AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0591370


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0591370 MtrunA17_CPg0492991 94.915 236 6 1 1 230 1 236 1.75e-168 463
Msa0591370 MtrunA17_Chr4g0015601 94.915 236 6 1 1 230 1 236 2.00e-168 463
Msa0591370 MtrunA17_Chr4g0016691 98.496 133 2 0 98 230 1 133 6.92e-95 273
Msa0591370 MtrunA17_Chr7g0275161 90.722 97 9 0 134 230 1 97 4.22e-60 184
Msa0591370 MtrunA17_Chr4g0016681 96.000 75 3 0 1 75 1 75 8.38e-50 157
Msa0591370 MtrunA17_Chr7g0275171 77.778 99 6 2 1 93 1 89 1.20e-48 155
Msa0591370 MtrunA17_Chr1g0178511 97.143 35 1 0 98 132 1 35 2.27e-16 74.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0591370 ATCG00160.1 87.234 235 24 1 1 229 1 235 9.78e-152 421

Find 37 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCTCATTTGGAAACATATC+TGG 0.181531 4_2:+15624254 Msa0591370:CDS
TTACGCTTTGCCGATATAAA+AGG 0.251568 4_2:-15623917 None:intergenic
ATGGAAGCTGGAGTTCATTT+TGG 0.255790 4_2:+15623860 Msa0591370:CDS
CAAGAGACAATTATCTCATT+TGG 0.294663 4_2:+15624242 Msa0591370:CDS
ATCAACGATTATTACAATAT+CGG 0.341941 4_2:-15624304 None:intergenic
TTTATCAGAAGCTTGTGATT+TGG 0.358806 4_2:+15623979 Msa0591370:CDS
CTAATTTGTTAAGAATTAAT+CGG 0.359442 4_2:-15624461 None:intergenic
ATCGAAATATCTGCTAGATC+TGG 0.363586 4_2:-15624408 None:intergenic
CTTCGAGAATGTATCACTTT+GGG 0.388824 4_2:+15624348 Msa0591370:CDS
GGAAAACAATTCTTAATTGT+TGG 0.390734 4_2:+15624022 Msa0591370:CDS
AAACGAGACTTCGTAAGTTC+AGG 0.412190 4_2:+15624154 Msa0591370:CDS
TGCAGCCCGTGTTACTGAAT+CGG 0.431042 4_2:-15624061 None:intergenic
TGATCAGCAAGAAGAATATA+CGG 0.437056 4_2:+15624323 Msa0591370:CDS
TCGGAGGTATGTTAACGAAT+TGG 0.448395 4_2:+15624121 Msa0591370:CDS
TTGGCCATGATACTCGGAAA+TGG 0.459897 4_2:+15623879 Msa0591370:CDS
TCTTCGAGAATGTATCACTT+TGG 0.477646 4_2:+15624347 Msa0591370:CDS
AACGAGACTTCGTAAGTTCA+GGG 0.478021 4_2:+15624155 Msa0591370:CDS
TCAACGATTATTACAATATC+GGG 0.480431 4_2:-15624303 None:intergenic
TTGAGAACGGAGCAAAAGAC+AGG 0.482432 4_2:+15624180 Msa0591370:CDS
GATTCCATTTCCGAGTATCA+TGG 0.488914 4_2:-15623883 None:intergenic
TTTGAAGAGATGATGGAAGC+TGG 0.489132 4_2:+15623848 Msa0591370:CDS
GTATCGATTAAACAAATCGT+TGG 0.491426 4_2:-15624375 None:intergenic
GCTATAGCATCATCATTAGC+TGG 0.518853 4_2:-15624432 None:intergenic
TCGAAATATCTGCTAGATCT+GGG 0.525094 4_2:-15624407 None:intergenic
TTTATATCGGCAAAGCGTAA+AGG 0.529937 4_2:+15623920 Msa0591370:CDS
GATATAAAAGGTGCCATTCG+AGG 0.542260 4_2:-15623905 None:intergenic
TCTCATTTGGAAACATATCT+GGG 0.550552 4_2:+15624255 Msa0591370:CDS
GGGTGGCATAAAATATATGA+CGG 0.585418 4_2:+15624275 Msa0591370:CDS
TAAGTTCAGGGACTTGAGAA+CGG 0.589134 4_2:+15624167 Msa0591370:CDS
GGTGGCATAAAATATATGAC+GGG 0.610359 4_2:+15624276 Msa0591370:CDS
AGCAGCCGATTCAGTAACAC+GGG 0.610911 4_2:+15624056 Msa0591370:intron
TCGGAAATGGAATCCTCGAA+TGG 0.635386 4_2:+15623892 Msa0591370:CDS
AAGCAGCCGATTCAGTAACA+CGG 0.653513 4_2:+15624055 Msa0591370:intron
TGAGAACGGAGCAAAAGACA+GGG 0.670658 4_2:+15624181 Msa0591370:CDS
CATTTGGAAACATATCTGGG+TGG 0.732935 4_2:+15624258 Msa0591370:CDS
GTGGCATAAAATATATGACG+GGG 0.737363 4_2:+15624277 Msa0591370:CDS
TAATTGTCTCTTGAACATAG+CGG 0.783646 4_2:-15624232 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTCATTATGTTAATAAAAAA+TGG + chr4_2:15624097-15624116 Msa0591370:CDS 15.0%
!!! CTAATTTGTTAAGAATTAAT+CGG - chr4_2:15624464-15624483 None:intergenic 15.0%
!! TATGTTAATAAAAAATGGCT+CGG + chr4_2:15624102-15624121 Msa0591370:CDS 20.0%
!! ATCAACGATTATTACAATAT+CGG - chr4_2:15624307-15624326 None:intergenic 20.0%
! GGAAAACAATTCTTAATTGT+TGG + chr4_2:15624022-15624041 Msa0591370:CDS 25.0%
! TCAACGATTATTACAATATC+GGG - chr4_2:15624306-15624325 None:intergenic 25.0%
!!! ATTAGTTTTTGCAATTTGTG+AGG + chr4_2:15624479-15624498 Msa0591370:CDS 25.0%
!!! TTAGTTTTTGCAATTTGTGA+GGG + chr4_2:15624480-15624499 Msa0591370:CDS 25.0%
!! CATAACTTTTGAAGAGATGA+TGG + chr4_2:15623841-15623860 Msa0591370:CDS 30.0%
TTTATCAGAAGCTTGTGATT+TGG + chr4_2:15623979-15623998 Msa0591370:CDS 30.0%
TAATTGTCTCTTGAACATAG+CGG - chr4_2:15624235-15624254 None:intergenic 30.0%
CAAGAGACAATTATCTCATT+TGG + chr4_2:15624242-15624261 Msa0591370:CDS 30.0%
ATCTCATTTGGAAACATATC+TGG + chr4_2:15624254-15624273 Msa0591370:CDS 30.0%
TCTCATTTGGAAACATATCT+GGG + chr4_2:15624255-15624274 Msa0591370:CDS 30.0%
TGATCAGCAAGAAGAATATA+CGG + chr4_2:15624323-15624342 Msa0591370:CDS 30.0%
!! GTATCGATTAAACAAATCGT+TGG - chr4_2:15624378-15624397 None:intergenic 30.0%
!! TTCATTTTGGCCATGATACT+CGG + chr4_2:15623873-15623892 Msa0591370:CDS 35.0%
! TCGAATGGCACCTTTTATAT+CGG + chr4_2:15623907-15623926 Msa0591370:CDS 35.0%
TTACGCTTTGCCGATATAAA+AGG - chr4_2:15623920-15623939 None:intergenic 35.0%
TTTATATCGGCAAAGCGTAA+AGG + chr4_2:15623920-15623939 Msa0591370:CDS 35.0%
! GTTAATAAAAAATGGCTCGG+AGG + chr4_2:15624105-15624124 Msa0591370:CDS 35.0%
GGGTGGCATAAAATATATGA+CGG + chr4_2:15624275-15624294 Msa0591370:CDS 35.0%
GGTGGCATAAAATATATGAC+GGG + chr4_2:15624276-15624295 Msa0591370:CDS 35.0%
GTGGCATAAAATATATGACG+GGG + chr4_2:15624277-15624296 Msa0591370:CDS 35.0%
TCTTCGAGAATGTATCACTT+TGG + chr4_2:15624347-15624366 Msa0591370:CDS 35.0%
CTTCGAGAATGTATCACTTT+GGG + chr4_2:15624348-15624367 Msa0591370:CDS 35.0%
TCGAAATATCTGCTAGATCT+GGG - chr4_2:15624410-15624429 None:intergenic 35.0%
ATCGAAATATCTGCTAGATC+TGG - chr4_2:15624411-15624430 None:intergenic 35.0%
!! TTTGAAGAGATGATGGAAGC+TGG + chr4_2:15623848-15623867 Msa0591370:CDS 40.0%
! ATGGAAGCTGGAGTTCATTT+TGG + chr4_2:15623860-15623879 Msa0591370:CDS 40.0%
GATTCCATTTCCGAGTATCA+TGG - chr4_2:15623886-15623905 None:intergenic 40.0%
!! GATATAAAAGGTGCCATTCG+AGG - chr4_2:15623908-15623927 None:intergenic 40.0%
! GTTTTTGATGCAGCAAGCAT+GGG + chr4_2:15624001-15624020 Msa0591370:CDS 40.0%
! TCGGAGGTATGTTAACGAAT+TGG + chr4_2:15624121-15624140 Msa0591370:CDS 40.0%
AAACGAGACTTCGTAAGTTC+AGG + chr4_2:15624154-15624173 Msa0591370:CDS 40.0%
AACGAGACTTCGTAAGTTCA+GGG + chr4_2:15624155-15624174 Msa0591370:CDS 40.0%
TAAGTTCAGGGACTTGAGAA+CGG + chr4_2:15624167-15624186 Msa0591370:CDS 40.0%
! AACATAGCGGCATCTCTTTT+TGG - chr4_2:15624222-15624241 None:intergenic 40.0%
CATTTGGAAACATATCTGGG+TGG + chr4_2:15624258-15624277 Msa0591370:CDS 40.0%
GCTATAGCATCATCATTAGC+TGG - chr4_2:15624435-15624454 None:intergenic 40.0%
TTGGCCATGATACTCGGAAA+TGG + chr4_2:15623879-15623898 Msa0591370:CDS 45.0%
TCGGAAATGGAATCCTCGAA+TGG + chr4_2:15623892-15623911 Msa0591370:CDS 45.0%
! GGTTTTTGATGCAGCAAGCA+TGG + chr4_2:15624000-15624019 Msa0591370:CDS 45.0%
! AAGCAGCCGATTCAGTAACA+CGG + chr4_2:15624055-15624074 Msa0591370:intron 45.0%
TTGAGAACGGAGCAAAAGAC+AGG + chr4_2:15624180-15624199 Msa0591370:CDS 45.0%
TGAGAACGGAGCAAAAGACA+GGG + chr4_2:15624181-15624200 Msa0591370:CDS 45.0%
! AGCAGCCGATTCAGTAACAC+GGG + chr4_2:15624056-15624075 Msa0591370:intron 50.0%
! TGCAGCCCGTGTTACTGAAT+CGG - chr4_2:15624064-15624083 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 15623821 15624530 15623821 ID=Msa0591370;Name=Msa0591370
chr4_2 mRNA 15623821 15624530 15623821 ID=Msa0591370-mRNA-1;Parent=Msa0591370;Name=Msa0591370-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|0|0|1|0|0.5|2|0|230
chr4_2 exon 15623821 15624043 15623821 ID=Msa0591370-mRNA-1:exon:4480;Parent=Msa0591370-mRNA-1
chr4_2 exon 15624061 15624530 15624061 ID=Msa0591370-mRNA-1:exon:4481;Parent=Msa0591370-mRNA-1
chr4_2 CDS 15623821 15624043 15623821 ID=Msa0591370-mRNA-1:cds;Parent=Msa0591370-mRNA-1
chr4_2 CDS 15624061 15624530 15624061 ID=Msa0591370-mRNA-1:cds;Parent=Msa0591370-mRNA-1
Gene Sequence

>Msa0591370

ATGACAAAAAGATATTGGAACATAACTTTTGAAGAGATGATGGAAGCTGGAGTTCATTTTGGCCATGATACTCGGAAATGGAATCCTCGAATGGCACCTTTTATATCGGCAAAGCGTAAAGGTATTCATATTACAAATCTTACTCGAACTGCTCGTTTTTTATCAGAAGCTTGTGATTTGGTTTTTGATGCAGCAAGCATGGGAAAACAATTCTTAATTGTTGCCGATTCAGTAACACGGGCTGCAATAAGAGCTCGATGTCATTATGTTAATAAAAAATGGCTCGGAGGTATGTTAACGAATTGGTATACTACAGAAACGAGACTTCGTAAGTTCAGGGACTTGAGAACGGAGCAAAAGACAGGGAAACTGAACTCTCTTCCAAAAAGAGATGCCGCTATGTTCAAGAGACAATTATCTCATTTGGAAACATATCTGGGTGGCATAAAATATATGACGGGGTTACCCGATATTGTAATAATCGTTGATCAGCAAGAAGAATATACGGCTCTTCGAGAATGTATCACTTTGGGAATTCCAACGATTTGTTTAATCGATACAAATTGTGACCCAGATCTAGCAGATATTTCGATTCCAGCTAATGATGATGCTATAGCTTCAATCCGATTAATTCTTAACAAATTAGTTTTTGCAATTTGTGAGGGTCGTTCTAGCTATATACGAAATTTTTGA

Protein sequence

>Msa0591370

MTKRYWNITFEEMMEAGVHFGHDTRKWNPRMAPFISAKRKGIHITNLTRTARFLSEACDLVFDAASMGKQFLIVADSVTRAAIRARCHYVNKKWLGGMLTNWYTTETRLRKFRDLRTEQKTGKLNSLPKRDAAMFKRQLSHLETYLGGIKYMTGLPDIVIIVDQQEEYTALRECITLGIPTICLIDTNCDPDLADISIPANDDAIASIRLILNKLVFAICEGRSSYIRNF*