AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1376450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1376450 MtrunA17_Chr4g0071941 97.241 145 4 0 54 198 6 150 9.25e-98 280
Msa1376450 MtrunA17_Chr5g0408251 63.874 191 61 2 8 198 18 200 4.03e-79 234
Msa1376450 MtrunA17_Chr7g0217621 62.051 195 70 3 6 198 10 202 3.81e-70 212
Msa1376450 MtrunA17_Chr4g0042491 38.636 176 92 6 25 197 17 179 3.97e-23 91.3
Msa1376450 MtrunA17_Chr7g0245371 46.067 89 47 1 108 195 84 172 1.10e-16 74.3
Msa1376450 MtrunA17_Chr2g0329371 29.744 195 116 4 19 194 11 203 1.08e-15 72.4
Msa1376450 MtrunA17_Chr4g0033601 47.761 67 35 0 129 195 77 143 6.17e-14 66.2
Msa1376450 MtrunA17_Chr7g0217611 74.419 43 11 0 94 136 1 43 2.52e-13 62.0
Msa1376450 MtrunA17_Chr4g0064231 48.000 75 35 1 125 195 144 218 1.35e-12 64.3
Msa1376450 MtrunA17_Chr3g0125311 41.053 95 51 1 99 193 70 159 2.41e-12 62.4
Msa1376450 MtrunA17_Chr3g0139311 49.180 61 31 0 129 189 114 174 2.64e-12 62.4
Msa1376450 MtrunA17_Chr7g0256171 50.820 61 30 0 134 194 82 142 2.96e-12 62.0
Msa1376450 MtrunA17_Chr8g0392951 32.090 134 58 4 76 196 47 160 2.10e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1376450 AT5G39670.1 48.000 200 91 6 2 198 15 204 1.35e-47 155
Msa1376450 AT3G29000.1 59.459 111 43 1 87 197 85 193 1.75e-37 129
Msa1376450 AT4G20780.1 60.000 65 26 0 130 194 120 184 9.71e-20 82.8
Msa1376450 AT5G44460.1 54.545 66 30 0 130 195 111 176 5.95e-17 75.5
Msa1376450 AT3G59440.1 30.000 190 112 6 19 195 7 188 1.04e-16 75.1
Msa1376450 AT3G47480.1 48.101 79 39 2 120 197 105 182 1.26e-16 74.7
Msa1376450 AT2G43290.1 37.719 114 67 3 83 194 96 207 3.95e-16 73.9
Msa1376450 AT4G03290.1 53.125 64 30 0 131 194 82 145 1.78e-15 70.9
Msa1376450 AT1G05990.1 50.769 65 32 0 131 195 80 144 3.33e-15 70.1
Msa1376450 AT3G07490.1 51.613 62 30 0 134 195 82 143 2.08e-14 68.2
Msa1376450 AT4G12860.1 50.000 62 31 0 134 195 82 143 4.23e-13 64.3
Msa1376450 AT1G21550.1 31.298 131 66 3 84 193 25 152 2.56e-12 62.4

Find 23 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAGAGAGTTCTTGTTATTT+TGG 0.121543 tig0019806:-91155 Msa1376450:CDS
AACTCAACTTCTCCCTTATT+TGG 0.181162 tig0019806:-91568 Msa1376450:CDS
CTTCTTTGCCAAATTCATTC+TGG 0.280945 tig0019806:-91472 Msa1376450:CDS
CTGAGCTACCAGAATGAATT+TGG 0.286669 tig0019806:+91464 None:intergenic
TGAAGAGAATGAGCCTAGTT+TGG 0.350779 tig0019806:-91245 Msa1376450:CDS
GCAAATGTTGGCAGAGATAA+TGG 0.359399 tig0019806:-91385 Msa1376450:CDS
TGAAAGAGATGAAGTGAAAA+TGG 0.369654 tig0019806:-91353 Msa1376450:CDS
AAGGTCTATGAAACCAAATA+AGG 0.374441 tig0019806:+91555 None:intergenic
CAGAATGAATTTGGCAAAGA+AGG 0.401758 tig0019806:+91473 None:intergenic
GAGGAACTTGAAGAAAAGTA+TGG 0.414511 tig0019806:-91292 Msa1376450:CDS
CTATTACTATGTGAAATTTG+AGG 0.460627 tig0019806:+91598 None:intergenic
AAACACTTCACAAAGCTCCT+TGG 0.468222 tig0019806:+91267 None:intergenic
AGGTCTATGAAACCAAATAA+GGG 0.516554 tig0019806:+91556 None:intergenic
AACAAACAAATCAGCAGAAG+TGG 0.517182 tig0019806:+91023 None:intergenic
TGCTTCAACTCCTCCAAACT+AGG 0.518183 tig0019806:+91232 None:intergenic
AGAGGTAAGAGATGAGAAGA+AGG 0.519907 tig0019806:-91443 Msa1376450:CDS
AGAGAATGAGCCTAGTTTGG+AGG 0.522617 tig0019806:-91242 Msa1376450:CDS
AAAATGTCAAGTATAGGAAA+AGG 0.526434 tig0019806:+91536 None:intergenic
GTGTAGCAGTCAAGAGAATG+AGG 0.533790 tig0019806:-91407 Msa1376450:CDS
CAAGAGAATGAGGCAAATGT+TGG 0.535719 tig0019806:-91397 Msa1376450:CDS
TGAAGAAAAGTATGGTTCCA+AGG 0.559713 tig0019806:-91284 Msa1376450:CDS
AGATGAAGTGAAAATGGTGA+TGG 0.595216 tig0019806:-91347 Msa1376450:CDS
AATTCATTCTGGTAGCTCAG+AGG 0.688478 tig0019806:-91461 Msa1376450:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATACTTGAGAAAAAATTG+TGG + tig0019806:91140-91159 None:intergenic 20.0%
!!! ACAATTTTTTCTCAAGTATA+TGG - tig0019806:91139-91158 Msa1376450:CDS 20.0%
!!! ATTTTTGATGAAAATCAAGA+TGG - tig0019806:91555-91574 Msa1376450:CDS 20.0%
! CTATTACTATGTGAAATTTG+AGG + tig0019806:91045-91064 None:intergenic 25.0%
! AAAATGTCAAGTATAGGAAA+AGG + tig0019806:91107-91126 None:intergenic 25.0%
! TGTTGAAAAATGTCAAGTAT+AGG + tig0019806:91113-91132 None:intergenic 25.0%
!!! AAAATGGTGATGGAAAAAAT+GGG - tig0019806:91303-91322 Msa1376450:CDS 25.0%
!! CAAAAATTGTGATCATCTTT+TGG + tig0019806:91542-91561 None:intergenic 25.0%
AGGTCTATGAAACCAAATAA+GGG + tig0019806:91087-91106 None:intergenic 30.0%
AAGGTCTATGAAACCAAATA+AGG + tig0019806:91088-91107 None:intergenic 30.0%
TGAAAGAGATGAAGTGAAAA+TGG - tig0019806:91287-91306 Msa1376450:CDS 30.0%
!! GAAAATGGTGATGGAAAAAA+TGG - tig0019806:91302-91321 Msa1376450:CDS 30.0%
! GTTTTTGATGAGAACAAAGA+TGG - tig0019806:91441-91460 Msa1376450:CDS 30.0%
!!! AGATGGTTTTATTGATGCAA+AGG - tig0019806:91458-91477 Msa1376450:CDS 30.0%
!!! CAGAGAGTTCTTGTTATTTT+GGG - tig0019806:91486-91505 Msa1376450:CDS 30.0%
!!! GTTATTTTGGGATTGAAACA+AGG - tig0019806:91498-91517 Msa1376450:CDS 30.0%
AACTCAACTTCTCCCTTATT+TGG - tig0019806:91072-91091 Msa1376450:CDS 35.0%
CAGAATGAATTTGGCAAAGA+AGG + tig0019806:91170-91189 None:intergenic 35.0%
CTTCTTTGCCAAATTCATTC+TGG - tig0019806:91168-91187 Msa1376450:CDS 35.0%
AGATGAAGTGAAAATGGTGA+TGG - tig0019806:91293-91312 Msa1376450:CDS 35.0%
GAGGAACTTGAAGAAAAGTA+TGG - tig0019806:91348-91367 Msa1376450:CDS 35.0%
! TGAAGAAAAGTATGGTTCCA+AGG - tig0019806:91356-91375 Msa1376450:CDS 35.0%
!!! GCAGAGAGTTCTTGTTATTT+TGG - tig0019806:91485-91504 Msa1376450:CDS 35.0%
CTGAGCTACCAGAATGAATT+TGG + tig0019806:91179-91198 None:intergenic 40.0%
AATTCATTCTGGTAGCTCAG+AGG - tig0019806:91179-91198 Msa1376450:CDS 40.0%
AGAGGTAAGAGATGAGAAGA+AGG - tig0019806:91197-91216 Msa1376450:CDS 40.0%
CAAGAGAATGAGGCAAATGT+TGG - tig0019806:91243-91262 Msa1376450:CDS 40.0%
GCAAATGTTGGCAGAGATAA+TGG - tig0019806:91255-91274 Msa1376450:CDS 40.0%
AAACACTTCACAAAGCTCCT+TGG + tig0019806:91376-91395 None:intergenic 40.0%
TGAAGAGAATGAGCCTAGTT+TGG - tig0019806:91395-91414 Msa1376450:CDS 40.0%
GTGTAGCAGTCAAGAGAATG+AGG - tig0019806:91233-91252 Msa1376450:CDS 45.0%
! CTTTTGCAGCTCAGAAAGTG+AGG - tig0019806:91329-91348 Msa1376450:CDS 45.0%
AGAGAATGAGCCTAGTTTGG+AGG - tig0019806:91398-91417 Msa1376450:CDS 45.0%
TGCTTCAACTCCTCCAAACT+AGG + tig0019806:91411-91430 None:intergenic 45.0%
Chromosome Type Strat End Strand Name
tig0019806 gene 91033 91629 91033 ID=Msa1376450;Name=Msa1376450
tig0019806 mRNA 91033 91629 91033 ID=Msa1376450-mRNA-1;Parent=Msa1376450;Name=Msa1376450-mRNA-1;_AED=0.35;_eAED=0.35;_QI=0|-1|0|1|-1|1|1|0|198
tig0019806 exon 91033 91629 91033 ID=Msa1376450-mRNA-1:exon:5176;Parent=Msa1376450-mRNA-1
tig0019806 CDS 91033 91629 91033 ID=Msa1376450-mRNA-1:cds;Parent=Msa1376450-mRNA-1
Gene Sequence

>Msa1376450

ATGGCTCTTCCTCAAATTTCACATAGTAATAGCATTAGCAACTCAACTTCTCCCTTATTTGGTTTCATAGACCTTTTCCTATACTTGACATTTTTCAACAAAATCCACAATTTTTTCTCAAGTATATGGTTTTTCCTTCTTTGCCAAATTCATTCTGGTAGCTCAGAGGTAAGAGATGAGAAGAAGGTTTCAGAATCTAAGTGTAGCAGTCAAGAGAATGAGGCAAATGTTGGCAGAGATAATGGTTACATGATTGAAAGAGATGAAGTGAAAATGGTGATGGAAAAAATGGGATTCTTTTGCAGCTCAGAAAGTGAGGAACTTGAAGAAAAGTATGGTTCCAAGGAGCTTTGTGAAGTGTTTGAAGAGAATGAGCCTAGTTTGGAGGAGTTGAAGCAAGCTTTTGATGTTTTTGATGAGAACAAAGATGGTTTTATTGATGCAAAGGAATTGCAGAGAGTTCTTGTTATTTTGGGATTGAAACAAGGATCAGAATTTGAGAATTGCCAAAAGATGATCACAATTTTTGATGAAAATCAAGATGGAAGAATTGATTTCATTGAGTTTGTAAATATTATGAAAAACCACTTCTGCTGA

Protein sequence

>Msa1376450

MALPQISHSNSISNSTSPLFGFIDLFLYLTFFNKIHNFFSSIWFFLLCQIHSGSSEVRDEKKVSESKCSSQENEANVGRDNGYMIERDEVKMVMEKMGFFCSSESEELEEKYGSKELCEVFEENEPSLEELKQAFDVFDENKDGFIDAKELQRVLVILGLKQGSEFENCQKMITIFDENQDGRIDFIEFVNIMKNHFC*