AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584030


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584030 MtrunA17_Chr8g0392251 99.286 140 1 0 1 140 1 140 2.40e-100 283
Msa0584030 MtrunA17_Chr8g0392191 99.286 140 1 0 1 140 1 140 2.40e-100 283
Msa0584030 MtrunA17_Chr5g0432551 98.571 140 2 0 1 140 1 140 6.11e-100 282
Msa0584030 MtrunA17_Chr4g0044571 94.286 140 8 0 1 140 4 143 7.79e-96 272
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584030 AT2G09990.1 89.209 139 15 0 2 140 8 146 1.92e-91 261
Msa0584030 AT5G18380.1 88.489 139 16 0 2 140 8 146 3.25e-91 261
Msa0584030 AT3G04230.1 83.453 139 23 0 2 140 8 146 6.19e-85 245
Msa0584030 AT5G18380.2 86.400 125 17 0 2 126 8 132 1.67e-78 229
Msa0584030 AT5G18380.3 86.111 108 15 0 2 109 8 115 5.55e-67 199

Find 38 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATCTAACGATAAGATTTC+TGG 0.210396 4_2:+2942025 None:intergenic
ACAGAGTAAGAAAGAGATTA+AGG 0.239341 4_2:-2942142 Msa0584030:CDS
CCGCAACGGCGTTCTTCTTC+CGG 0.308388 4_2:+2942406 None:intergenic
GCCTGAGATTCTTCGTTTCA+AGG 0.344740 4_2:-2942319 Msa0584030:CDS
CGCTGTGAGCCTAAGAAGTT+TGG 0.359075 4_2:-2942072 Msa0584030:CDS
TCAGAGTATTGCTAAGGCTT+TGG 0.386737 4_2:-2942193 Msa0584030:CDS
CCACGACCACCAAACTTCTT+AGG 0.436009 4_2:+2942063 None:intergenic
TACGAACCAATCCTCCTTCT+CGG 0.444217 4_2:-2942294 Msa0584030:CDS
GTTTCGCCGGCGTTGATATG+AGG 0.478501 4_2:-2942263 Msa0584030:CDS
GCCTTGAAACGAAGAATCTC+AGG 0.478888 4_2:+2942318 None:intergenic
CTCGGAAGACACCGTTTCGC+CGG 0.484088 4_2:-2942276 Msa0584030:CDS
ATGGAACAAGTGCAATGCTT+TGG 0.487256 4_2:-2942429 Msa0584030:CDS
CAACGGCTGTCCAATCGAAC+TGG 0.488470 4_2:-2942346 Msa0584030:CDS
GTGGTCGTGGTGCTCGTGCT+AGG 0.502073 4_2:-2942050 Msa0584030:CDS
CCTAAGAAGTTTGGTGGTCG+TGG 0.511400 4_2:-2942063 Msa0584030:CDS
AGGATCCGTGTGAAGGGAGG+AGG 0.521481 4_2:-2942243 Msa0584030:CDS
TCATATCAACGCCGGCGAAA+CGG 0.524265 4_2:+2942265 None:intergenic
TCAGGCTCAACCAGTTCGAT+TGG 0.524396 4_2:+2942336 None:intergenic
AACAAGTGCAATGCTTTGGC+CGG 0.546867 4_2:-2942425 Msa0584030:CDS
AACGGTGTCTTCCGAGAAGG+AGG 0.549270 4_2:+2942283 None:intergenic
TGTGAGCCTAAGAAGTTTGG+TGG 0.558448 4_2:-2942069 Msa0584030:CDS
GACCGCGACCTCTCTTGCAG+TGG 0.558828 4_2:+2942379 None:intergenic
ACCCACTGCAAGAGAGGTCG+CGG 0.562945 4_2:-2942381 Msa0584030:CDS
CATTCGTCAGAGTATTGCTA+AGG 0.576627 4_2:-2942199 Msa0584030:CDS
TGATATGAGGATCCGTGTGA+AGG 0.579448 4_2:-2942250 Msa0584030:CDS
GCGGTAACCCACTGCAAGAG+AGG 0.580471 4_2:-2942387 Msa0584030:CDS
TTCTTAGGCTCACAGCGTCT+AGG 0.590494 4_2:+2942078 None:intergenic
TGTCTTCCGAGAAGGAGGAT+TGG 0.592227 4_2:+2942288 None:intergenic
GATATGAGGATCCGTGTGAA+GGG 0.594162 4_2:-2942249 Msa0584030:CDS
CTTGCAGTGGGTTACCGCAA+CGG 0.599991 4_2:+2942392 None:intergenic
ACCGCGACCTCTCTTGCAGT+GGG 0.603590 4_2:+2942380 None:intergenic
CGCGGTCTGATCAAGATCAA+CGG 0.609302 4_2:-2942363 Msa0584030:CDS
CTTAGCAATACTCTGACGAA+TGG 0.614188 4_2:+2942200 None:intergenic
ATGAGGATCCGTGTGAAGGG+AGG 0.615322 4_2:-2942246 Msa0584030:CDS
CGAAACGGTGTCTTCCGAGA+AGG 0.622095 4_2:+2942280 None:intergenic
TGTGACCTCCTCCCTTCACA+CGG 0.629480 4_2:+2942238 None:intergenic
CCGGAAGAAGAACGCCGTTG+CGG 0.651449 4_2:-2942406 Msa0584030:CDS
ACGGATCCTCATATCAACGC+CGG 0.685813 4_2:+2942257 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ACAGAGTAAGAAAGAGATTA+AGG - chr4_2:2942316-2942335 Msa0584030:CDS 30.0%
ATGGAACAAGTGCAATGCTT+TGG - chr4_2:2942029-2942048 Msa0584030:CDS 40.0%
CTTAGCAATACTCTGACGAA+TGG + chr4_2:2942261-2942280 None:intergenic 40.0%
!! CATTCGTCAGAGTATTGCTA+AGG - chr4_2:2942259-2942278 Msa0584030:CDS 40.0%
!! TCAGAGTATTGCTAAGGCTT+TGG - chr4_2:2942265-2942284 Msa0584030:CDS 40.0%
AACAAGTGCAATGCTTTGGC+CGG - chr4_2:2942033-2942052 Msa0584030:CDS 45.0%
GCCTGAGATTCTTCGTTTCA+AGG - chr4_2:2942139-2942158 Msa0584030:CDS 45.0%
GCCTTGAAACGAAGAATCTC+AGG + chr4_2:2942143-2942162 None:intergenic 45.0%
TACGAACCAATCCTCCTTCT+CGG - chr4_2:2942164-2942183 Msa0584030:CDS 45.0%
TGATATGAGGATCCGTGTGA+AGG - chr4_2:2942208-2942227 Msa0584030:CDS 45.0%
GATATGAGGATCCGTGTGAA+GGG - chr4_2:2942209-2942228 Msa0584030:CDS 45.0%
TGTGAGCCTAAGAAGTTTGG+TGG - chr4_2:2942389-2942408 Msa0584030:CDS 45.0%
CGCGGTCTGATCAAGATCAA+CGG - chr4_2:2942095-2942114 Msa0584030:CDS 50.0%
TCAGGCTCAACCAGTTCGAT+TGG + chr4_2:2942125-2942144 None:intergenic 50.0%
TGTCTTCCGAGAAGGAGGAT+TGG + chr4_2:2942173-2942192 None:intergenic 50.0%
TCATATCAACGCCGGCGAAA+CGG + chr4_2:2942196-2942215 None:intergenic 50.0%
ACGGATCCTCATATCAACGC+CGG + chr4_2:2942204-2942223 None:intergenic 50.0%
TTCTTAGGCTCACAGCGTCT+AGG + chr4_2:2942383-2942402 None:intergenic 50.0%
CGCTGTGAGCCTAAGAAGTT+TGG - chr4_2:2942386-2942405 Msa0584030:CDS 50.0%
CCACGACCACCAAACTTCTT+AGG + chr4_2:2942398-2942417 None:intergenic 50.0%
! CCTAAGAAGTTTGGTGGTCG+TGG - chr4_2:2942395-2942414 Msa0584030:CDS 50.0%
!! CTTGCAGTGGGTTACCGCAA+CGG + chr4_2:2942069-2942088 None:intergenic 55.0%
CAACGGCTGTCCAATCGAAC+TGG - chr4_2:2942112-2942131 Msa0584030:CDS 55.0%
AACGGTGTCTTCCGAGAAGG+AGG + chr4_2:2942178-2942197 None:intergenic 55.0%
CGAAACGGTGTCTTCCGAGA+AGG + chr4_2:2942181-2942200 None:intergenic 55.0%
!! GTTTCGCCGGCGTTGATATG+AGG - chr4_2:2942195-2942214 Msa0584030:CDS 55.0%
ATGAGGATCCGTGTGAAGGG+AGG - chr4_2:2942212-2942231 Msa0584030:CDS 55.0%
TGTGACCTCCTCCCTTCACA+CGG + chr4_2:2942223-2942242 None:intergenic 55.0%
CCGCAACGGCGTTCTTCTTC+CGG + chr4_2:2942055-2942074 None:intergenic 60.0%
CCGGAAGAAGAACGCCGTTG+CGG - chr4_2:2942052-2942071 Msa0584030:CDS 60.0%
GCGGTAACCCACTGCAAGAG+AGG - chr4_2:2942071-2942090 Msa0584030:CDS 60.0%
ACCCACTGCAAGAGAGGTCG+CGG - chr4_2:2942077-2942096 Msa0584030:CDS 60.0%
ACCGCGACCTCTCTTGCAGT+GGG + chr4_2:2942081-2942100 None:intergenic 60.0%
CTCGGAAGACACCGTTTCGC+CGG - chr4_2:2942182-2942201 Msa0584030:CDS 60.0%
AGGATCCGTGTGAAGGGAGG+AGG - chr4_2:2942215-2942234 Msa0584030:CDS 60.0%
GACCGCGACCTCTCTTGCAG+TGG + chr4_2:2942082-2942101 None:intergenic 65.0%
GTGGTCGTGGTGCTCGTGCT+AGG - chr4_2:2942408-2942427 Msa0584030:CDS 65.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 2942029 2942451 2942029 ID=Msa0584030;Name=Msa0584030
chr4_2 mRNA 2942029 2942451 2942029 ID=Msa0584030-mRNA-1;Parent=Msa0584030;Name=Msa0584030-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|140
chr4_2 exon 2942029 2942451 2942029 ID=Msa0584030-mRNA-1:exon:846;Parent=Msa0584030-mRNA-1
chr4_2 CDS 2942029 2942451 2942029 ID=Msa0584030-mRNA-1:cds;Parent=Msa0584030-mRNA-1
Gene Sequence

>Msa0584030

ATGGAACAAGTGCAATGCTTTGGCCGGAAGAAGAACGCCGTTGCGGTAACCCACTGCAAGAGAGGTCGCGGTCTGATCAAGATCAACGGCTGTCCAATCGAACTGGTTGAGCCTGAGATTCTTCGTTTCAAGGCATACGAACCAATCCTCCTTCTCGGAAGACACCGTTTCGCCGGCGTTGATATGAGGATCCGTGTGAAGGGAGGAGGTCACACTTCTCAGATCTACGCCATTCGTCAGAGTATTGCTAAGGCTTTGGTTGCTTACTATCAGAAATTTGTTGATGAACAGAGTAAGAAAGAGATTAAGGATATTCTTGTTCGTTATGATCGTACTCTTCTTGTTGCTGATCCTAGACGCTGTGAGCCTAAGAAGTTTGGTGGTCGTGGTGCTCGTGCTAGGTTCCAGAAATCTTATCGTTAG

Protein sequence

>Msa0584030

MEQVQCFGRKKNAVAVTHCKRGRGLIKINGCPIELVEPEILRFKAYEPILLLGRHRFAGVDMRIRVKGGGHTSQIYAIRQSIAKALVAYYQKFVDEQSKKEIKDILVRYDRTLLVADPRRCEPKKFGGRGARARFQKSYR*