AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0150920


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0150920 MtrunA17_Chr1g0159211 74.537 216 4 2 1 165 8 223 3.81e-105 300
Msa0150920 MtrunA17_Chr1g0159221 70.698 215 13 1 1 165 9 223 1.06e-98 283
Msa0150920 MtrunA17_Chr3g0126121 51.852 216 53 1 1 165 7 222 1.08e-69 210
Msa0150920 MtrunA17_Chr1g0187451 23.404 188 90 2 28 165 19 202 8.54e-13 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0150920 AT1G21360.1 38.028 213 81 2 2 164 11 222 1.69e-42 141
Msa0150920 AT3G21260.3 38.991 218 78 2 2 164 15 232 1.33e-35 124
Msa0150920 AT1G21360.3 53.704 108 49 1 2 109 11 117 1.89e-33 117
Msa0150920 AT3G21260.2 34.014 147 47 1 68 164 2 148 8.89e-12 60.1

Find 24 sgRNAs with CRISPR-Local

Find 119 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCCTCTCTATATGTTATT+TGG 0.165815 1_4:-12664906 Msa0150920:CDS
TTTAGTTGAAATATTGAAAT+TGG 0.200840 1_4:-12663356 Msa0150920:CDS
CTAATAATTACAGATAAAAT+AGG 0.259826 1_4:-12664748 Msa0150920:intron
TAAGCAGAAAATGCAAATAT+TGG 0.279728 1_4:-12662727 Msa0150920:CDS
TATAGAGAGGAAAGGCTTAA+TGG 0.297643 1_4:+12664916 None:intergenic
GTTGTGATAGTTAAACCTTC+TGG 0.315301 1_4:-12664965 Msa0150920:CDS
ATAGAGAGGAAAGGCTTAAT+GGG 0.342416 1_4:+12664917 None:intergenic
TATTTGGTTCTACAAGTTCT+TGG 0.346372 1_4:-12664890 Msa0150920:intron
ACTAAATTTAGATTTGTTGT+TGG 0.392467 1_4:+12663373 None:intergenic
GGTGGCTCTAAGATTAGTTC+CGG 0.420560 1_4:-12662805 Msa0150920:CDS
TGTCTCAAAACAGCCATTGT+TGG 0.436087 1_4:+12664724 None:intergenic
TAATAATTACAGATAAAATA+GGG 0.451699 1_4:-12664747 Msa0150920:intron
AACAGAAGGCAATGCAAAGA+AGG 0.452284 1_4:-12663329 Msa0150920:CDS
TTTGCAGAGATTATATAACT+TGG 0.500380 1_4:-12662555 Msa0150920:intron
CAATGGATATCCTCAAGAAA+AGG 0.520025 1_4:+12662690 None:intergenic
ACAGAAGGCAATGCAAAGAA+GGG 0.552195 1_4:-12663328 Msa0150920:CDS
CAAAGCTTACTAGGATACAA+TGG 0.561451 1_4:+12662673 None:intergenic
AGATGTGTATCAAAATATCA+AGG 0.576462 1_4:-12664701 Msa0150920:intron
TTGAAATTGGAAGCAACAGA+AGG 0.584098 1_4:-12663343 Msa0150920:CDS
GAACCAAATAACATATAGAG+AGG 0.617617 1_4:+12664903 None:intergenic
AGATAAAATAGGGCCAACAA+TGG 0.630676 1_4:-12664737 Msa0150920:CDS
AAATAACATATAGAGAGGAA+AGG 0.630937 1_4:+12664908 None:intergenic
CAGAAGGCAATGCAAAGAAG+GGG 0.645808 1_4:-12663327 Msa0150920:CDS
TAGAGAGGAAAGGCTTAATG+GGG 0.674382 1_4:+12664918 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATAATTACAGATAAAATA+GGG - chr1_4:12662801-12662820 Msa0150920:CDS 10.0%
!! TAGATAATTAAAGATATTAA+CGG + chr1_4:12663545-12663564 None:intergenic 10.0%
!! TATATATTAGTTAAAAAGTA+TGG - chr1_4:12663641-12663660 Msa0150920:intron 10.0%
!!! TTCTTTTTTCATTATAATAT+GGG - chr1_4:12664027-12664046 Msa0150920:intron 10.0%
!! TATTGAAGAAATTTATAAAT+AGG - chr1_4:12664355-12664374 Msa0150920:intron 10.0%
!! CTAATAATTACAGATAAAAT+AGG - chr1_4:12662800-12662819 Msa0150920:CDS 15.0%
!! ACAAAATTATAATAAGAGAA+GGG + chr1_4:12662943-12662962 None:intergenic 15.0%
!! AACAAAATTATAATAAGAGA+AGG + chr1_4:12662944-12662963 None:intergenic 15.0%
!! ATAAATAACAATGCTTAAAA+AGG + chr1_4:12663191-12663210 None:intergenic 15.0%
!!! AACCAATAAAATTTGTTATT+TGG - chr1_4:12663251-12663270 Msa0150920:intron 15.0%
!! AGGTATAAAAAAATTTGTAT+AGG + chr1_4:12663793-12663812 None:intergenic 15.0%
!! TAAGAAGAAATTTAACATAA+AGG - chr1_4:12663970-12663989 Msa0150920:intron 15.0%
!! AAGAAGAAATTTAACATAAA+GGG - chr1_4:12663971-12663990 Msa0150920:intron 15.0%
!!! CTTCTTTTTTCATTATAATA+TGG - chr1_4:12664026-12664045 Msa0150920:intron 15.0%
!!! TCTTTTTTCATTATAATATG+GGG - chr1_4:12664028-12664047 Msa0150920:intron 15.0%
!! TTTAGTTGAAATATTGAAAT+TGG - chr1_4:12664192-12664211 Msa0150920:intron 15.0%
!!! AGGTGTTATTATATTATTAT+AGG + chr1_4:12664290-12664309 None:intergenic 15.0%
!!! ATTAGAGAAGTATTATTATT+AGG + chr1_4:12664310-12664329 None:intergenic 15.0%
!!! AGGTATCATTTTATAATTTA+TGG - chr1_4:12664375-12664394 Msa0150920:intron 15.0%
!! AAAAAATATATACACACATA+AGG + chr1_4:12664945-12664964 None:intergenic 15.0%
!!! TAGATGTTTTGTTTTTTTTG+AGG + chr1_4:12662768-12662787 None:intergenic 20.0%
!! ATGAATGATGTTAGTTATTA+GGG - chr1_4:12662991-12663010 Msa0150920:intron 20.0%
!! CTATTAATCTAATAACTACT+TGG + chr1_4:12663099-12663118 None:intergenic 20.0%
!! TTCTCCAATAGTTAAAATTA+TGG - chr1_4:12663148-12663167 Msa0150920:intron 20.0%
!!! TCAACCATAATTTTAACTAT+TGG + chr1_4:12663155-12663174 None:intergenic 20.0%
!!! CAATAAAATTTGTTATTTGG+CGG - chr1_4:12663254-12663273 Msa0150920:intron 20.0%
!! AAGCTACTCAAATTATTAAA+AGG + chr1_4:12663384-12663403 None:intergenic 20.0%
!!! ATACGAAATAGAATGTTTTT+AGG - chr1_4:12663419-12663438 Msa0150920:intron 20.0%
!!! TACGAAATAGAATGTTTTTA+GGG - chr1_4:12663420-12663439 Msa0150920:intron 20.0%
!! TTTAATACACAACTAATCAT+TGG + chr1_4:12664112-12664131 None:intergenic 20.0%
!!! ACTAAATTTAGATTTGTTGT+TGG + chr1_4:12664178-12664197 None:intergenic 20.0%
!!! CATATATTCTGAAAAGAAAA+TGG - chr1_4:12664403-12664422 Msa0150920:intron 20.0%
!! ATGAAATTACATTAAAACCA+TGG - chr1_4:12664447-12664466 Msa0150920:intron 20.0%
!! TGAAACGCAATATATATTTA+GGG + chr1_4:12664723-12664742 None:intergenic 20.0%
!!! GTGTGTATATATTTTTTTGA+AGG - chr1_4:12664948-12664967 Msa0150920:CDS 20.0%
!! TTTTATTGAAGAGCTTTCTA+TGG - chr1_4:12662561-12662580 Msa0150920:intron 25.0%
! AAATAACATATAGAGAGGAA+AGG + chr1_4:12662643-12662662 None:intergenic 25.0%
! TTTCCTCTCTATATGTTATT+TGG - chr1_4:12662642-12662661 Msa0150920:intron 25.0%
! AGATGTGTATCAAAATATCA+AGG - chr1_4:12662847-12662866 Msa0150920:intron 25.0%
! TAATAAGAGAAGGGTTAAAT+GGG + chr1_4:12662934-12662953 None:intergenic 25.0%
! ATAATAAGAGAAGGGTTAAA+TGG + chr1_4:12662935-12662954 None:intergenic 25.0%
! GATGAATGATGTTAGTTATT+AGG - chr1_4:12662990-12663009 Msa0150920:intron 25.0%
! ATAGACATCATAACTACAAT+TGG - chr1_4:12663115-12663134 Msa0150920:intron 25.0%
! TAGACATCATAACTACAATT+GGG - chr1_4:12663116-12663135 Msa0150920:intron 25.0%
!! CGCCAAATAACAAATTTTAT+TGG + chr1_4:12663256-12663275 None:intergenic 25.0%
! ATAGTGCATATTGCAAAAAT+TGG - chr1_4:12663682-12663701 Msa0150920:intron 25.0%
!!! ATTGGACATGTATTTTGAAA+AGG - chr1_4:12663700-12663719 Msa0150920:intron 25.0%
! AATCTACAAACTTAGATCAA+TGG + chr1_4:12663895-12663914 None:intergenic 25.0%
! TAACATAAAGGGTTAACTTA+AGG - chr1_4:12663982-12664001 Msa0150920:intron 25.0%
! AACATAAAGGGTTAACTTAA+GGG - chr1_4:12663983-12664002 Msa0150920:intron 25.0%
! TAACTTAAGGGTTATAAGTT+AGG - chr1_4:12663995-12664014 Msa0150920:intron 25.0%
! TAGTATTTCATGCTATTAGA+TGG - chr1_4:12664540-12664559 Msa0150920:intron 25.0%
! CTGAAACGCAATATATATTT+AGG + chr1_4:12664724-12664743 None:intergenic 25.0%
! CTAAATATATATTGCGTTTC+AGG - chr1_4:12664722-12664741 Msa0150920:CDS 25.0%
!! TCAATGAATGTTTTACTTTC+CGG + chr1_4:12664765-12664784 None:intergenic 25.0%
! TAAGCAGAAAATGCAAATAT+TGG - chr1_4:12664821-12664840 Msa0150920:intron 25.0%
! ATTGATAAACAAAGCTTACT+AGG + chr1_4:12664887-12664906 None:intergenic 25.0%
!!! AGTAAGCTTTGTTTATCAAT+TGG - chr1_4:12664887-12664906 Msa0150920:intron 25.0%
! GGTAAAGTTTGCAATATTTA+GGG + chr1_4:12664924-12664943 None:intergenic 25.0%
! AGGTAAAGTTTGCAATATTT+AGG + chr1_4:12664925-12664944 None:intergenic 25.0%
! AAAACAAATACACACACATA+AGG + chr1_4:12664976-12664995 None:intergenic 25.0%
! TTTGCAGAGATTATATAACT+TGG - chr1_4:12664993-12665012 Msa0150920:CDS 25.0%
GAACCAAATAACATATAGAG+AGG + chr1_4:12662648-12662667 None:intergenic 30.0%
!! TATTTGGTTCTACAAGTTCT+TGG - chr1_4:12662658-12662677 Msa0150920:intron 30.0%
AATGGTGTGTAATTAAGGAA+AGG - chr1_4:12663291-12663310 Msa0150920:intron 30.0%
ATGAGAAATGATAGTTACAG+TGG + chr1_4:12663360-12663379 None:intergenic 30.0%
!! CTTGGACATGTATTTTGAAA+CGG + chr1_4:12663487-12663506 None:intergenic 30.0%
CAAAGATAAGACACATGTTA+AGG + chr1_4:12663813-12663832 None:intergenic 30.0%
CTTAACATGTGTCTTATCTT+TGG - chr1_4:12663811-12663830 Msa0150920:intron 30.0%
AAGTGTGCGAGAAAAAAAAT+TGG + chr1_4:12663860-12663879 None:intergenic 30.0%
ATTACATTAAAACCATGGCA+TGG - chr1_4:12664452-12664471 Msa0150920:intron 30.0%
AATATATATTGCGTTTCAGG+TGG - chr1_4:12664725-12664744 Msa0150920:CDS 30.0%
GTTGTGATAGTTAAACCTTC+TGG - chr1_4:12662583-12662602 Msa0150920:intron 35.0%
ATAGAGAGGAAAGGCTTAAT+GGG + chr1_4:12662634-12662653 None:intergenic 35.0%
TATAGAGAGGAAAGGCTTAA+TGG + chr1_4:12662635-12662654 None:intergenic 35.0%
AGATAAAATAGGGCCAACAA+TGG - chr1_4:12662811-12662830 Msa0150920:intron 35.0%
AGTTATTAGGGTTTGAACCT+TGG - chr1_4:12663003-12663022 Msa0150920:intron 35.0%
GTTTGAACCTTGGATTTCTT+AGG - chr1_4:12663013-12663032 Msa0150920:intron 35.0%
!! TTGTTATTTGGCGGAAATCA+AGG - chr1_4:12663263-12663282 Msa0150920:intron 35.0%
! TGTTATTTGGCGGAAATCAA+GGG - chr1_4:12663264-12663283 Msa0150920:intron 35.0%
! GAGGTAATGGTGTGTAATTA+AGG - chr1_4:12663286-12663305 Msa0150920:intron 35.0%
!!! GACATGTATTTTGAAACGGA+GGG + chr1_4:12663483-12663502 None:intergenic 35.0%
CATATGTGAAATGGTTGACT+TGG + chr1_4:12663505-12663524 None:intergenic 35.0%
TAACGGTCAAAATTGTGCAT+GGG + chr1_4:12663528-12663547 None:intergenic 35.0%
TTAACGGTCAAAATTGTGCA+TGG + chr1_4:12663529-12663548 None:intergenic 35.0%
CTTAAGGGTTATAAGTTAGG+TGG - chr1_4:12663998-12664017 Msa0150920:intron 35.0%
!!! TATGGGGATTGTTTTTGTGT+CGG - chr1_4:12664044-12664063 Msa0150920:intron 35.0%
TTCCAATCTCTGCAATCAAA+CGG + chr1_4:12664137-12664156 None:intergenic 35.0%
TTGAAATTGGAAGCAACAGA+AGG - chr1_4:12664205-12664224 Msa0150920:intron 35.0%
! TTTTCTGCTTAAGCATGTCA+CGG + chr1_4:12664812-12664831 None:intergenic 35.0%
CAATGGATATCCTCAAGAAA+AGG + chr1_4:12664861-12664880 None:intergenic 35.0%
CAAAGCTTACTAGGATACAA+TGG + chr1_4:12664878-12664897 None:intergenic 35.0%
! GCTTCAAGATTTTCTCCAGA+AGG + chr1_4:12662601-12662620 None:intergenic 40.0%
TAGAGAGGAAAGGCTTAATG+GGG + chr1_4:12662633-12662652 None:intergenic 40.0%
TGTCTCAAAACAGCCATTGT+TGG + chr1_4:12662827-12662846 None:intergenic 40.0%
TAAGAGAAGGGTTAAATGGG+TGG + chr1_4:12662931-12662950 None:intergenic 40.0%
GGTACTACCTAAGAAATCCA+AGG + chr1_4:12663023-12663042 None:intergenic 40.0%
GTAAGTTGTGGGACACAAAA+GGG + chr1_4:12663044-12663063 None:intergenic 40.0%
AGTAAGTTGTGGGACACAAA+AGG + chr1_4:12663045-12663064 None:intergenic 40.0%
AGTGTCAAGCAGTAAGTTGT+GGG + chr1_4:12663055-12663074 None:intergenic 40.0%
TAGTGTCAAGCAGTAAGTTG+TGG + chr1_4:12663056-12663075 None:intergenic 40.0%
!!! GGACATGTATTTTGAAACGG+AGG + chr1_4:12663484-12663503 None:intergenic 40.0%
TTCCGTTTGATTGCAGAGAT+TGG - chr1_4:12664132-12664151 Msa0150920:intron 40.0%
AACAGAAGGCAATGCAAAGA+AGG - chr1_4:12664219-12664238 Msa0150920:intron 40.0%
ACAGAAGGCAATGCAAAGAA+GGG - chr1_4:12664220-12664239 Msa0150920:intron 40.0%
CATTAAAACCATGGCATGGA+TGG - chr1_4:12664456-12664475 Msa0150920:intron 40.0%
! TCTACTTGTGCCTTTTCTTG+AGG - chr1_4:12664848-12664867 Msa0150920:intron 40.0%
TATTTGGCGGAAATCAAGGG+AGG - chr1_4:12663267-12663286 Msa0150920:intron 45.0%
GTGCATGGGCATATGTGAAA+TGG + chr1_4:12663514-12663533 None:intergenic 45.0%
!!! GGGATTGTTTTTGTGTCGGA+CGG - chr1_4:12664048-12664067 Msa0150920:intron 45.0%
!!! GGATTGTTTTTGTGTCGGAC+GGG - chr1_4:12664049-12664068 Msa0150920:intron 45.0%
CAGAAGGCAATGCAAAGAAG+GGG - chr1_4:12664221-12664240 Msa0150920:intron 45.0%
GCTGCAGTAAAGCCTTTGTT+TGG - chr1_4:12664248-12664267 Msa0150920:intron 45.0%
! AAGCCTTTGTTTGGCTCACA+AGG - chr1_4:12664257-12664276 Msa0150920:intron 45.0%
TCACCTTGTGAGCCAAACAA+AGG + chr1_4:12664263-12664282 None:intergenic 45.0%
GATGAAATCCATCCATGCCA+TGG + chr1_4:12664467-12664486 None:intergenic 45.0%
!! GGTGGCTCTAAGATTAGTTC+CGG - chr1_4:12664743-12664762 Msa0150920:intron 45.0%
!!! TCTATTTTTATAAAATATTT+AGG - chr1_4:12664618-12664637 Msa0150920:intron 5.0%
GCGGAAATCAAGGGAGGTAA+TGG - chr1_4:12663273-12663292 Msa0150920:intron 50.0%
Chromosome Type Strat End Strand Name
chr1_4 gene 12662535 12665035 12662535 ID=Msa0150920;Name=Msa0150920
chr1_4 mRNA 12662535 12665035 12662535 ID=Msa0150920-mRNA-1;Parent=Msa0150920;Name=Msa0150920-mRNA-1;_AED=0.19;_eAED=0.19;_QI=0|0|0|1|1|1|5|0|165
chr1_4 exon 12664891 12665035 12664891 ID=Msa0150920-mRNA-1:exon:5090;Parent=Msa0150920-mRNA-1
chr1_4 exon 12664702 12664757 12664702 ID=Msa0150920-mRNA-1:exon:5089;Parent=Msa0150920-mRNA-1
chr1_4 exon 12663306 12663422 12663306 ID=Msa0150920-mRNA-1:exon:5088;Parent=Msa0150920-mRNA-1
chr1_4 exon 12662683 12662826 12662683 ID=Msa0150920-mRNA-1:exon:5087;Parent=Msa0150920-mRNA-1
chr1_4 exon 12662535 12662570 12662535 ID=Msa0150920-mRNA-1:exon:5086;Parent=Msa0150920-mRNA-1
chr1_4 CDS 12664891 12665035 12664891 ID=Msa0150920-mRNA-1:cds;Parent=Msa0150920-mRNA-1
chr1_4 CDS 12664702 12664757 12664702 ID=Msa0150920-mRNA-1:cds;Parent=Msa0150920-mRNA-1
chr1_4 CDS 12663306 12663422 12663306 ID=Msa0150920-mRNA-1:cds;Parent=Msa0150920-mRNA-1
chr1_4 CDS 12662683 12662826 12662683 ID=Msa0150920-mRNA-1:cds;Parent=Msa0150920-mRNA-1
chr1_4 CDS 12662535 12662570 12662535 ID=Msa0150920-mRNA-1:cds;Parent=Msa0150920-mRNA-1
Gene Sequence

>Msa0150920

ATGGAGAAGAAATCAGAGATAAGTTGTTTTATTGAAGAGCTTTCTATGGTTGTGATAGTTAAACCTTCTGGAGAAAATCTTGAAGCTGCTCATATCCCCATTAAGCCTTTCCTCTCTATATGTTATTTGGTTCTACAAGTTCTTGATAAAATAGGGCCAACAATGGCTGTTTTGAGACAAGATGTGTATCAAAATATCAAGAGATTGGAACTAATGCATGAATCAAATCCAACAACAAATCTAAATTTAGTTGAAATATTGAAATTGGAAGCAACAGAAGGCAATGCAAAGAAGGGGTCTAGCTGCAGTAAAGCCTTTGTGGCTCTAAGATTAGTTCCGGAAAGTAAAACATTCATTGATCTTCTTAAGACTGAAGATGAAGACCGTGACATGCTTAAGCAGAAAATGCAAATATTGGTTTCTCTACTTGTGCCTTTTCTTGAGGATATCCATTGTATCCTAAGATTATATAACTTGGACAAGCTGAAATCAACATGA

Protein sequence

>Msa0150920

MEKKSEISCFIEELSMVVIVKPSGENLEAAHIPIKPFLSICYLVLQVLDKIGPTMAVLRQDVYQNIKRLELMHESNPTTNLNLVEILKLEATEGNAKKGSSCSKAFVALRLVPESKTFIDLLKTEDEDRDMLKQKMQILVSLLVPFLEDIHCILRLYNLDKLKST*