 111 4.49e-11 57.8

Find 21 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTCCTCTGAACCTGAATT+TGG 0.134136 tig0023872:-5610 None:intergenic
CTTCAACAACCCTTTGAATA+TGG 0.147562 tig0023872:+5954 Msa1412130:CDS
CCTCACAACTCAACGATTCT+TGG 0.288929 tig0023872:+5792 Msa1412130:CDS
TGTTCAACACTTCCAAATTC+AGG 0.300497 tig0023872:+5598 Msa1412130:CDS
CTTGGATGATCTTGCTGTTC+AGG 0.305122 tig0023872:+5723 Msa1412130:CDS
TCTTCAAGTGGAACATCTTC+AGG 0.306987 tig0023872:+5574 Msa1412130:CDS
TTCAACAACCCTTTGAATAT+GGG 0.356244 tig0023872:+5955 Msa1412130:CDS
TTGTCATTATTATTATCAAC+AGG 0.406404 tig0023872:-5928 None:intergenic
TTATTTGAACCAACCAATCA+TGG 0.433242 tig0023872:+5978 Msa1412130:CDS
TTCAAATAACCCATATTCAA+AGG 0.450188 tig0023872:-5964 None:intergenic
GAGATCTTCTTGCTGATTCG+CGG 0.468319 tig0023872:-5681 None:intergenic
ATATCTGCAGAAGCCATGAT+TGG 0.469872 tig0023872:-5991 None:intergenic
GGAAGATTTGATGCTTCTGA+TGG 0.470481 tig0023872:+5627 Msa1412130:CDS
TCAAATAACCCATATTCAAA+GGG 0.472163 tig0023872:-5963 None:intergenic
CTGTTCAGGTGAGTCAACTA+AGG 0.511341 tig0023872:+5737 Msa1412130:CDS
CTGCAGAAGCCATGATTGGT+TGG 0.535667 tig0023872:-5987 None:intergenic
AACTTCATGAATGTTGCAAA+TGG 0.546215 tig0023872:+5895 Msa1412130:CDS
TCTCACATGGCTTCTTCAAG+TGG 0.568523 tig0023872:+5562 None:intergenic
ACTTCCAAATTCAGGTTCAG+AGG 0.572504 tig0023872:+5606 Msa1412130:CDS
CAGCAAGAAGATCTCGAATG+AGG 0.587735 tig0023872:+5689 Msa1412130:CDS
CCAAGAATCGTTGAGTTGTG+AGG 0.599678 tig0023872:-5792 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTCATTATTATTATCAAC+AGG - tig0023872:5931-5950 None:intergenic 20.0%
! TCAAATAACCCATATTCAAA+GGG - tig0023872:5966-5985 None:intergenic 25.0%
! TTCAAATAACCCATATTCAA+AGG - tig0023872:5967-5986 None:intergenic 25.0%
AATGAGGAAACAAAAACACT+TGG + tig0023872:5705-5724 Msa1412130:CDS 30.0%
AACTTCATGAATGTTGCAAA+TGG + tig0023872:5895-5914 Msa1412130:CDS 30.0%
TTCAACAACCCTTTGAATAT+GGG + tig0023872:5955-5974 Msa1412130:CDS 30.0%
TTATTTGAACCAACCAATCA+TGG + tig0023872:5978-5997 Msa1412130:CDS 30.0%
TGTTCAACACTTCCAAATTC+AGG + tig0023872:5598-5617 Msa1412130:CDS 35.0%
CTTCAACAACCCTTTGAATA+TGG + tig0023872:5954-5973 Msa1412130:CDS 35.0%
TCTTCAAGTGGAACATCTTC+AGG + tig0023872:5574-5593 Msa1412130:CDS 40.0%
! ACTTCCAAATTCAGGTTCAG+AGG + tig0023872:5606-5625 Msa1412130:CDS 40.0%
TCTTCCTCTGAACCTGAATT+TGG - tig0023872:5613-5632 None:intergenic 40.0%
GGAAGATTTGATGCTTCTGA+TGG + tig0023872:5627-5646 Msa1412130:CDS 40.0%
ATATCTGCAGAAGCCATGAT+TGG - tig0023872:5994-6013 None:intergenic 40.0%
!! GAGATCTTCTTGCTGATTCG+CGG - tig0023872:5684-5703 None:intergenic 45.0%
CAGCAAGAAGATCTCGAATG+AGG + tig0023872:5689-5708 Msa1412130:CDS 45.0%
!! CTTGGATGATCTTGCTGTTC+AGG + tig0023872:5723-5742 Msa1412130:CDS 45.0%
CTGTTCAGGTGAGTCAACTA+AGG + tig0023872:5737-5756 Msa1412130:CDS 45.0%
! CCAAGAATCGTTGAGTTGTG+AGG - tig0023872:5795-5814 None:intergenic 45.0%
CCTCACAACTCAACGATTCT+TGG + tig0023872:5792-5811 Msa1412130:CDS 45.0%
CTGCAGAAGCCATGATTGGT+TGG - tig0023872:5990-6009 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0023872 gene 5568 6032 5568 ID=Msa1412130;Name=Msa1412130
tig0023872 mRNA 5568 6032 5568 ID=Msa1412130-mRNA-1;Parent=Msa1412130;Name=Msa1412130-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|154
tig0023872 exon 5568 6032 5568 ID=Msa1412130-mRNA-1:exon:20451;Parent=Msa1412130-mRNA-1
tig0023872 CDS 5568 6032 5568 ID=Msa1412130-mRNA-1:cds;Parent=Msa1412130-mRNA-1
Gene Sequence

>Msa1412130

ATGGCTTCTTCAAGTGGAACATCTTCAGGCTGTTCAACACTTCCAAATTCAGGTTCAGAGGAAGATTTGATGCTTCTGATGGATCAAAGAAAAAGAAAGAGAATGATATCAAACCGCGAATCAGCAAGAAGATCTCGAATGAGGAAACAAAAACACTTGGATGATCTTGCTGTTCAGGTGAGTCAACTAAGGAATGAGAATCAACAGATTCTAACTTCAGTGAACCTCACAACTCAACGATTCTTGGCTGTTGAATCTGAAAACTCTGTGCTTAGAGCTCAACTGAATGAACTCAACAGCAGATTTGAGTCTTTGAATGAGATCATCAACTTCATGAATGTTGCAAATGGTGTTTTTGAACCTGTTGATAATAATAATGACAATTACTTCAACAACCCTTTGAATATGGGTTATTTGAACCAACCAATCATGGCTTCTGCAGATATGAACATGATACATTATTGA

Protein sequence

>Msa1412130

MASSSGTSSGCSTLPNSGSEEDLMLLMDQRKRKRMISNRESARRSRMRKQKHLDDLAVQVSQLRNENQQILTSVNLTTQRFLAVESENSVLRAQLNELNSRFESLNEIINFMNVANGVFEPVDNNNDNYFNNPLNMGYLNQPIMASADMNMIHY*