AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1425260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1425260 MtrunA17_Chr3g0144941 97.419 155 3 1 1 154 1 155 1.34e-106 300
Msa1425260 MtrunA17_Chr4g0035414 71.895 153 39 1 1 149 1 153 8.97e-65 194
Msa1425260 MtrunA17_Chr1g0155551 61.491 161 50 4 1 151 1 159 3.75e-57 176
Msa1425260 MtrunA17_Chr8g0378901 53.416 161 67 5 1 154 1 160 1.73e-46 148
Msa1425260 MtrunA17_Chr3g0141881 59.341 91 34 1 17 107 53 140 3.91e-30 107
Msa1425260 MtrunA17_Chr1g0194681 44.545 110 58 1 1 110 1 107 4.33e-25 94.0
Msa1425260 MtrunA17_Chr6g0456061 44.118 102 47 2 26 124 86 180 3.21e-18 77.4
Msa1425260 MtrunA17_Chr8g0341311 50.685 73 36 0 26 98 70 142 2.54e-17 74.7
Msa1425260 MtrunA17_Chr7g0225661 44.444 99 51 2 1 98 57 152 2.61e-17 74.7
Msa1425260 MtrunA17_Chr7g0220571 51.250 80 39 0 19 98 76 155 4.44e-17 74.3
Msa1425260 MtrunA17_Chr4g0054291 39.091 110 60 1 7 109 45 154 6.39e-16 70.9
Msa1425260 MtrunA17_Chr5g0400901 41.053 95 48 1 27 121 58 144 2.04e-14 66.6
Msa1425260 MtrunA17_Chr7g0269951 45.000 120 60 2 27 146 19 132 4.51e-13 62.4
Msa1425260 MtrunA17_Chr3g0139301 34.259 108 67 1 6 109 98 205 1.14e-12 63.9
Msa1425260 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
Msa1425260 AT1G75390.1 53.459 159 58 4 2 147 9 164 2.83e-48 154
Msa1425260 AT4G34590.1 57.143 133 47 2 26 148 23 155 5.19e-44 142
Msa1425260 AT2G18160.1 47.020 151 56 5 22 151 23 170 7.83e-37 125
Msa1425260 AT1G75390.2 60.825 97 34 2 2 94 9 105 1.21e-32 112
Msa1425260 AT3G62420.1 44.526 137 75 1 13 149 8 143 1.29e-30 108
Msa1425260 AT2G04038.1 48.837 86 41 1 16 98 57 142 4.39e-18 76.6
Msa1425260 AT5G15830.1 34.932 146 79 3 9 154 55 184 8.82e-18 76.3
Msa1425260 AT1G13600.1 45.361 97 48 2 16 107 70 166 1.16e-16 73.6
Msa1425260 AT3G30530.1 52.055 73 35 0 26 98 77 149 2.79e-16 72.0
Msa1425260 AT5G38800.1 47.500 80 42 0 19 98 61 140 1.48e-15 70.1
Msa1425260 AT5G49450.1 36.190 105 64 1 27 128 13 117 1.96e-12 61.2
Msa1425260 AT4G37730.1 45.000 80 37 1 26 98 193 272 4.52e-12 62.8
Msa1425260 AT2G22850.1 37.079 89 56 0 23 111 122 210 2.78e-11 59.7
Msa1425260 AT2G22850.2 37.079 89 56 0 23 111 122 210 2.78e-11 59.7
Msa1425260 AT3G49760.1 55.814 43 19 0 28 70 70 112 4.41e-11 58.2
Msa1425260 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 tig0025831:+62314 None:intergenic
CTTCAACAACCCTTTGAATA+TGG 0.147562 tig0025831:-61970 Msa1425260:CDS
CCTCACAACTCAACGATTCT+TGG 0.288929 tig0025831:-62132 Msa1425260:CDS
TGTTCAACACTTCCAAATTC+AGG 0.300497 tig0025831:-62326 Msa1425260:CDS
CTTGGATGATCTTGCTGTTC+AGG 0.305122 tig0025831:-62201 Msa1425260:CDS
TCTTCAAGTGGAACATCTTC+AGG 0.306987 tig0025831:-62350 Msa1425260:CDS
TTCAACAACCCTTTGAATAT+GGG 0.356244 tig0025831:-61969 Msa1425260:CDS
TTGTCATTATTATTATCAAC+AGG 0.406404 tig0025831:+61996 None:intergenic
TTATTTGAACCAACCAATCA+TGG 0.433242 tig0025831:-61946 Msa1425260:CDS
TTCAAATAACCCATATTCAA+AGG 0.450188 tig0025831:+61960 None:intergenic
GAGATCTTCTTGCTGATTCG+CGG 0.468319 tig0025831:+62243 None:intergenic
ATATCTGCAGAAGCCATGAT+TGG 0.469872 tig0025831:+61933 None:intergenic
GGAAGATTTGATGCTTCTGA+TGG 0.470481 tig0025831:-62297 Msa1425260:CDS
TCAAATAACCCATATTCAAA+GGG 0.472163 tig0025831:+61961 None:intergenic
CTGTTCAGGTGAGTCAACTA+AGG 0.511341 tig0025831:-62187 Msa1425260:CDS
CTGCAGAAGCCATGATTGGT+TGG 0.535667 tig0025831:+61937 None:intergenic
AACTTCATGAATGTTGCAAA+TGG 0.546215 tig0025831:-62029 Msa1425260:CDS
TCTCACATGGCTTCTTCAAG+TGG 0.568523 tig0025831:-62362 None:intergenic
ACTTCCAAATTCAGGTTCAG+AGG 0.572504 tig0025831:-62318 Msa1425260:CDS
CAGCAAGAAGATCTCGAATG+AGG 0.587735 tig0025831:-62235 Msa1425260:CDS
CCAAGAATCGTTGAGTTGTG+AGG 0.599678 tig0025831:+62132 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTCATTATTATTATCAAC+AGG + tig0025831:62277-62296 None:intergenic 20.0%
! TCAAATAACCCATATTCAAA+GGG + tig0025831:62312-62331 None:intergenic 25.0%
! TTCAAATAACCCATATTCAA+AGG + tig0025831:62313-62332 None:intergenic 25.0%
AATGAGGAAACAAAAACACT+TGG - tig0025831:62051-62070 Msa1425260:CDS 30.0%
AACTTCATGAATGTTGCAAA+TGG - tig0025831:62241-62260 Msa1425260:CDS 30.0%
TTCAACAACCCTTTGAATAT+GGG - tig0025831:62301-62320 Msa1425260:CDS 30.0%
TTATTTGAACCAACCAATCA+TGG - tig0025831:62324-62343 Msa1425260:CDS 30.0%
TGTTCAACACTTCCAAATTC+AGG - tig0025831:61944-61963 Msa1425260:CDS 35.0%
CTTCAACAACCCTTTGAATA+TGG - tig0025831:62300-62319 Msa1425260:CDS 35.0%
TCTTCAAGTGGAACATCTTC+AGG - tig0025831:61920-61939 Msa1425260:CDS 40.0%
! ACTTCCAAATTCAGGTTCAG+AGG - tig0025831:61952-61971 Msa1425260:CDS 40.0%
TCTTCCTCTGAACCTGAATT+TGG + tig0025831:61959-61978 None:intergenic 40.0%
GGAAGATTTGATGCTTCTGA+TGG - tig0025831:61973-61992 Msa1425260:CDS 40.0%
ATATCTGCAGAAGCCATGAT+TGG + tig0025831:62340-62359 None:intergenic 40.0%
!! GAGATCTTCTTGCTGATTCG+CGG + tig0025831:62030-62049 None:intergenic 45.0%
CAGCAAGAAGATCTCGAATG+AGG - tig0025831:62035-62054 Msa1425260:CDS 45.0%
!! CTTGGATGATCTTGCTGTTC+AGG - tig0025831:62069-62088 Msa1425260:CDS 45.0%
CTGTTCAGGTGAGTCAACTA+AGG - tig0025831:62083-62102 Msa1425260:CDS 45.0%
! CCAAGAATCGTTGAGTTGTG+AGG + tig0025831:62141-62160 None:intergenic 45.0%
CCTCACAACTCAACGATTCT+TGG - tig0025831:62138-62157 Msa1425260:CDS 45.0%
CTGCAGAAGCCATGATTGGT+TGG + tig0025831:62336-62355 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0025831 gene 61914 62378 61914 ID=Msa1425260;Name=Msa1425260
tig0025831 mRNA 61914 62378 61914 ID=Msa1425260-mRNA-1;Parent=Msa1425260;Name=Msa1425260-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|154
tig0025831 exon 61914 62378 61914 ID=Msa1425260-mRNA-1:exon:4200;Parent=Msa1425260-mRNA-1
tig0025831 CDS 61914 62378 61914 ID=Msa1425260-mRNA-1:cds;Parent=Msa1425260-mRNA-1
Gene Sequence

>Msa1425260

ATGGCTTCTTCAAGTGGAACATCTTCAGGCTGTTCAACACTTCCAAATTCAGGTTCAGAGGAAGATTTGATGCTTCTGATGGATCAAAGAAAAAGAAAGAGAATGATATCAAACCGCGAATCAGCAAGAAGATCTCGAATGAGGAAACAAAAACACTTGGATGATCTTGCTGTTCAGGTGAGTCAACTAAGGAATGAGAATCAACAGATTCTAACTTCAGTGAACCTCACAACTCAACGATTCTTGGCTGTTGAATCTGAAAACTCTGTGCTTAGAGCTCAACTGAATGAACTCAACAGCAGATTTGAGTCTTTGAATGAGATCATCAACTTCATGAATGTTGCAAATGGTGTTTTTGAACCTGTTGATAATAATAATGACAATTACTTCAACAACCCTTTGAATATGGGTTATTTGAACCAACCAATCATGGCTTCTGCAGATATGAACATGATACATTATTGA

Protein sequence

>Msa1425260

MASSSGTSSGCSTLPNSGSEEDLMLLMDQRKRKRMISNRESARRSRMRKQKHLDDLAVQVSQLRNENQQILTSVNLTTQRFLAVESENSVLRAQLNELNSRFESLNEIINFMNVANGVFEPVDNNNDNYFNNPLNMGYLNQPIMASADMNMIHY*