AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0179220

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0179220 MtrunA17_Chr1g0212471 86.170 188 25 1 1 187 1 188 1.90e-119 337
Msa0179220 MtrunA17_Chr4g0022641 62.441 213 71 4 1 205 1 212 7.59e-89 266
Msa0179220 MtrunA17_Chr4g0059631 54.709 223 82 5 1 205 1 222 9.35e-76 228
Msa0179220 MtrunA17_Chr2g0303981 45.596 193 93 4 3 193 5 187 4.94e-54 171
Msa0179220 MtrunA17_Chr6g0457851 37.975 158 96 1 1 156 11 168 2.54e-37 132
Msa0179220 MtrunA17_Chr1g0212151 39.130 161 90 2 1 156 1 158 1.38e-35 128
Msa0179220 MtrunA17_Chr6g0449851 36.842 171 106 2 1 169 1 171 9.43e-35 125
Msa0179220 MtrunA17_Chr6g0449861 33.520 179 117 2 1 177 9 187 8.70e-33 120
Msa0179220 MtrunA17_Chr3g0107381 27.273 176 112 5 1 166 1 170 7.94e-13 65.1
Msa0179220 MtrunA17_Chr3g0107461 29.268 164 103 4 1 155 1 160 1.36e-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
Msa0179220 AT5G55690.1 34.899 149 81 4 1 143 1 139 2.58e-16 75.9
Msa0179220 AT5G55690.2 34.899 149 81 4 1 143 1 139 2.58e-16 75.9
Msa0179220 AT1G22590.2 31.056 161 98 6 1 154 1 155 9.13e-12 61.2
Msa0179220 AT5G58890.1 25.561 223 133 9 6 209 6 214 1.27e-11 62.8

Find 38 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTTCCATGTTAACCAAATT+TGG 0.129467 1_4:+66640089 None:intergenic
TCCAACCTGGCATCCAAATT+TGG 0.186789 1_4:-66640102 Msa0179220:CDS
CGGTCTTCTGGCCATGTTAT+TGG 0.230397 1_4:+66640278 None:intergenic
TTTACCATTGTACGGTCTTC+TGG 0.269305 1_4:+66640266 None:intergenic
GTCGTTGACATCAAATATCT+TGG 0.367645 1_4:+66640199 None:intergenic
ACCGGACTTGACAGTGTATT+GGG 0.378449 1_4:+66640352 None:intergenic
CACCGGACTTGACAGTGTAT+TGG 0.384830 1_4:+66640351 None:intergenic
GTGATTACAAGCTTGAATCT+TGG 0.389216 1_4:+66640031 None:intergenic
ATGAGGCAAAACAGCATGAT+TGG 0.423445 1_4:+66639878 None:intergenic
TGTATGACACTGAGTGGGCT+TGG 0.425893 1_4:+66639957 None:intergenic
ATCATATGTTTAAATCAAGT+TGG 0.439931 1_4:+66639841 None:intergenic
TGATGTGTTGTTGCATTTGA+GGG 0.441139 1_4:+66639928 None:intergenic
GATGATATCTTTATGCACTT+TGG 0.458740 1_4:+66640136 None:intergenic
GTTAACCAAATTTGGATGCC+AGG 0.463541 1_4:+66640097 None:intergenic
ACCAAATTTGGATGCCAGGT+TGG 0.474376 1_4:+66640101 None:intergenic
TTGATGTGTTGTTGCATTTG+AGG 0.494636 1_4:+66639927 None:intergenic
TCCCAATACACTGTCAAGTC+CGG 0.494797 1_4:-66640353 Msa0179220:CDS
ACTTTCAAGCAAAGAAAAGC+TGG 0.495334 1_4:-66640392 Msa0179220:CDS
TGGTTTGTTGATGAATTATG+AGG 0.510382 1_4:+66639861 None:intergenic
GCATCCAAATTTGGTTAACA+TGG 0.520385 1_4:-66640093 Msa0179220:CDS
CTTTGAAATTAAGAAAGCTA+AGG 0.524267 1_4:-66640174 Msa0179220:CDS
TTTGTTTGTAGAATGGGTCG+TGG 0.527118 1_4:-66640461 None:intergenic
TCGTTGACATCAAATATCTT+GGG 0.530959 1_4:+66640200 None:intergenic
GCATGGAGTTTACCATTGTA+CGG 0.551323 1_4:+66640258 None:intergenic
ATGCTCATACTCTTGAAGCA+TGG 0.571710 1_4:+66640241 None:intergenic
CAATCATGTTAGTGAGATGG+TGG 0.574738 1_4:-66639907 Msa0179220:CDS
ATTGTGTATGATGATGATGA+TGG 0.576451 1_4:-66640314 Msa0179220:CDS
CATCAATCATGTTAGTGAGA+TGG 0.579763 1_4:-66639910 Msa0179220:CDS
CATGTTGAAAAGTGAGATGG+TGG 0.605793 1_4:-66640000 Msa0179220:CDS
CAACATGTTGAAAAGTGAGA+TGG 0.617799 1_4:-66640003 Msa0179220:CDS
TGATGATGATGGCAATAATG+TGG 0.630960 1_4:-66640303 Msa0179220:CDS
CAGCACTTAAGTCTCTGAGC+TGG 0.631241 1_4:+66640063 None:intergenic
TCAATATCAAATATCCAACC+TGG 0.635175 1_4:-66640115 Msa0179220:CDS
ATAATGTGGGACCAATAACA+TGG 0.642393 1_4:-66640289 Msa0179220:CDS
GATGATGATGGCAATAATGT+GGG 0.668464 1_4:-66640302 Msa0179220:CDS
TGCTATGTATGACACTGAGT+GGG 0.671421 1_4:+66639952 None:intergenic
ATGCTATGTATGACACTGAG+TGG 0.718974 1_4:+66639951 None:intergenic
ATGGCCAGAAGACCGTACAA+TGG 0.724325 1_4:-66640270 Msa0179220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTTTGAAATTAAGAAAGCTA+AGG - chr1_4:66640117-66640136 Msa0179220:CDS 25.0%
! ATTGTGTATGATGATGATGA+TGG - chr1_4:66639977-66639996 Msa0179220:CDS 30.0%
TCGTTGACATCAAATATCTT+GGG + chr1_4:66640094-66640113 None:intergenic 30.0%
GATGATATCTTTATGCACTT+TGG + chr1_4:66640158-66640177 None:intergenic 30.0%
TCAATATCAAATATCCAACC+TGG - chr1_4:66640176-66640195 Msa0179220:CDS 30.0%
!! TGGTTTGTTGATGAATTATG+AGG + chr1_4:66640433-66640452 None:intergenic 30.0%
ACTTTCAAGCAAAGAAAAGC+TGG - chr1_4:66639899-66639918 Msa0179220:CDS 35.0%
! AATCAAACAAGCTTTTGCAC+CGG + chr1_4:66639960-66639979 None:intergenic 35.0%
!! TGATGATGATGGCAATAATG+TGG - chr1_4:66639988-66640007 Msa0179220:CDS 35.0%
!! GATGATGATGGCAATAATGT+GGG - chr1_4:66639989-66640008 Msa0179220:CDS 35.0%
ATAATGTGGGACCAATAACA+TGG - chr1_4:66640002-66640021 Msa0179220:CDS 35.0%
GTCGTTGACATCAAATATCT+TGG + chr1_4:66640095-66640114 None:intergenic 35.0%
GCATCCAAATTTGGTTAACA+TGG - chr1_4:66640198-66640217 Msa0179220:CDS 35.0%
GCTTCCATGTTAACCAAATT+TGG + chr1_4:66640205-66640224 None:intergenic 35.0%
GTGATTACAAGCTTGAATCT+TGG + chr1_4:66640263-66640282 None:intergenic 35.0%
CAACATGTTGAAAAGTGAGA+TGG - chr1_4:66640288-66640307 Msa0179220:CDS 35.0%
! TGATGTGTTGTTGCATTTGA+GGG + chr1_4:66640366-66640385 None:intergenic 35.0%
! TTGATGTGTTGTTGCATTTG+AGG + chr1_4:66640367-66640386 None:intergenic 35.0%
CATCAATCATGTTAGTGAGA+TGG - chr1_4:66640381-66640400 Msa0179220:CDS 35.0%
TTTACCATTGTACGGTCTTC+TGG + chr1_4:66640028-66640047 None:intergenic 40.0%
GCATGGAGTTTACCATTGTA+CGG + chr1_4:66640036-66640055 None:intergenic 40.0%
ATGCTCATACTCTTGAAGCA+TGG + chr1_4:66640053-66640072 None:intergenic 40.0%
GTTAACCAAATTTGGATGCC+AGG + chr1_4:66640197-66640216 None:intergenic 40.0%
CATGTTGAAAAGTGAGATGG+TGG - chr1_4:66640291-66640310 Msa0179220:CDS 40.0%
TGCTATGTATGACACTGAGT+GGG + chr1_4:66640342-66640361 None:intergenic 40.0%
ATGCTATGTATGACACTGAG+TGG + chr1_4:66640343-66640362 None:intergenic 40.0%
CAATCATGTTAGTGAGATGG+TGG - chr1_4:66640384-66640403 Msa0179220:CDS 40.0%
ATGAGGCAAAACAGCATGAT+TGG + chr1_4:66640416-66640435 None:intergenic 40.0%
TCCCAATACACTGTCAAGTC+CGG - chr1_4:66639938-66639957 Msa0179220:CDS 45.0%
ACCGGACTTGACAGTGTATT+GGG + chr1_4:66639942-66639961 None:intergenic 45.0%
TCCAACCTGGCATCCAAATT+TGG - chr1_4:66640189-66640208 Msa0179220:CDS 45.0%
ACCAAATTTGGATGCCAGGT+TGG + chr1_4:66640193-66640212 None:intergenic 45.0%
CACCGGACTTGACAGTGTAT+TGG + chr1_4:66639943-66639962 None:intergenic 50.0%
CGGTCTTCTGGCCATGTTAT+TGG + chr1_4:66640016-66640035 None:intergenic 50.0%
ATGGCCAGAAGACCGTACAA+TGG - chr1_4:66640021-66640040 Msa0179220:CDS 50.0%
CAGCACTTAAGTCTCTGAGC+TGG + chr1_4:66640231-66640250 None:intergenic 50.0%
! TGTATGACACTGAGTGGGCT+TGG + chr1_4:66640337-66640356 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 66639842 66640471 66639842 ID=Msa0179220;Name=Msa0179220
chr1_4 mRNA 66639842 66640471 66639842 ID=Msa0179220-mRNA-1;Parent=Msa0179220;Name=Msa0179220-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|209
chr1_4 exon 66639842 66640471 66639842 ID=Msa0179220-mRNA-1:exon:21896;Parent=Msa0179220-mRNA-1
chr1_4 CDS 66639842 66640471 66639842 ID=Msa0179220-mRNA-1:cds;Parent=Msa0179220-mRNA-1
Gene Sequence

>Msa0179220

ATGGGTCGTGGAAAAATAACTATGAAATACATCAAAAATGCGAAAGTACGCAAACAAACTTTCAAGCAAAGAAAAGCTGGACTAATGAAAAAAATTTCCCAATACACTGTCAAGTCCGGTGCAAAAGCTTGTTTGATTGTGTATGATGATGATGATGGCAATAATGTGGGACCAATAACATGGCCAGAAGACCGTACAATGGTAAACTCCATGCTTCAAGAGTATGAGCATCAAAAGATTGAGAATACACCCAAGATATTTGATGTCAACGACTACTTTGAAATTAAGAAAGCTAAGGTTAAAGCTGAAATTACCAAAGTGCATAAAGATATCATCAATATCAAATATCCAACCTGGCATCCAAATTTGGTTAACATGGAAGCGAGCCAGCTCAGAGACTTAAGTGCTGTTGTAGATGCCAAGATTCAAGCTTGTAATCACAAAATCAACATGTTGAAAAGTGAGATGGTGGAAGAGAATGTTGTTTTGAATCCAAGCCCACTCAGTGTCATACATAGCATCCCTCAAATGCAACAACACATCAATCATGTTAGTGAGATGGTGGATATGACCAATCATGCTGTTTTGCCTCATAATTCATCAACAAACCAACTTGATTTAAACATATGA
Protein sequence

>Msa0179220

MGRGKITMKYIKNAKVRKQTFKQRKAGLMKKISQYTVKSGAKACLIVYDDDDGNNVGPITWPEDRTMVNSMLQEYEHQKIENTPKIFDVNDYFEIKKAKVKAEITKVHKDIINIKYPTWHPNLVNMEASQLRDLSAVVDAKIQACNHKINMLKSEMVEENVVLNPSPLSVIHSIPQMQQHINHVSEMVDMTNHAVLPHNSSTNQLDLNI*