AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0445090

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0445090 MtrunA17_Chr3g0085321 92.063 189 10 1 1 184 1 189 3.61e-124 347
Msa0445090 MtrunA17_Chr3g0085301 80.423 189 32 1 1 184 6 194 2.71e-109 310
Msa0445090 MtrunA17_Chr3g0090231 71.739 184 42 2 3 181 4 182 1.84e-94 272
Msa0445090 MtrunA17_Chr4g0040551 71.196 184 43 2 3 181 4 182 7.31e-94 271
Msa0445090 MtrunA17_Chr3g0085311 62.963 189 65 1 1 184 1 189 1.96e-84 247
Msa0445090 MtrunA17_Chr3g0085291 61.905 189 65 3 1 184 1 187 3.89e-80 236
Msa0445090 MtrunA17_Chr1g0177051 49.162 179 85 4 7 181 7 183 9.29e-49 156
Msa0445090 MtrunA17_Chr1g0175911 45.506 178 91 4 6 181 16 189 1.83e-45 148
Msa0445090 MtrunA17_Chr4g0005081 47.973 148 75 1 36 181 47 194 5.43e-43 142
Msa0445090 MtrunA17_Chr4g0005031 46.622 148 77 1 36 181 71 218 9.02e-42 139
Msa0445090 MtrunA17_Chr4g0005071 45.270 148 79 1 36 181 46 193 1.40e-40 136
Msa0445090 MtrunA17_Chr4g0005041 43.243 148 82 1 36 181 48 195 1.96e-39 133
Msa0445090 MtrunA17_Chr4g0005011 43.836 146 78 2 38 181 51 194 3.24e-38 130
Msa0445090 MtrunA17_Chr7g0259071 40.107 187 92 5 1 179 12 186 5.79e-38 129
Msa0445090 MtrunA17_Chr7g0259091 39.130 184 106 3 1 181 11 191 5.30e-37 127
Msa0445090 MtrunA17_Chr7g0243501 42.282 149 85 1 34 181 41 189 1.14e-36 125
Msa0445090 MtrunA17_Chr4g0005111 40.645 155 91 1 29 182 34 188 3.03e-36 124
Msa0445090 MtrunA17_Chr7g0259121 45.161 155 74 4 36 181 38 190 7.52e-36 124
Msa0445090 MtrunA17_Chr7g0259101 46.309 149 77 2 36 181 43 191 2.29e-35 127
Msa0445090 MtrunA17_Chr7g0259101 44.898 147 78 2 36 179 242 388 1.07e-34 125
Msa0445090 MtrunA17_Chr5g0446751 38.710 186 103 5 2 181 6 186 5.54e-34 119
Msa0445090 MtrunA17_Chr4g0037481 37.500 152 92 1 33 181 38 189 1.18e-33 118
Msa0445090 MtrunA17_Chr3g0136631 42.000 150 80 4 38 181 38 186 1.14e-30 110
Msa0445090 MtrunA17_Chr4g0005131 36.709 158 95 2 29 182 33 189 7.60e-30 108
Msa0445090 MtrunA17_Chr3g0136641 42.282 149 80 4 38 181 38 185 8.57e-29 105
Msa0445090 MtrunA17_Chr4g0068391 35.542 166 92 4 4 165 9 163 1.34e-23 92.0
Msa0445090 MtrunA17_Chr4g0024951 31.690 142 95 1 45 184 37 178 7.91e-22 87.4
Msa0445090 MtrunA17_Chr4g0024961 33.803 142 92 1 45 184 37 178 1.58e-21 86.7
Msa0445090 MtrunA17_Chr4g0068381 37.398 123 73 2 41 160 35 156 2.18e-20 83.6
Msa0445090 MtrunA17_Chr4g0005091 31.319 182 104 4 7 182 7 173 3.67e-19 80.5
Msa0445090 MtrunA17_Chr1g0169281 36.634 101 63 1 59 159 129 228 7.78e-13 64.7
Msa0445090 MtrunA17_Chr1g0169511 39.326 89 53 1 71 159 135 222 3.11e-12 63.2
Msa0445090 MtrunA17_Chr1g0169291 39.326 89 53 1 71 159 135 222 3.76e-12 62.8
Msa0445090 MtrunA17_Chr1g0212861 37.363 91 54 2 72 159 235 325 7.92e-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
Msa0445090 AT1G22900.1 42.775 173 94 3 10 179 19 189 6.06e-44 145
Msa0445090 AT1G65870.1 42.262 168 93 2 16 181 22 187 6.14e-44 144
Msa0445090 AT5G42500.1 41.509 159 89 3 23 179 25 181 7.63e-41 136
Msa0445090 AT5G42510.1 42.484 153 80 3 31 179 30 178 1.45e-40 135
Msa0445090 AT2G21100.1 43.421 152 82 2 33 181 35 185 2.47e-38 130
Msa0445090 AT2G21100.2 43.421 152 82 2 33 181 35 185 2.47e-38 130
Msa0445090 AT1G58170.1 38.333 180 100 4 6 179 6 180 6.35e-37 126
Msa0445090 AT3G13650.1 40.411 146 86 1 36 181 39 183 7.53e-35 121
Msa0445090 AT1G55210.1 43.750 128 71 1 36 163 40 166 1.23e-33 118
Msa0445090 AT1G55210.2 43.750 128 71 1 36 163 40 166 1.23e-33 118
Msa0445090 AT5G49040.1 40.458 131 74 2 36 163 41 170 4.96e-32 114
Msa0445090 AT3G58090.1 49.524 105 53 0 77 181 165 269 1.03e-30 113
Msa0445090 AT3G13662.1 39.844 128 76 1 36 163 38 164 6.96e-30 108
Msa0445090 AT5G49030.3 40.458 131 74 2 36 163 41 170 1.28e-29 114
Msa0445090 AT4G38700.1 38.562 153 84 4 38 181 36 187 3.10e-28 104
Msa0445090 AT2G21110.1 35.714 154 91 2 35 181 31 183 4.92e-26 99.0
Msa0445090 AT3G13660.1 40.000 115 69 0 67 181 8 122 2.05e-24 92.8
Msa0445090 AT4G11210.1 28.889 180 115 6 9 181 6 179 9.53e-14 66.6
Msa0445090 AT4G11190.1 26.816 179 120 6 9 181 6 179 4.96e-12 62.0

Find 38 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATCCATTTGGTACATTTAT+TGG 0.153260 3_3:+18836298 None:intergenic
CTTTCTTCACTTCAAGATCT+TGG 0.247590 3_3:-18836187 Msa0445090:CDS
TACTCAACAACAAAATGTTC+AGG 0.343328 3_3:+18835983 None:intergenic
ATAAATGTACCAAATGGATT+TGG 0.359511 3_3:-18836295 Msa0445090:CDS
GGAAGAGCTCAAGGGTTGTT+TGG 0.380080 3_3:-18836211 Msa0445090:CDS
TAATGTCATGGTAGTAGAAA+TGG 0.395728 3_3:+18836362 None:intergenic
CTCACACTCATTTCCACAAA+TGG 0.403874 3_3:-18836454 Msa0445090:CDS
ATGCCTATTGTTGGTGGAAC+TGG 0.410474 3_3:-18836064 Msa0445090:CDS
TGTGTCAATGATTTGTACTA+TGG 0.414022 3_3:+18836321 None:intergenic
AAAGTTGAACCAAATCCATT+TGG 0.421388 3_3:+18836286 None:intergenic
AAAATGTTCAGGGGTAGAAA+TGG 0.424631 3_3:+18835994 None:intergenic
GGAAGTAGTCTTAGTATGTT+GGG 0.434106 3_3:-18836118 Msa0445090:CDS
ACACCAGTTCCACCAACAAT+AGG 0.442036 3_3:+18836061 None:intergenic
TTGTGAGAAAACTCCATTTG+TGG 0.447942 3_3:+18836441 None:intergenic
TGTGTTAGTTTCTCTGTTCG+TGG 0.453538 3_3:+18836388 None:intergenic
CTCTGTTCGTGGTTGTTCTG+AGG 0.455164 3_3:+18836399 None:intergenic
TCTGTTCGTGGTTGTTCTGA+GGG 0.458437 3_3:+18836400 None:intergenic
TGGAAGTAGTCTTAGTATGT+TGG 0.463038 3_3:-18836119 Msa0445090:CDS
ACACCAATAAATGTACCAAA+TGG 0.472256 3_3:-18836301 Msa0445090:CDS
AATAGAGAAATGCCTATTGT+TGG 0.476777 3_3:-18836073 Msa0445090:CDS
TTCTGAGGGTAATATGATGT+TGG 0.478821 3_3:+18836414 None:intergenic
AGAGAAATGCCTATTGTTGG+TGG 0.518085 3_3:-18836070 Msa0445090:CDS
ATGTGATTTGAACTTAACTC+TGG 0.531516 3_3:+18836235 None:intergenic
TCAATGATTTGTACTATGGT+GGG 0.533940 3_3:+18836325 None:intergenic
ACTCAACAACAAAATGTTCA+GGG 0.537652 3_3:+18835984 None:intergenic
AAATGAGTGTGAGGGAGAAG+AGG 0.539387 3_3:+18836464 None:intergenic
AATCACATTGGAAGAGCTCA+AGG 0.541975 3_3:-18836220 Msa0445090:CDS
GTCAATGATTTGTACTATGG+TGG 0.552285 3_3:+18836324 None:intergenic
TTTAAGGAAGGGGAATATGG+TGG 0.575067 3_3:-18836139 Msa0445090:CDS
CAATGATTTGTACTATGGTG+GGG 0.575820 3_3:+18836326 None:intergenic
GTAGTCTTAGTATGTTGGGA+AGG 0.607491 3_3:-18836114 Msa0445090:CDS
ATGGATGATGCAATGACTGA+AGG 0.615844 3_3:-18836259 Msa0445090:CDS
TGGATGATGCAATGACTGAA+GGG 0.619095 3_3:-18836258 Msa0445090:CDS
CTCAACAACAAAATGTTCAG+GGG 0.634579 3_3:+18835985 None:intergenic
GAGTTAAGTTCAAATCACAT+TGG 0.654375 3_3:-18836232 Msa0445090:CDS
CATTTGTGGAAATGAGTGTG+AGG 0.677634 3_3:+18836455 None:intergenic
ATCACATTGGAAGAGCTCAA+GGG 0.681788 3_3:-18836219 Msa0445090:CDS
ATTTGTGGAAATGAGTGTGA+GGG 0.692176 3_3:+18836456 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTGACAAATTTTGTTTTTA+AGG - chr3_3:18836293-18836312 Msa0445090:CDS 20.0%
!!! ACAAATTTTGTTTTTAAGGA+AGG - chr3_3:18836297-18836316 Msa0445090:CDS 20.0%
!!! CAAATTTTGTTTTTAAGGAA+GGG - chr3_3:18836298-18836317 Msa0445090:CDS 20.0%
!!! AAATTTTGTTTTTAAGGAAG+GGG - chr3_3:18836299-18836318 Msa0445090:CDS 20.0%
! AATCCATTTGGTACATTTAT+TGG + chr3_3:18836153-18836172 None:intergenic 25.0%
!! ATAAATGTACCAAATGGATT+TGG - chr3_3:18836153-18836172 Msa0445090:CDS 25.0%
!!! ATTTGGTTCAACTTTTATGA+TGG - chr3_3:18836170-18836189 Msa0445090:CDS 25.0%
!! TCTCTATTTTGTTCAGAAAT+AGG + chr3_3:18836363-18836382 None:intergenic 25.0%
TAATGTCATGGTAGTAGAAA+TGG + chr3_3:18836089-18836108 None:intergenic 30.0%
!! TTTTGTTGTCTCTAATGTCA+TGG + chr3_3:18836101-18836120 None:intergenic 30.0%
! TCAATGATTTGTACTATGGT+GGG + chr3_3:18836126-18836145 None:intergenic 30.0%
! TGTGTCAATGATTTGTACTA+TGG + chr3_3:18836130-18836149 None:intergenic 30.0%
ACACCAATAAATGTACCAAA+TGG - chr3_3:18836147-18836166 Msa0445090:CDS 30.0%
AAAGTTGAACCAAATCCATT+TGG + chr3_3:18836165-18836184 None:intergenic 30.0%
ATGTGATTTGAACTTAACTC+TGG + chr3_3:18836216-18836235 None:intergenic 30.0%
GAGTTAAGTTCAAATCACAT+TGG - chr3_3:18836216-18836235 Msa0445090:CDS 30.0%
AATAGAGAAATGCCTATTGT+TGG - chr3_3:18836375-18836394 Msa0445090:CDS 30.0%
!!! GTGTTTTTAGATTTGCTAGA+GGG - chr3_3:18836406-18836425 Msa0445090:CDS 30.0%
ACTCAACAACAAAATGTTCA+GGG + chr3_3:18836467-18836486 None:intergenic 30.0%
TACTCAACAACAAAATGTTC+AGG + chr3_3:18836468-18836487 None:intergenic 30.0%
ATTTGTGGAAATGAGTGTGA+GGG + chr3_3:18835995-18836014 None:intergenic 35.0%
TTGTGAGAAAACTCCATTTG+TGG + chr3_3:18836010-18836029 None:intergenic 35.0%
! TTCTGAGGGTAATATGATGT+TGG + chr3_3:18836037-18836056 None:intergenic 35.0%
! CAATGATTTGTACTATGGTG+GGG + chr3_3:18836125-18836144 None:intergenic 35.0%
! GTCAATGATTTGTACTATGG+TGG + chr3_3:18836127-18836146 None:intergenic 35.0%
CTTTCTTCACTTCAAGATCT+TGG - chr3_3:18836261-18836280 Msa0445090:CDS 35.0%
!! GTTTTTAAGGAAGGGGAATA+TGG - chr3_3:18836306-18836325 Msa0445090:CDS 35.0%
! TGGAAGTAGTCTTAGTATGT+TGG - chr3_3:18836329-18836348 Msa0445090:CDS 35.0%
! GGAAGTAGTCTTAGTATGTT+GGG - chr3_3:18836330-18836349 Msa0445090:CDS 35.0%
!!! GGTGTTTTTAGATTTGCTAG+AGG - chr3_3:18836405-18836424 Msa0445090:CDS 35.0%
AAAATGTTCAGGGGTAGAAA+TGG + chr3_3:18836457-18836476 None:intergenic 35.0%
CTCAACAACAAAATGTTCAG+GGG + chr3_3:18836466-18836485 None:intergenic 35.0%
CATTTGTGGAAATGAGTGTG+AGG + chr3_3:18835996-18836015 None:intergenic 40.0%
CTCACACTCATTTCCACAAA+TGG - chr3_3:18835994-18836013 Msa0445090:CDS 40.0%
! TGTGTTAGTTTCTCTGTTCG+TGG + chr3_3:18836063-18836082 None:intergenic 40.0%
ATGGATGATGCAATGACTGA+AGG - chr3_3:18836189-18836208 Msa0445090:CDS 40.0%
TGGATGATGCAATGACTGAA+GGG - chr3_3:18836190-18836209 Msa0445090:CDS 40.0%
AATCACATTGGAAGAGCTCA+AGG - chr3_3:18836228-18836247 Msa0445090:CDS 40.0%
ATCACATTGGAAGAGCTCAA+GGG - chr3_3:18836229-18836248 Msa0445090:CDS 40.0%
TTTAAGGAAGGGGAATATGG+TGG - chr3_3:18836309-18836328 Msa0445090:CDS 40.0%
! GTAGTCTTAGTATGTTGGGA+AGG - chr3_3:18836334-18836353 Msa0445090:CDS 40.0%
AGAGAAATGCCTATTGTTGG+TGG - chr3_3:18836378-18836397 Msa0445090:CDS 40.0%
AAATGAGTGTGAGGGAGAAG+AGG + chr3_3:18835987-18836006 None:intergenic 45.0%
TCTGTTCGTGGTTGTTCTGA+GGG + chr3_3:18836051-18836070 None:intergenic 45.0%
! ATGCCTATTGTTGGTGGAAC+TGG - chr3_3:18836384-18836403 Msa0445090:CDS 45.0%
ACACCAGTTCCACCAACAAT+AGG + chr3_3:18836390-18836409 None:intergenic 45.0%
CTCTGTTCGTGGTTGTTCTG+AGG + chr3_3:18836052-18836071 None:intergenic 50.0%
GGAAGAGCTCAAGGGTTGTT+TGG - chr3_3:18836237-18836256 Msa0445090:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 18835958 18836512 18835958 ID=Msa0445090;Name=Msa0445090
chr3_3 mRNA 18835958 18836512 18835958 ID=Msa0445090-mRNA-1;Parent=Msa0445090;Name=Msa0445090-mRNA-1;_AED=0.41;_eAED=0.42;_QI=0|-1|0|1|-1|1|1|0|184
chr3_3 exon 18835958 18836512 18835958 ID=Msa0445090-mRNA-1:exon:4013;Parent=Msa0445090-mRNA-1
chr3_3 CDS 18835958 18836512 18835958 ID=Msa0445090-mRNA-1:cds;Parent=Msa0445090-mRNA-1
Gene Sequence

>Msa0445090

ATGACACTTTCACATAGTTTCTTTTTCCTCTTCTCCCTCACACTCATTTCCACAAATGGAGTTTTCTCACAACAATCCAACATCATATTACCCTCAGAACAACCACGAACAGAGAAACTAACACATATCCATTTCTACTACCATGACATTAGAGACAACAAAAGCCCCACCATAGTACAAATCATTGACACACCAATAAATGTACCAAATGGATTTGGTTCAACTTTTATGATGGATGATGCAATGACTGAAGGGCCAGAGTTAAGTTCAAATCACATTGGAAGAGCTCAAGGGTTGTTTGGTCTTTCTTCACTTCAAGATCTTGGAATGTTTATGTTGACAAATTTTGTTTTTAAGGAAGGGGAATATGGTGGAAGTAGTCTTAGTATGTTGGGAAGGAATCCTATTTCTGAACAAAATAGAGAAATGCCTATTGTTGGTGGAACTGGTGTTTTTAGATTTGCTAGAGGGTATGCTATTGCAAATAGTGTTGATTCCATTTCTACCCCTGAACATTTTGTTGTTGAGTATAATATTACTGTTTCTCTTCCCTAA
Protein sequence

>Msa0445090

MTLSHSFFFLFSLTLISTNGVFSQQSNIILPSEQPRTEKLTHIHFYYHDIRDNKSPTIVQIIDTPINVPNGFGSTFMMDDAMTEGPELSSNHIGRAQGLFGLSSLQDLGMFMLTNFVFKEGEYGGSSLSMLGRNPISEQNREMPIVGGTGVFRFARGYAIANSVDSISTPEHFVVEYNITVSLP*