AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1452390

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1452390 MtrunA17_Chr2g0278721 83.810 210 22 1 1 198 593 802 9.30e-116 352
Msa1452390 MtrunA17_Chr2g0278721 47.087 206 99 4 1 198 88 291 9.08e-54 184
Msa1452390 MtrunA17_Chr2g0278741 50.000 206 93 5 1 198 170 373 1.21e-60 198
Msa1452390 MtrunA17_Chr6g0477011 48.000 200 100 3 1 198 88 285 8.49e-59 187
Msa1452390 MtrunA17_Chr4g0039881 46.734 199 104 1 2 198 65 263 5.75e-57 186
Msa1452390 MtrunA17_Chr6g0464091 46.009 213 93 5 1 198 91 296 2.55e-56 185
Msa1452390 MtrunA17_Chr4g0069611 48.276 203 95 5 2 198 88 286 3.88e-56 184
Msa1452390 MtrunA17_Chr2g0302851 44.279 201 108 2 1 198 88 287 4.31e-56 184
Msa1452390 MtrunA17_Chr6g0466841 44.279 201 106 2 2 198 91 289 6.36e-51 171
Msa1452390 MtrunA17_Chr6g0466831 43.284 201 108 2 2 198 91 289 7.45e-50 168
Msa1452390 MtrunA17_Chr8g0367221 33.495 206 126 3 2 198 1362 1565 3.51e-32 122
Msa1452390 MtrunA17_Chr8g0367221 33.659 205 126 3 2 198 86 288 4.25e-30 116
Msa1452390 MtrunA17_Chr8g0367221 30.288 208 130 4 2 198 872 1075 1.69e-27 109
Msa1452390 MtrunA17_Chr7g0241801 33.333 204 109 4 1 200 82 262 1.62e-27 107
Msa1452390 MtrunA17_Chr7g0241781 35.000 200 107 4 1 198 82 260 1.70e-26 105
Msa1452390 MtrunA17_Chr8g0336321 30.144 209 133 5 1 198 82 288 2.02e-24 99.8
Msa1452390 MtrunA17_Chr8g0336251 30.144 209 133 5 1 198 82 288 2.04e-24 99.8
Msa1452390 MtrunA17_Chr3g0092021 47.253 91 48 0 2 92 91 181 1.41e-17 77.0
Msa1452390 MtrunA17_Chr4g0029151 29.016 193 115 8 16 198 102 282 9.66e-16 75.1
Msa1452390 MtrunA17_Chr2g0283041 30.806 211 121 9 2 200 80 277 3.09e-15 73.6
Msa1452390 MtrunA17_Chr4g0029161 26.531 196 120 6 14 198 92 274 3.87e-15 73.2
Msa1452390 MtrunA17_Chr4g0029131 26.531 196 120 6 14 198 92 274 6.86e-15 72.8
Msa1452390 MtrunA17_Chr1g0196851 26.943 193 127 4 14 198 128 314 6.75e-14 69.7
Msa1452390 MtrunA17_Chr4g0040711 29.187 209 129 9 2 200 81 280 9.27e-14 69.3
Msa1452390 MtrunA17_Chr4g0040691 26.794 209 130 8 2 198 81 278 9.30e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1452390 AT2G22590.1 38.725 204 115 4 2 198 91 291 7.27e-45 155
Msa1452390 AT5G49690.1 37.745 204 119 2 1 198 83 284 3.05e-42 148
Msa1452390 AT5G65550.1 34.135 208 124 4 2 198 82 287 2.56e-33 124
Msa1452390 AT5G54060.1 27.619 210 133 7 2 200 86 287 1.05e-16 78.2
Msa1452390 AT5G54010.1 25.628 199 140 3 2 200 79 269 4.99e-13 67.4
Msa1452390 AT4G27570.1 25.490 204 133 8 2 200 80 269 1.06e-11 63.5
Msa1452390 AT1G64920.1 25.373 201 132 6 2 200 79 263 1.31e-11 63.2
Msa1452390 AT4G27560.1 25.123 203 135 7 2 200 80 269 2.18e-11 62.8
Msa1452390 AT5G53990.1 25.126 199 131 7 2 198 79 261 7.11e-11 61.2

Find 38 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGTTGTTTACATTGCATT+TGG 0.241228 tig0033858:+8554 Msa1452390:CDS
ATTACTATGGTCCACCTAAA+TGG 0.278800 tig0033858:+8222 Msa1452390:CDS
GAGAATCATAGGCTAGTTTA+AGG 0.286651 tig0033858:-7985 None:intergenic
GTAGGAAATGAAATCCATTT+AGG 0.287213 tig0033858:-8236 None:intergenic
GATATCAAAGTTAATGAAAC+AGG 0.297992 tig0033858:+8302 Msa1452390:CDS
GGTGGACCATAGTAATCTTC+AGG 0.323318 tig0033858:-8215 None:intergenic
CTGTTGTTTACATTGCATTT+GGG 0.330299 tig0033858:+8555 Msa1452390:CDS
TTATCAGAAGAATCTCTTCT+TGG 0.349435 tig0033858:-8470 None:intergenic
GGTCTTAAACCAATCTTTGT+AGG 0.350025 tig0033858:-8254 None:intergenic
TCAAAACTTCAAATCCTGAT+TGG 0.352979 tig0033858:+8032 Msa1452390:CDS
ATTTCATTTCCTACAAAGAT+TGG 0.364052 tig0033858:+8245 Msa1452390:CDS
GATTGGTTTAAGACCTTATG+AGG 0.366338 tig0033858:+8262 Msa1452390:CDS
CAAAACTTCAAATCCTGATT+GGG 0.372669 tig0033858:+8033 Msa1452390:CDS
TTTAAGGTAATAGAGTTTGT+TGG 0.391137 tig0033858:-7969 None:intergenic
GCTTTGATTTGAATCCAATC+AGG 0.403409 tig0033858:-8506 None:intergenic
AGATTCTTGAAGAGAATCAT+AGG 0.444248 tig0033858:-7996 None:intergenic
AAGAAGAGATTCTTCTGATA+AGG 0.451469 tig0033858:+8472 Msa1452390:CDS
AACAAGCCTGTGATTCCTGT+TGG 0.452927 tig0033858:+8437 Msa1452390:CDS
ATTTCAGTCCTTGTCCTGCA+TGG 0.453347 tig0033858:+8128 Msa1452390:intron
CAAGAGATCTTGAAGGAGAA+TGG 0.456587 tig0033858:+8390 Msa1452390:CDS
AAATCATAGAAAACCCAATC+AGG 0.471854 tig0033858:-8046 None:intergenic
ACAAATCCTGAAGATTACTA+TGG 0.475322 tig0033858:+8209 Msa1452390:CDS
TCAGAAGAATCTCTTCTTGG+TGG 0.486888 tig0033858:-8467 None:intergenic
CTTGGTGGAAGCAATCCAAC+AGG 0.516343 tig0033858:-8452 None:intergenic
AGAAGTTCAAGAGATCTTGA+AGG 0.518118 tig0033858:+8383 Msa1452390:CDS
AGGTAGATCATAGTCCTGAT+TGG 0.518241 tig0033858:+8492 Msa1452390:CDS
AAGGTAATAGAGTTTGTTGG+AGG 0.543704 tig0033858:-7966 None:intergenic
AGCAATCCAACAGGAATCAC+AGG 0.548846 tig0033858:-8443 None:intergenic
TTTGTTGGAGGGAATATCCA+TGG 0.553087 tig0033858:-7954 None:intergenic
TTACATTGCATTTGGGAGTG+AGG 0.565933 tig0033858:+8562 Msa1452390:CDS
ATTGGATTCAAATCAAAGCA+TGG 0.575062 tig0033858:+8510 Msa1452390:CDS
AAGAAGCATATGCTCCATGC+AGG 0.575969 tig0033858:-8142 None:intergenic
GGAAATGAAATCCATTTAGG+TGG 0.580262 tig0033858:-8233 None:intergenic
CATATGCTCCATGCAGGACA+AGG 0.580512 tig0033858:-8136 None:intergenic
TTCAAACTCTTTGCTAACTG+TGG 0.586550 tig0033858:-8085 None:intergenic
AGGTAATAGAGTTTGTTGGA+GGG 0.602069 tig0033858:-7965 None:intergenic
ATATCAAAGTTAATGAAACA+GGG 0.645990 tig0033858:+8303 Msa1452390:CDS
TATCAAAGTTAATGAAACAG+GGG 0.659935 tig0033858:+8304 Msa1452390:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATATCAAAGTTAATGAAACA+GGG + tig0033858:8303-8322 Msa1452390:CDS 20.0%
!! TTTAAGGTAATAGAGTTTGT+TGG - tig0033858:7972-7991 None:intergenic 25.0%
! TTGATACACCAAAAAACAAT+TGG + tig0033858:8164-8183 Msa1452390:CDS 25.0%
! ATTTCATTTCCTACAAAGAT+TGG + tig0033858:8245-8264 Msa1452390:CDS 25.0%
! GATATCAAAGTTAATGAAAC+AGG + tig0033858:8302-8321 Msa1452390:CDS 25.0%
! TATCAAAGTTAATGAAACAG+GGG + tig0033858:8304-8323 Msa1452390:CDS 25.0%
AGATTCTTGAAGAGAATCAT+AGG - tig0033858:7999-8018 None:intergenic 30.0%
TCAAAACTTCAAATCCTGAT+TGG + tig0033858:8032-8051 Msa1452390:CDS 30.0%
CAAAACTTCAAATCCTGATT+GGG + tig0033858:8033-8052 Msa1452390:CDS 30.0%
AAATCATAGAAAACCCAATC+AGG - tig0033858:8049-8068 None:intergenic 30.0%
!!! CATCATCACCAATTGTTTTT+TGG - tig0033858:8175-8194 None:intergenic 30.0%
ACAAATCCTGAAGATTACTA+TGG + tig0033858:8209-8228 Msa1452390:CDS 30.0%
GTAGGAAATGAAATCCATTT+AGG - tig0033858:8239-8258 None:intergenic 30.0%
! AGCAATTTTCTTACCTCATA+AGG - tig0033858:8278-8297 None:intergenic 30.0%
TCTGTTTAGATCAAAAACAG+GGG - tig0033858:8333-8352 None:intergenic 30.0%
CTCTGTTTAGATCAAAAACA+GGG - tig0033858:8334-8353 None:intergenic 30.0%
TTATCAGAAGAATCTCTTCT+TGG - tig0033858:8473-8492 None:intergenic 30.0%
AAGAAGAGATTCTTCTGATA+AGG + tig0033858:8472-8491 Msa1452390:CDS 30.0%
ATTGGATTCAAATCAAAGCA+TGG + tig0033858:8510-8529 Msa1452390:CDS 30.0%
! TCTGTTGTTTACATTGCATT+TGG + tig0033858:8554-8573 Msa1452390:CDS 30.0%
! CTGTTGTTTACATTGCATTT+GGG + tig0033858:8555-8574 Msa1452390:CDS 30.0%
!! AGGTAATAGAGTTTGTTGGA+GGG - tig0033858:7968-7987 None:intergenic 35.0%
!! AAGGTAATAGAGTTTGTTGG+AGG - tig0033858:7969-7988 None:intergenic 35.0%
!! GAGAATCATAGGCTAGTTTA+AGG - tig0033858:7988-8007 None:intergenic 35.0%
! TCTATGATTTTGCAGCTAGT+TGG + tig0033858:8059-8078 Msa1452390:CDS 35.0%
TTCAAACTCTTTGCTAACTG+TGG - tig0033858:8088-8107 None:intergenic 35.0%
ATTACTATGGTCCACCTAAA+TGG + tig0033858:8222-8241 Msa1452390:CDS 35.0%
GGAAATGAAATCCATTTAGG+TGG - tig0033858:8236-8255 None:intergenic 35.0%
GGTCTTAAACCAATCTTTGT+AGG - tig0033858:8257-8276 None:intergenic 35.0%
!! GATTGGTTTAAGACCTTATG+AGG + tig0033858:8262-8281 Msa1452390:CDS 35.0%
GCTCTGTTTAGATCAAAAAC+AGG - tig0033858:8335-8354 None:intergenic 35.0%
AGAAGTTCAAGAGATCTTGA+AGG + tig0033858:8383-8402 Msa1452390:CDS 35.0%
! GGAGAATGGTTAGATTTTCT+TGG + tig0033858:8404-8423 Msa1452390:CDS 35.0%
!! GCTTTGATTTGAATCCAATC+AGG - tig0033858:8509-8528 None:intergenic 35.0%
CAAGAGATCTTGAAGGAGAA+TGG + tig0033858:8390-8409 Msa1452390:CDS 40.0%
TCAGAAGAATCTCTTCTTGG+TGG - tig0033858:8470-8489 None:intergenic 40.0%
AGGTAGATCATAGTCCTGAT+TGG + tig0033858:8492-8511 Msa1452390:CDS 40.0%
TTACATTGCATTTGGGAGTG+AGG + tig0033858:8562-8581 Msa1452390:CDS 40.0%
ATTTCAGTCCTTGTCCTGCA+TGG + tig0033858:8128-8147 Msa1452390:intron 45.0%
! AAGAAGCATATGCTCCATGC+AGG - tig0033858:8145-8164 None:intergenic 45.0%
GGTGGACCATAGTAATCTTC+AGG - tig0033858:8218-8237 None:intergenic 45.0%
AACAAGCCTGTGATTCCTGT+TGG + tig0033858:8437-8456 Msa1452390:CDS 45.0%
AGCAATCCAACAGGAATCAC+AGG - tig0033858:8446-8465 None:intergenic 45.0%
CATATGCTCCATGCAGGACA+AGG - tig0033858:8139-8158 None:intergenic 50.0%
CTTGGTGGAAGCAATCCAAC+AGG - tig0033858:8455-8474 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
tig0033858 gene 7956 8610 7956 ID=Msa1452390;Name=Msa1452390
tig0033858 mRNA 7956 8610 7956 ID=Msa1452390-mRNA-1;Parent=Msa1452390;Name=Msa1452390-mRNA-1;_AED=0.39;_eAED=0.40;_QI=0|0|0|1|1|1|2|0|206
tig0033858 exon 7956 8100 7956 ID=Msa1452390-mRNA-1:exon:18552;Parent=Msa1452390-mRNA-1
tig0033858 exon 8135 8610 8135 ID=Msa1452390-mRNA-1:exon:18553;Parent=Msa1452390-mRNA-1
tig0033858 CDS 7956 8100 7956 ID=Msa1452390-mRNA-1:cds;Parent=Msa1452390-mRNA-1
tig0033858 CDS 8135 8610 8135 ID=Msa1452390-mRNA-1:cds;Parent=Msa1452390-mRNA-1
Gene Sequence

>Msa1452390

ATGGATATTCCCTCCAACAAACTCTATTACCTTAAACTAGCCTATGATTCTCTTCAAGAATCTCTAGCTGAAATACTCAAAACTTCAAATCCTGATTGGGTTTTCTATGATTTTGCAGCTAGTTGGTTACCACAGTTAGCAAAGATCCTTGTCCTGCATGGAGCATATGCTTCTTTGATACACCAAAAAACAATTGGTGATGATGTTGCAACTACTAGAACAAATCCTGAAGATTACTATGGTCCACCTAAATGGATTTCATTTCCTACAAAGATTGGTTTAAGACCTTATGAGGTAAGAAAATTGCTTGAAGATATCAAAGTTAATGAAACAGGGGCATCCCCTGTTTTTGATCTAAACAGAGCAAATTCAGATTGTGATATGTTTGTTATTAGAAGTTCAAGAGATCTTGAAGGAGAATGGTTAGATTTTCTTGGTGAGTTTTACAACAAGCCTGTGATTCCTGTTGGATTGCTTCCACCAAGAAGAGATTCTTCTGATAAGGTAGATCATAGTCCTGATTGGATTCAAATCAAAGCATGGTTAGACACACAAAAGAGTTCATCTGTTGTTTACATTGCATTTGGGAGTGAGGAAATTGAGCCAAGAAAATCTCAATGA
Protein sequence

>Msa1452390

MDIPSNKLYYLKLAYDSLQESLAEILKTSNPDWVFYDFAASWLPQLAKILVLHGAYASLIHQKTIGDDVATTRTNPEDYYGPPKWISFPTKIGLRPYEVRKLLEDIKVNETGASPVFDLNRANSDCDMFVIRSSRDLEGEWLDFLGEFYNKPVIPVGLLPPRRDSSDKVDHSPDWIQIKAWLDTQKSSSVVYIAFGSEEIEPRKSQ*