AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0619980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0619980 MtrunA17_Chr8g0385691 78.846 52 2 1 1 52 1 43 7.98e-20 78.6
Msa0619980 MtrunA17_Chr8g0385681 70.000 50 10 1 3 52 2 46 3.71e-14 63.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 12 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGATTGTAACAAAGATTT+AGG 0.103636 4_2:-71293869 Msa0619980:CDS
GGCTCTCACAAGACGGATTT+TGG 0.212306 4_2:+71293808 None:intergenic
AAGATTGTAACAAAGATTTA+GGG 0.318005 4_2:-71293868 Msa0619980:CDS
AACACAAGATCCATCTTCTA+AGG 0.389643 4_2:-71293777 Msa0619980:intron
GCGGTGAAGGGTTGCAAGAA+GGG 0.478500 4_2:-71293902 Msa0619980:CDS
AAGAATGGAAGAAGCGGTGA+AGG 0.530292 4_2:-71293915 None:intergenic
TTAGGTAGTACCTTAGAAGA+TGG 0.534695 4_2:+71293767 None:intergenic
AGCGGTGAAGGGTTGCAAGA+AGG 0.555388 4_2:-71293903 Msa0619980:CDS
TGGATCTTGTGTTTCAACAA+AGG 0.574409 4_2:+71293787 None:intergenic
CAACAAAGGCTCTCACAAGA+CGG 0.602126 4_2:+71293801 None:intergenic
AAGCAAAAGAATGGAAGAAG+CGG 0.630933 4_2:-71293921 None:intergenic
AGAATGGAAGAAGCGGTGAA+GGG 0.656513 4_2:-71293914 Msa0619980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATTTTTCTGATATTTA+AGG - chr4_2:71292860-71292879 Msa0619980:intron 10.0%
!!! ATAAATTTTTCTGATATTTA+AGG - chr4_2:71292860-71292879 Msa0619980:intron 10.0%
!!! TTACAAATTTTTGTATCATA+TGG - chr4_2:71292723-71292742 Msa0619980:intron 15.0%
!!! AACTGATATTTTACATTTTT+AGG - chr4_2:71292972-71292991 Msa0619980:intron 15.0%
!!! AAATAAATTTTTGTGCTTTT+TGG - chr4_2:71292999-71293018 Msa0619980:intron 15.0%
!!! AATAAATTTTTGTGCTTTTT+GGG - chr4_2:71293000-71293019 Msa0619980:intron 15.0%
!!! TAACAAGAATTACTATTTTT+AGG + chr4_2:71293542-71293561 None:intergenic 15.0%
!!! TTACAAATTTTTGTATCATA+TGG - chr4_2:71292723-71292742 Msa0619980:intron 15.0%
!!! AACTGATATTTTACATTTTT+AGG - chr4_2:71292972-71292991 Msa0619980:intron 15.0%
!!! AAATAAATTTTTGTGCTTTT+TGG - chr4_2:71292999-71293018 Msa0619980:intron 15.0%
!!! AATAAATTTTTGTGCTTTTT+GGG - chr4_2:71293000-71293019 Msa0619980:intron 15.0%
!!! TAACAAGAATTACTATTTTT+AGG + chr4_2:71293542-71293561 None:intergenic 15.0%
!! AAGATTGTAACAAAGATTTA+GGG - chr4_2:71292569-71292588 Msa0619980:intron 20.0%
!!! ATTTTTGTATCATATGGTAA+TGG - chr4_2:71292729-71292748 Msa0619980:intron 20.0%
!!! AGAAAAATTTATTTCTCAGT+TGG + chr4_2:71292852-71292871 None:intergenic 20.0%
!! AATAAAAAAACCTTCAACAT+CGG + chr4_2:71292938-71292957 None:intergenic 20.0%
!!! TATCATATTATCCTTTTTGA+AGG - chr4_2:71293714-71293733 Msa0619980:intron 20.0%
!! AAGATTGTAACAAAGATTTA+GGG - chr4_2:71292569-71292588 Msa0619980:intron 20.0%
!!! ATTTTTGTATCATATGGTAA+TGG - chr4_2:71292729-71292748 Msa0619980:intron 20.0%
!!! AGAAAAATTTATTTCTCAGT+TGG + chr4_2:71292852-71292871 None:intergenic 20.0%
!! AATAAAAAAACCTTCAACAT+CGG + chr4_2:71292938-71292957 None:intergenic 20.0%
!!! TATCATATTATCCTTTTTGA+AGG - chr4_2:71293714-71293733 Msa0619980:intron 20.0%
! GAAGATTGTAACAAAGATTT+AGG - chr4_2:71292568-71292587 Msa0619980:intron 25.0%
! AAATTATGTATGAAGAGGTT+AGG + chr4_2:71292691-71292710 None:intergenic 25.0%
! TGACTATACATGTGAAATAT+AGG + chr4_2:71292771-71292790 None:intergenic 25.0%
! AAACAATGAATTCATCATAG+AGG + chr4_2:71293169-71293188 None:intergenic 25.0%
! GAATATTTGAGCACTTTATT+TGG - chr4_2:71293754-71293773 Msa0619980:intron 25.0%
! TTTATTTGGACACACATATT+TGG - chr4_2:71293768-71293787 Msa0619980:intron 25.0%
! CTTACTTGATCACAAATATT+TGG + chr4_2:71293864-71293883 None:intergenic 25.0%
! GAAGATTGTAACAAAGATTT+AGG - chr4_2:71292568-71292587 Msa0619980:intron 25.0%
! AAATTATGTATGAAGAGGTT+AGG + chr4_2:71292691-71292710 None:intergenic 25.0%
! TGACTATACATGTGAAATAT+AGG + chr4_2:71292771-71292790 None:intergenic 25.0%
! AAACAATGAATTCATCATAG+AGG + chr4_2:71293169-71293188 None:intergenic 25.0%
! GAATATTTGAGCACTTTATT+TGG - chr4_2:71293754-71293773 Msa0619980:intron 25.0%
! TTTATTTGGACACACATATT+TGG - chr4_2:71293768-71293787 Msa0619980:intron 25.0%
! CTTACTTGATCACAAATATT+TGG + chr4_2:71293864-71293883 None:intergenic 25.0%
GACGTAAATTATGTATGAAG+AGG + chr4_2:71292696-71292715 None:intergenic 30.0%
!! TGTATCATATGGTAATGGTT+TGG - chr4_2:71292734-71292753 Msa0619980:intron 30.0%
ATACATGTGAAATATAGGTG+AGG + chr4_2:71292766-71292785 None:intergenic 30.0%
ATGATTACTTAGTGAACTTG+TGG + chr4_2:71293061-71293080 None:intergenic 30.0%
TTTGTCGGAAAATATCAAGA+TGG + chr4_2:71293116-71293135 None:intergenic 30.0%
TAAAACGAGAAGACAAAGAA+TGG - chr4_2:71293231-71293250 Msa0619980:intron 30.0%
! GAAAATTAGCTCTTCAACTT+TGG - chr4_2:71293358-71293377 Msa0619980:intron 30.0%
AAGCAATACTTCCTTCAAAA+AGG + chr4_2:71293728-71293747 None:intergenic 30.0%
!!! TTTTTGAAGGAAGTATTGCT+TGG - chr4_2:71293727-71293746 Msa0619980:intron 30.0%
CAGAGAGAAAGAAATAAAGA+GGG + chr4_2:71293896-71293915 None:intergenic 30.0%
TCAGAGAGAAAGAAATAAAG+AGG + chr4_2:71293897-71293916 None:intergenic 30.0%
GACGTAAATTATGTATGAAG+AGG + chr4_2:71292696-71292715 None:intergenic 30.0%
!! TGTATCATATGGTAATGGTT+TGG - chr4_2:71292734-71292753 Msa0619980:intron 30.0%
ATACATGTGAAATATAGGTG+AGG + chr4_2:71292766-71292785 None:intergenic 30.0%
ATGATTACTTAGTGAACTTG+TGG + chr4_2:71293061-71293080 None:intergenic 30.0%
TTTGTCGGAAAATATCAAGA+TGG + chr4_2:71293116-71293135 None:intergenic 30.0%
TAAAACGAGAAGACAAAGAA+TGG - chr4_2:71293231-71293250 Msa0619980:intron 30.0%
! GAAAATTAGCTCTTCAACTT+TGG - chr4_2:71293358-71293377 Msa0619980:intron 30.0%
AAGCAATACTTCCTTCAAAA+AGG + chr4_2:71293728-71293747 None:intergenic 30.0%
!!! TTTTTGAAGGAAGTATTGCT+TGG - chr4_2:71293727-71293746 Msa0619980:intron 30.0%
CAGAGAGAAAGAAATAAAGA+GGG + chr4_2:71293896-71293915 None:intergenic 30.0%
TCAGAGAGAAAGAAATAAAG+AGG + chr4_2:71293897-71293916 None:intergenic 30.0%
TGGATCTTGTGTTTCAACAA+AGG + chr4_2:71292653-71292672 None:intergenic 35.0%
AACACAAGATCCATCTTCTA+AGG - chr4_2:71292660-71292679 Msa0619980:intron 35.0%
TTAGGTAGTACCTTAGAAGA+TGG + chr4_2:71292673-71292692 None:intergenic 35.0%
TATTTCTCAGTTGGACAACT+AGG + chr4_2:71292843-71292862 None:intergenic 35.0%
!!! GATATTTTGACCGATGTTGA+AGG - chr4_2:71292925-71292944 Msa0619980:intron 35.0%
TGTCACGGTTGATTATTTGT+CGG + chr4_2:71293131-71293150 None:intergenic 35.0%
ATTGAAAAACACGACTGTCA+CGG + chr4_2:71293146-71293165 None:intergenic 35.0%
! ACAAGAGTGTACTGAAATAG+AGG - chr4_2:71293309-71293328 Msa0619980:intron 35.0%
!! CTCTTTTATTTGTCGTGTGT+CGG + chr4_2:71293400-71293419 None:intergenic 35.0%
TTGGACACACATATTTGGAA+AGG - chr4_2:71293773-71293792 Msa0619980:intron 35.0%
TGGACACACATATTTGGAAA+GGG - chr4_2:71293774-71293793 Msa0619980:intron 35.0%
! TTTCTTTCTCTCTGAAGATG+AGG - chr4_2:71293902-71293921 Msa0619980:CDS 35.0%
TGGATCTTGTGTTTCAACAA+AGG + chr4_2:71292653-71292672 None:intergenic 35.0%
AACACAAGATCCATCTTCTA+AGG - chr4_2:71292660-71292679 Msa0619980:intron 35.0%
TTAGGTAGTACCTTAGAAGA+TGG + chr4_2:71292673-71292692 None:intergenic 35.0%
TATTTCTCAGTTGGACAACT+AGG + chr4_2:71292843-71292862 None:intergenic 35.0%
!!! GATATTTTGACCGATGTTGA+AGG - chr4_2:71292925-71292944 Msa0619980:intron 35.0%
TGTCACGGTTGATTATTTGT+CGG + chr4_2:71293131-71293150 None:intergenic 35.0%
ATTGAAAAACACGACTGTCA+CGG + chr4_2:71293146-71293165 None:intergenic 35.0%
! ACAAGAGTGTACTGAAATAG+AGG - chr4_2:71293309-71293328 Msa0619980:intron 35.0%
!! CTCTTTTATTTGTCGTGTGT+CGG + chr4_2:71293400-71293419 None:intergenic 35.0%
TTGGACACACATATTTGGAA+AGG - chr4_2:71293773-71293792 Msa0619980:intron 35.0%
TGGACACACATATTTGGAAA+GGG - chr4_2:71293774-71293793 Msa0619980:intron 35.0%
! TTTCTTTCTCTCTGAAGATG+AGG - chr4_2:71293902-71293921 Msa0619980:CDS 35.0%
GTGTACTGAAATAGAGGAGA+CGG - chr4_2:71293315-71293334 Msa0619980:intron 40.0%
! GACGGTTTCTGAAAGTCATT+TGG - chr4_2:71293333-71293352 Msa0619980:intron 40.0%
CGACACACGACAAATAAAAG+AGG - chr4_2:71293398-71293417 Msa0619980:intron 40.0%
GTGTACTGAAATAGAGGAGA+CGG - chr4_2:71293315-71293334 Msa0619980:intron 40.0%
! GACGGTTTCTGAAAGTCATT+TGG - chr4_2:71293333-71293352 Msa0619980:intron 40.0%
CGACACACGACAAATAAAAG+AGG - chr4_2:71293398-71293417 Msa0619980:intron 40.0%
CAACAAAGGCTCTCACAAGA+CGG + chr4_2:71292639-71292658 None:intergenic 45.0%
CAACAAAGGCTCTCACAAGA+CGG + chr4_2:71292639-71292658 None:intergenic 45.0%
!! TATCATTTAAAAAAATTAAA+TGG + chr4_2:71292909-71292928 None:intergenic 5.0%
!! TATCATTTAAAAAAATTAAA+TGG + chr4_2:71292909-71292928 None:intergenic 5.0%
!! GGCTCTCACAAGACGGATTT+TGG + chr4_2:71292632-71292651 None:intergenic 50.0%
!! GGCTCTCACAAGACGGATTT+TGG + chr4_2:71292632-71292651 None:intergenic 50.0%
AGCGGTGAAGGGTTGCAAGA+AGG - chr4_2:71292534-71292553 Msa0619980:intron 55.0%
GCGGTGAAGGGTTGCAAGAA+GGG - chr4_2:71292535-71292554 Msa0619980:intron 55.0%
AGCGGTGAAGGGTTGCAAGA+AGG - chr4_2:71292534-71292553 Msa0619980:intron 55.0%
GCGGTGAAGGGTTGCAAGAA+GGG - chr4_2:71292535-71292554 Msa0619980:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 71292526 71293933 71292526 ID=Msa0619980;Name=Msa0619980
chr4_2 mRNA 71292526 71293933 71292526 ID=Msa0619980-mRNA-1;Parent=Msa0619980;Name=Msa0619980-mRNA-1;_AED=0.49;_eAED=0.52;_QI=0|0|0|0.5|1|1|2|0|56
chr4_2 exon 71293778 71293933 71293778 ID=Msa0619980-mRNA-1:exon:21113;Parent=Msa0619980-mRNA-1
chr4_2 exon 71292526 71292540 71292526 ID=Msa0619980-mRNA-1:exon:21112;Parent=Msa0619980-mRNA-1
chr4_2 CDS 71293778 71293933 71293778 ID=Msa0619980-mRNA-1:cds;Parent=Msa0619980-mRNA-1
chr4_2 CDS 71292526 71292540 71292526 ID=Msa0619980-mRNA-1:cds;Parent=Msa0619980-mRNA-1
Gene Sequence

>Msa0619980

ATGGAAGAAGCGGTGAAGGGTTGCAAGAAGGGAACAAGATTAGAAGATTGTAACAAAGATTTAGGGTATGCTGCAAACGATGTTGTTACAGAAACTGAACTGACCAAAATCCGTCTTGTGAGAGCCTTTGTTGAAACACAAGATCCATCTTCTAAGATGAGGAACAAGTAA

Protein sequence

>Msa0619980

MEEAVKGCKKGTRLEDCNKDLGYAANDVVTETELTKIRLVRAFVETQDPSSKMRNK*