AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0803310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0803310 MtrunA17_Chr5g0411241 99.167 120 1 0 1 120 1 120 7.02e-83 238
Msa0803310 MtrunA17_Chr5g0411231 83.333 120 20 0 1 120 1 120 6.47e-69 202
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 27 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGGGCCTTCAGTCTTGAAAA+TGG 0.356723 5_3:+18413419 None:intergenic
TTATGCAGTGATGGTGGAGC+TGG 0.397441 5_3:-18413516 Msa0803310:intron
CTTGCTCTTGAGTGAAGCTC+TGG 0.411535 5_3:+18414303 None:intergenic
TCACTGCTACTCTCAATAAC+TGG 0.438274 5_3:+18413489 None:intergenic
CCCTTGCCAGAGTTTACACC+AGG 0.459349 5_3:+18413399 None:intergenic
AGGACTGAAGGGCCTGATGC+TGG 0.490624 5_3:-18414025 Msa0803310:CDS
GGCAATGTGTTGTGCAAGAC+AGG 0.514042 5_3:-18414073 Msa0803310:CDS
ACAACACATTGCCCAAGCCC+TGG 0.525921 5_3:+18414083 None:intergenic
CCCTGGTGTAAACTCTGGCA+AGG 0.541663 5_3:-18413400 Msa0803310:CDS
TATGCAGTGATGGTGGAGCT+GGG 0.557903 5_3:-18413515 Msa0803310:intron
ACATTCTGCAAGTGTGGTGA+AGG 0.561546 5_3:-18413453 Msa0803310:CDS
ATTGAGAGTAGCAGTGACAA+TGG 0.563224 5_3:-18413483 Msa0803310:CDS
CAGAGCTTCACTCAAGAGCA+AGG 0.567749 5_3:-18414302 Msa0803310:CDS
TTGCTCTTGAGTGAAGCTCT+GGG 0.573531 5_3:+18414304 None:intergenic
GTTGGACATGTGTTATAACT+AGG 0.581816 5_3:-18414045 Msa0803310:CDS
GTGTTATAACTAGGACTGAA+GGG 0.595455 5_3:-18414036 Msa0803310:CDS
TGTGCAAGACAGGTAAAGGT+TGG 0.598871 5_3:-18414063 Msa0803310:CDS
AAACTCTTATGCAGTGATGG+TGG 0.602169 5_3:-18413522 Msa0803310:intron
GAAGGCCCTGGTGTAAACTC+TGG 0.603912 5_3:-18413405 Msa0803310:CDS
TGTGTTATAACTAGGACTGA+AGG 0.610701 5_3:-18414037 Msa0803310:CDS
CCTGGTGTAAACTCTGGCAA+GGG 0.620143 5_3:-18413399 Msa0803310:CDS
GTGTTGTGCAAGACAGGTAA+AGG 0.626364 5_3:-18414067 Msa0803310:CDS
AGAGCTTCACTCAAGAGCAA+GGG 0.651871 5_3:-18414301 Msa0803310:intron
TCTGCAAGTGTGGTGAAGGG+TGG 0.652623 5_3:-18413449 Msa0803310:CDS
AGTGAAACATTCTGCAAGTG+TGG 0.671634 5_3:-18413459 Msa0803310:CDS
CATTCTGCAAGTGTGGTGAA+GGG 0.681189 5_3:-18413452 Msa0803310:CDS
CCTTGCCAGAGTTTACACCA+GGG 0.773669 5_3:+18413400 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTATTTGTTTGTAATA+TGG - chr5_3:18413839-18413858 Msa0803310:intron 10.0%
!! TTAATTATTTGTTTGTAATA+TGG - chr5_3:18413839-18413858 Msa0803310:intron 10.0%
!! TAATATGAAATTGAGATTTA+AGG + chr5_3:18413962-18413981 None:intergenic 15.0%
!! TAATATGAAATTGAGATTTA+AGG + chr5_3:18413962-18413981 None:intergenic 15.0%
!! AAACTGTAAAGATGAAATAA+AGG + chr5_3:18413405-18413424 None:intergenic 20.0%
!! TAAAATAATAATAAGAGGAG+TGG + chr5_3:18413719-18413738 None:intergenic 20.0%
!! GCAGTTAAAATAATAATAAG+AGG + chr5_3:18413724-18413743 None:intergenic 20.0%
!! TATCGTGGAAAAAAAATATA+AGG - chr5_3:18413769-18413788 Msa0803310:intron 20.0%
!! TTATTAGGTAAAAGTTCAAT+AGG + chr5_3:18413909-18413928 None:intergenic 20.0%
!! AATTTATCGTTCAACTTATT+AGG + chr5_3:18413924-18413943 None:intergenic 20.0%
!! TTCTATAAGCATAAAATTAG+TGG + chr5_3:18414034-18414053 None:intergenic 20.0%
!! AAACTGTAAAGATGAAATAA+AGG + chr5_3:18413405-18413424 None:intergenic 20.0%
!! TAAAATAATAATAAGAGGAG+TGG + chr5_3:18413719-18413738 None:intergenic 20.0%
!! GCAGTTAAAATAATAATAAG+AGG + chr5_3:18413724-18413743 None:intergenic 20.0%
!! TATCGTGGAAAAAAAATATA+AGG - chr5_3:18413769-18413788 Msa0803310:intron 20.0%
!! TTATTAGGTAAAAGTTCAAT+AGG + chr5_3:18413909-18413928 None:intergenic 20.0%
!! AATTTATCGTTCAACTTATT+AGG + chr5_3:18413924-18413943 None:intergenic 20.0%
!! TTCTATAAGCATAAAATTAG+TGG + chr5_3:18414034-18414053 None:intergenic 20.0%
!!! ACGAAAATAGAGCATTATTT+TGG + chr5_3:18413492-18413511 None:intergenic 25.0%
!!! TTAACCAATAAGTTTTGTGT+AGG - chr5_3:18413529-18413548 Msa0803310:intron 25.0%
!!! ACGAAAATAGAGCATTATTT+TGG + chr5_3:18413492-18413511 None:intergenic 25.0%
!!! TTAACCAATAAGTTTTGTGT+AGG - chr5_3:18413529-18413548 Msa0803310:intron 25.0%
CTTTCCTACACAAAACTTAT+TGG + chr5_3:18413536-18413555 None:intergenic 30.0%
!! GCAATCATTTTAACAATGGT+TGG + chr5_3:18413866-18413885 None:intergenic 30.0%
!! TGGTGCAATCATTTTAACAA+TGG + chr5_3:18413870-18413889 None:intergenic 30.0%
CTTTCCTACACAAAACTTAT+TGG + chr5_3:18413536-18413555 None:intergenic 30.0%
!! GCAATCATTTTAACAATGGT+TGG + chr5_3:18413866-18413885 None:intergenic 30.0%
!! TGGTGCAATCATTTTAACAA+TGG + chr5_3:18413870-18413889 None:intergenic 30.0%
! CTGAGTTTTTATCTTGAGCT+GGG + chr5_3:18413560-18413579 None:intergenic 35.0%
GTTGGACATGTGTTATAACT+AGG - chr5_3:18413619-18413638 Msa0803310:intron 35.0%
TGTGTTATAACTAGGACTGA+AGG - chr5_3:18413627-18413646 Msa0803310:intron 35.0%
GTGTTATAACTAGGACTGAA+GGG - chr5_3:18413628-18413647 Msa0803310:intron 35.0%
! GGCAAAGTTTTTGCTAAATG+TGG - chr5_3:18413660-18413679 Msa0803310:intron 35.0%
ATTTGACAAGAAAGCTATCG+TGG - chr5_3:18413754-18413773 Msa0803310:intron 35.0%
TAGGTAAGATCTTCATGTCA+TGG + chr5_3:18413890-18413909 None:intergenic 35.0%
ATCAAACTCTTATGCAGTGA+TGG - chr5_3:18414139-18414158 Msa0803310:intron 35.0%
!! TGTTCCATTTTCAAGACTGA+AGG - chr5_3:18414241-18414260 Msa0803310:intron 35.0%
! CTGAGTTTTTATCTTGAGCT+GGG + chr5_3:18413560-18413579 None:intergenic 35.0%
GTTGGACATGTGTTATAACT+AGG - chr5_3:18413619-18413638 Msa0803310:intron 35.0%
TGTGTTATAACTAGGACTGA+AGG - chr5_3:18413627-18413646 Msa0803310:intron 35.0%
GTGTTATAACTAGGACTGAA+GGG - chr5_3:18413628-18413647 Msa0803310:intron 35.0%
! GGCAAAGTTTTTGCTAAATG+TGG - chr5_3:18413660-18413679 Msa0803310:intron 35.0%
ATTTGACAAGAAAGCTATCG+TGG - chr5_3:18413754-18413773 Msa0803310:intron 35.0%
TAGGTAAGATCTTCATGTCA+TGG + chr5_3:18413890-18413909 None:intergenic 35.0%
ATCAAACTCTTATGCAGTGA+TGG - chr5_3:18414139-18414158 Msa0803310:intron 35.0%
!! TGTTCCATTTTCAAGACTGA+AGG - chr5_3:18414241-18414260 Msa0803310:intron 35.0%
! CCTGAGTTTTTATCTTGAGC+TGG + chr5_3:18413561-18413580 None:intergenic 40.0%
CCAGCTCAAGATAAAAACTC+AGG - chr5_3:18413558-18413577 Msa0803310:intron 40.0%
TCAAGATAAAAACTCAGGCC+AGG - chr5_3:18413563-18413582 Msa0803310:intron 40.0%
CAAGATAAAAACTCAGGCCA+GGG - chr5_3:18413564-18413583 Msa0803310:intron 40.0%
AAACTCTTATGCAGTGATGG+TGG - chr5_3:18414142-18414161 Msa0803310:intron 40.0%
TCACTGCTACTCTCAATAAC+TGG + chr5_3:18414178-18414197 None:intergenic 40.0%
ATTGAGAGTAGCAGTGACAA+TGG - chr5_3:18414181-18414200 Msa0803310:intron 40.0%
AGTGAAACATTCTGCAAGTG+TGG - chr5_3:18414205-18414224 Msa0803310:intron 40.0%
! CCTGAGTTTTTATCTTGAGC+TGG + chr5_3:18413561-18413580 None:intergenic 40.0%
CCAGCTCAAGATAAAAACTC+AGG - chr5_3:18413558-18413577 Msa0803310:intron 40.0%
TCAAGATAAAAACTCAGGCC+AGG - chr5_3:18413563-18413582 Msa0803310:intron 40.0%
CAAGATAAAAACTCAGGCCA+GGG - chr5_3:18413564-18413583 Msa0803310:intron 40.0%
AAACTCTTATGCAGTGATGG+TGG - chr5_3:18414142-18414161 Msa0803310:intron 40.0%
TCACTGCTACTCTCAATAAC+TGG + chr5_3:18414178-18414197 None:intergenic 40.0%
ATTGAGAGTAGCAGTGACAA+TGG - chr5_3:18414181-18414200 Msa0803310:intron 40.0%
AGTGAAACATTCTGCAAGTG+TGG - chr5_3:18414205-18414224 Msa0803310:intron 40.0%
TTGCTCTTGAGTGAAGCTCT+GGG + chr5_3:18413363-18413382 None:intergenic 45.0%
AGAGCTTCACTCAAGAGCAA+GGG - chr5_3:18413363-18413382 Msa0803310:CDS 45.0%
GTGTTGTGCAAGACAGGTAA+AGG - chr5_3:18413597-18413616 Msa0803310:intron 45.0%
TGTGCAAGACAGGTAAAGGT+TGG - chr5_3:18413601-18413620 Msa0803310:intron 45.0%
GCAAAAACTTTGCCAGCATC+AGG + chr5_3:18413654-18413673 None:intergenic 45.0%
ACATTCTGCAAGTGTGGTGA+AGG - chr5_3:18414211-18414230 Msa0803310:intron 45.0%
CATTCTGCAAGTGTGGTGAA+GGG - chr5_3:18414212-18414231 Msa0803310:intron 45.0%
AGGGCCTTCAGTCTTGAAAA+TGG + chr5_3:18414248-18414267 None:intergenic 45.0%
!! ATTTTCAAGACTGAAGGCCC+TGG - chr5_3:18414247-18414266 Msa0803310:intron 45.0%
TTGCTCTTGAGTGAAGCTCT+GGG + chr5_3:18413363-18413382 None:intergenic 45.0%
AGAGCTTCACTCAAGAGCAA+GGG - chr5_3:18413363-18413382 Msa0803310:CDS 45.0%
GTGTTGTGCAAGACAGGTAA+AGG - chr5_3:18413597-18413616 Msa0803310:intron 45.0%
TGTGCAAGACAGGTAAAGGT+TGG - chr5_3:18413601-18413620 Msa0803310:intron 45.0%
GCAAAAACTTTGCCAGCATC+AGG + chr5_3:18413654-18413673 None:intergenic 45.0%
ACATTCTGCAAGTGTGGTGA+AGG - chr5_3:18414211-18414230 Msa0803310:intron 45.0%
CATTCTGCAAGTGTGGTGAA+GGG - chr5_3:18414212-18414231 Msa0803310:intron 45.0%
AGGGCCTTCAGTCTTGAAAA+TGG + chr5_3:18414248-18414267 None:intergenic 45.0%
!! ATTTTCAAGACTGAAGGCCC+TGG - chr5_3:18414247-18414266 Msa0803310:intron 45.0%
CTTGCTCTTGAGTGAAGCTC+TGG + chr5_3:18413364-18413383 None:intergenic 50.0%
CAGAGCTTCACTCAAGAGCA+AGG - chr5_3:18413362-18413381 Msa0803310:CDS 50.0%
TAAAAACTCAGGCCAGGGCT+TGG - chr5_3:18413569-18413588 Msa0803310:intron 50.0%
AAAAACTCAGGCCAGGGCTT+GGG - chr5_3:18413570-18413589 Msa0803310:intron 50.0%
GGCAATGTGTTGTGCAAGAC+AGG - chr5_3:18413591-18413610 Msa0803310:intron 50.0%
!! TTATGCAGTGATGGTGGAGC+TGG - chr5_3:18414148-18414167 Msa0803310:intron 50.0%
!! TATGCAGTGATGGTGGAGCT+GGG - chr5_3:18414149-18414168 Msa0803310:intron 50.0%
CCTTGCCAGAGTTTACACCA+GGG + chr5_3:18414267-18414286 None:intergenic 50.0%
CCTGGTGTAAACTCTGGCAA+GGG - chr5_3:18414265-18414284 Msa0803310:intron 50.0%
CTTGCTCTTGAGTGAAGCTC+TGG + chr5_3:18413364-18413383 None:intergenic 50.0%
CAGAGCTTCACTCAAGAGCA+AGG - chr5_3:18413362-18413381 Msa0803310:CDS 50.0%
TAAAAACTCAGGCCAGGGCT+TGG - chr5_3:18413569-18413588 Msa0803310:intron 50.0%
AAAAACTCAGGCCAGGGCTT+GGG - chr5_3:18413570-18413589 Msa0803310:intron 50.0%
GGCAATGTGTTGTGCAAGAC+AGG - chr5_3:18413591-18413610 Msa0803310:intron 50.0%
!! TTATGCAGTGATGGTGGAGC+TGG - chr5_3:18414148-18414167 Msa0803310:intron 50.0%
!! TATGCAGTGATGGTGGAGCT+GGG - chr5_3:18414149-18414168 Msa0803310:intron 50.0%
CCTTGCCAGAGTTTACACCA+GGG + chr5_3:18414267-18414286 None:intergenic 50.0%
CCTGGTGTAAACTCTGGCAA+GGG - chr5_3:18414265-18414284 Msa0803310:intron 50.0%
ACAACACATTGCCCAAGCCC+TGG + chr5_3:18413584-18413603 None:intergenic 55.0%
TCTGCAAGTGTGGTGAAGGG+TGG - chr5_3:18414215-18414234 Msa0803310:intron 55.0%
GAAGGCCCTGGTGTAAACTC+TGG - chr5_3:18414259-18414278 Msa0803310:intron 55.0%
CCCTGGTGTAAACTCTGGCA+AGG - chr5_3:18414264-18414283 Msa0803310:intron 55.0%
CCCTTGCCAGAGTTTACACC+AGG + chr5_3:18414268-18414287 None:intergenic 55.0%
ACAACACATTGCCCAAGCCC+TGG + chr5_3:18413584-18413603 None:intergenic 55.0%
TCTGCAAGTGTGGTGAAGGG+TGG - chr5_3:18414215-18414234 Msa0803310:intron 55.0%
GAAGGCCCTGGTGTAAACTC+TGG - chr5_3:18414259-18414278 Msa0803310:intron 55.0%
CCCTGGTGTAAACTCTGGCA+AGG - chr5_3:18414264-18414283 Msa0803310:intron 55.0%
CCCTTGCCAGAGTTTACACC+AGG + chr5_3:18414268-18414287 None:intergenic 55.0%
AGGACTGAAGGGCCTGATGC+TGG - chr5_3:18413639-18413658 Msa0803310:intron 60.0%
AGGACTGAAGGGCCTGATGC+TGG - chr5_3:18413639-18413658 Msa0803310:intron 60.0%
Chromosome Type Strat End Strand Name
chr5_3 gene 18413353 18414333 18413353 ID=Msa0803310;Name=Msa0803310
chr5_3 mRNA 18413353 18414333 18413353 ID=Msa0803310-mRNA-1;Parent=Msa0803310;Name=Msa0803310-mRNA-1;_AED=0.37;_eAED=0.37;_QI=0|0|0|1|1|1|3|0|120
chr5_3 exon 18414302 18414333 18414302 ID=Msa0803310-mRNA-1:exon:7554;Parent=Msa0803310-mRNA-1
chr5_3 exon 18413983 18414135 18413983 ID=Msa0803310-mRNA-1:exon:7553;Parent=Msa0803310-mRNA-1
chr5_3 exon 18413353 18413530 18413353 ID=Msa0803310-mRNA-1:exon:7552;Parent=Msa0803310-mRNA-1
chr5_3 CDS 18414302 18414333 18414302 ID=Msa0803310-mRNA-1:cds;Parent=Msa0803310-mRNA-1
chr5_3 CDS 18413983 18414135 18413983 ID=Msa0803310-mRNA-1:cds;Parent=Msa0803310-mRNA-1
chr5_3 CDS 18413353 18413530 18413353 ID=Msa0803310-mRNA-1:cds;Parent=Msa0803310-mRNA-1
Gene Sequence

>Msa0803310

ATGGAGTCCCAGAGCTTCACTCAAGAGCAAGGGAAAGTCCCAGCTCAAGATAAAAACTCAGGCCAGGGCTTGGGCAATGTGTTGTGCAAGACAGGTAAAGGTTGGACATGTGTTATAACTAGGACTGAAGGGCCTGATGCTGGCAAAGTTTTTGCTAAATGTGGTGAAAATTGCAACTGCACGCTTGATGGTGGAGCTGGGTCACCAGTTATTGAGAGTAGCAGTGACAATGGCAGTGAAACATTCTGCAAGTGTGGTGAAGGGTGGAGTTGTTCCATTTTCAAGACTGAAGGCCCTGGTGTAAACTCTGGCAAGGGCTTTGCTGAATGCACTCAACAGTATAACTGTGCTTGTAACTGTTGA

Protein sequence

>Msa0803310

MESQSFTQEQGKVPAQDKNSGQGLGNVLCKTGKGWTCVITRTEGPDAGKVFAKCGENCNCTLDGGAGSPVIESSSDNGSETFCKCGEGWSCSIFKTEGPGVNSGKGFAECTQQYNCACNC*