AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0899760


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0899760 MtrunA17_Chr6g0485491 57.237 152 65 0 65 216 4 155 2.82e-58 181
Msa0899760 MtrunA17_Chr6g0485481 64.662 133 46 1 23 154 1 133 9.23e-58 179
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0899760 AT1G79310.1 27.807 187 102 6 8 172 2 177 3.47e-14 70.9

Find 44 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATGCTGACCATATAATATT+TGG 0.112509 6_1:+95122501 None:intergenic
AAGATGAAAATATTGATTAT+TGG 0.166905 6_1:-95123052 Msa0899760:CDS
GACTGACTCTTCATCCCTTT+TGG 0.219963 6_1:+95122616 None:intergenic
ACTATTAAAGCTCTCTTTGT+AGG 0.282700 6_1:+95123158 None:intergenic
GAGTCAGTCAGAGGTTCTTT+TGG 0.365713 6_1:-95122602 Msa0899760:CDS
AGTATCACCTGGCTTTGATA+TGG 0.372210 6_1:+95122953 None:intergenic
CAAAGAATCCAAATATTATA+TGG 0.376669 6_1:-95122509 Msa0899760:CDS
TTCTGTTCACATCTTCCAAA+AGG 0.402019 6_1:-95122631 Msa0899760:CDS
TTATCTCATCAGTGGCATAA+AGG 0.413830 6_1:+95122459 None:intergenic
TCTTGACACCGTCAGCCATT+TGG 0.425544 6_1:+95122717 None:intergenic
CTCATCAGTGGCATAAAGGT+TGG 0.445387 6_1:+95122463 None:intergenic
TTCATGATTGATGCTTGTTA+CGG 0.446394 6_1:-95122689 Msa0899760:CDS
ATTGATGCTTGTTACGGAGG+GGG 0.492034 6_1:-95122683 Msa0899760:CDS
TGATTGATGCTTGTTACGGA+GGG 0.498805 6_1:-95122685 Msa0899760:CDS
AGTTACCTTGTTGCAGCCAA+TGG 0.499386 6_1:-95122882 Msa0899760:CDS
TCATCAGTGGCATAAAGGTT+GGG 0.512161 6_1:+95122464 None:intergenic
TCTGTTCACATCTTCCAAAA+GGG 0.518903 6_1:-95122630 Msa0899760:CDS
ACCATGTAAAGGAGTTCCAT+TGG 0.542081 6_1:+95122866 None:intergenic
TTAATTACCATATCAAAGCC+AGG 0.542624 6_1:-95122960 Msa0899760:CDS
TTGAGGAAGTTACCATGTAA+AGG 0.542838 6_1:+95122855 None:intergenic
GTGGCATAAAGGTTGGGTAG+TGG 0.543095 6_1:+95122470 None:intergenic
GACAGAAACGATGGAGGACC+TGG 0.548548 6_1:-95123026 Msa0899760:CDS
ATGATTGATGCTTGTTACGG+AGG 0.558998 6_1:-95122686 Msa0899760:CDS
CAAATATTATATGGTCAGCA+TGG 0.561520 6_1:-95122500 Msa0899760:CDS
GCCAATGGAACTCCTTTACA+TGG 0.561635 6_1:-95122867 Msa0899760:intron
TTGATGCTTGTTACGGAGGG+GGG 0.576592 6_1:-95122682 Msa0899760:CDS
TCGGAATATGTATTGAGTGT+AGG 0.587606 6_1:+95123116 None:intergenic
GATTGATGCTTGTTACGGAG+GGG 0.589936 6_1:-95122684 Msa0899760:CDS
TAGAATCAAGTTAAGAGAGT+GGG 0.593682 6_1:-95122416 Msa0899760:three_prime_UTR
ATGTGAACAGAACAACTTTG+TGG 0.596681 6_1:+95122642 None:intergenic
GATTGTGTTAATGATTACAC+TGG 0.597418 6_1:-95122554 Msa0899760:CDS
CATGGTAACTATCAACAAAG+AGG 0.608307 6_1:-95122909 Msa0899760:CDS
AAAAGTTTGCTAATAAACCG+TGG 0.617749 6_1:-95123080 Msa0899760:CDS
ATAGAATCAAGTTAAGAGAG+TGG 0.627109 6_1:-95122417 Msa0899760:exon
ATGGTAACTATCAACAAAGA+GGG 0.636257 6_1:-95122908 Msa0899760:CDS
AGGGATGAAGAGTCAGTCAG+AGG 0.636514 6_1:-95122611 Msa0899760:CDS
GAGTTCCATTGGCTGCAACA+AGG 0.637602 6_1:+95122877 None:intergenic
ACACTCAATACATATTCCGA+TGG 0.646069 6_1:-95123113 Msa0899760:CDS
TATTGGCAAGACAGAAACGA+TGG 0.655578 6_1:-95123035 Msa0899760:CDS
TCAGCATCAATAAGGAAACC+AGG 0.656233 6_1:+95123008 None:intergenic
TGAACAGAACAACTTTGTGG+TGG 0.661409 6_1:+95122645 None:intergenic
GTGTTAGACCAAATGGCTGA+CGG 0.670017 6_1:-95122725 Msa0899760:CDS
GAACAGAACAACTTTGTGGT+GGG 0.698434 6_1:+95122646 None:intergenic
TGGCAAGACAGAAACGATGG+AGG 0.703781 6_1:-95123032 Msa0899760:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGATGAAAATATTGATTAT+TGG - chr6_1:95122500-95122519 Msa0899760:CDS 15.0%
!!! AAGATGAAAATATTGATTAT+TGG - chr6_1:95122500-95122519 Msa0899760:CDS 15.0%
!!! TATTTTCATCTTTAAATCCA+CGG + chr6_1:95122492-95122511 None:intergenic 20.0%
!!! ACTTTATTTTTTCATTTCAG+TGG - chr6_1:95122619-95122638 Msa0899760:CDS 20.0%
!! CAAAGAATCCAAATATTATA+TGG - chr6_1:95123043-95123062 Msa0899760:CDS 20.0%
!!! TATTTTCATCTTTAAATCCA+CGG + chr6_1:95122492-95122511 None:intergenic 20.0%
!!! ACTTTATTTTTTCATTTCAG+TGG - chr6_1:95122619-95122638 Msa0899760:CDS 20.0%
!! CAAAGAATCCAAATATTATA+TGG - chr6_1:95123043-95123062 Msa0899760:CDS 20.0%
!! TGAAAAAATAAAGTATCACC+TGG + chr6_1:95122613-95122632 None:intergenic 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG - chr6_1:95122820-95122839 Msa0899760:intron 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG + chr6_1:95123104-95123123 None:intergenic 25.0%
!! TGAAAAAATAAAGTATCACC+TGG + chr6_1:95122613-95122632 None:intergenic 25.0%
!!! TAAAAAAGTGTTAGACCAAA+TGG - chr6_1:95122820-95122839 Msa0899760:intron 25.0%
!!! AGAATTTTTTATCTCATCAG+TGG + chr6_1:95123104-95123123 None:intergenic 25.0%
ACTATTAAAGCTCTCTTTGT+AGG + chr6_1:95122397-95122416 None:intergenic 30.0%
!! AAAAGTTTGCTAATAAACCG+TGG - chr6_1:95122472-95122491 Msa0899760:CDS 30.0%
! GTATTTTGTCAGCATCAATA+AGG + chr6_1:95122555-95122574 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG - chr6_1:95122592-95122611 Msa0899760:CDS 30.0%
!!! TTTTTTCATTTCAGTGGACA+TGG - chr6_1:95122625-95122644 Msa0899760:CDS 30.0%
ATGGTAACTATCAACAAAGA+GGG - chr6_1:95122644-95122663 Msa0899760:CDS 30.0%
TATTTGTGATTCTCAATGCA+TGG - chr6_1:95122748-95122767 Msa0899760:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG - chr6_1:95122863-95122882 Msa0899760:intron 30.0%
GATTGTGTTAATGATTACAC+TGG - chr6_1:95122998-95123017 Msa0899760:CDS 30.0%
CATGCTGACCATATAATATT+TGG + chr6_1:95123054-95123073 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG - chr6_1:95123052-95123071 Msa0899760:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG - chr6_1:95123135-95123154 Msa0899760:CDS 30.0%
TAGAATCAAGTTAAGAGAGT+GGG - chr6_1:95123136-95123155 Msa0899760:CDS 30.0%
ACTATTAAAGCTCTCTTTGT+AGG + chr6_1:95122397-95122416 None:intergenic 30.0%
!! AAAAGTTTGCTAATAAACCG+TGG - chr6_1:95122472-95122491 Msa0899760:CDS 30.0%
! GTATTTTGTCAGCATCAATA+AGG + chr6_1:95122555-95122574 None:intergenic 30.0%
TTAATTACCATATCAAAGCC+AGG - chr6_1:95122592-95122611 Msa0899760:CDS 30.0%
!!! TTTTTTCATTTCAGTGGACA+TGG - chr6_1:95122625-95122644 Msa0899760:CDS 30.0%
ATGGTAACTATCAACAAAGA+GGG - chr6_1:95122644-95122663 Msa0899760:CDS 30.0%
TATTTGTGATTCTCAATGCA+TGG - chr6_1:95122748-95122767 Msa0899760:intron 30.0%
! TTCATGATTGATGCTTGTTA+CGG - chr6_1:95122863-95122882 Msa0899760:intron 30.0%
GATTGTGTTAATGATTACAC+TGG - chr6_1:95122998-95123017 Msa0899760:CDS 30.0%
CATGCTGACCATATAATATT+TGG + chr6_1:95123054-95123073 None:intergenic 30.0%
CAAATATTATATGGTCAGCA+TGG - chr6_1:95123052-95123071 Msa0899760:CDS 30.0%
ATAGAATCAAGTTAAGAGAG+TGG - chr6_1:95123135-95123154 Msa0899760:CDS 30.0%
TAGAATCAAGTTAAGAGAGT+GGG - chr6_1:95123136-95123155 Msa0899760:CDS 30.0%
TCGGAATATGTATTGAGTGT+AGG + chr6_1:95122439-95122458 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG - chr6_1:95122439-95122458 Msa0899760:CDS 35.0%
! ACTTTTTATCTTCGCACCAT+CGG + chr6_1:95122458-95122477 None:intergenic 35.0%
CATGGTAACTATCAACAAAG+AGG - chr6_1:95122643-95122662 Msa0899760:CDS 35.0%
TTGAGGAAGTTACCATGTAA+AGG + chr6_1:95122700-95122719 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG + chr6_1:95122717-95122736 None:intergenic 35.0%
ATGTGAACAGAACAACTTTG+TGG + chr6_1:95122913-95122932 None:intergenic 35.0%
TTCTGTTCACATCTTCCAAA+AGG - chr6_1:95122921-95122940 Msa0899760:CDS 35.0%
TCTGTTCACATCTTCCAAAA+GGG - chr6_1:95122922-95122941 Msa0899760:CDS 35.0%
TTATCTCATCAGTGGCATAA+AGG + chr6_1:95123096-95123115 None:intergenic 35.0%
TCGGAATATGTATTGAGTGT+AGG + chr6_1:95122439-95122458 None:intergenic 35.0%
ACACTCAATACATATTCCGA+TGG - chr6_1:95122439-95122458 Msa0899760:CDS 35.0%
! ACTTTTTATCTTCGCACCAT+CGG + chr6_1:95122458-95122477 None:intergenic 35.0%
CATGGTAACTATCAACAAAG+AGG - chr6_1:95122643-95122662 Msa0899760:CDS 35.0%
TTGAGGAAGTTACCATGTAA+AGG + chr6_1:95122700-95122719 None:intergenic 35.0%
TATTAGCATGAGATGTGTTG+AGG + chr6_1:95122717-95122736 None:intergenic 35.0%
ATGTGAACAGAACAACTTTG+TGG + chr6_1:95122913-95122932 None:intergenic 35.0%
TTCTGTTCACATCTTCCAAA+AGG - chr6_1:95122921-95122940 Msa0899760:CDS 35.0%
TCTGTTCACATCTTCCAAAA+GGG - chr6_1:95122922-95122941 Msa0899760:CDS 35.0%
TTATCTCATCAGTGGCATAA+AGG + chr6_1:95123096-95123115 None:intergenic 35.0%
TATTGGCAAGACAGAAACGA+TGG - chr6_1:95122517-95122536 Msa0899760:CDS 40.0%
TCAGCATCAATAAGGAAACC+AGG + chr6_1:95122547-95122566 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG + chr6_1:95122602-95122621 None:intergenic 40.0%
ACCATGTAAAGGAGTTCCAT+TGG + chr6_1:95122689-95122708 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG - chr6_1:95122866-95122885 Msa0899760:intron 40.0%
! TGATTGATGCTTGTTACGGA+GGG - chr6_1:95122867-95122886 Msa0899760:intron 40.0%
GAACAGAACAACTTTGTGGT+GGG + chr6_1:95122909-95122928 None:intergenic 40.0%
TGAACAGAACAACTTTGTGG+TGG + chr6_1:95122910-95122929 None:intergenic 40.0%
TCATCAGTGGCATAAAGGTT+GGG + chr6_1:95123091-95123110 None:intergenic 40.0%
TATTGGCAAGACAGAAACGA+TGG - chr6_1:95122517-95122536 Msa0899760:CDS 40.0%
TCAGCATCAATAAGGAAACC+AGG + chr6_1:95122547-95122566 None:intergenic 40.0%
!! AGTATCACCTGGCTTTGATA+TGG + chr6_1:95122602-95122621 None:intergenic 40.0%
ACCATGTAAAGGAGTTCCAT+TGG + chr6_1:95122689-95122708 None:intergenic 40.0%
! ATGATTGATGCTTGTTACGG+AGG - chr6_1:95122866-95122885 Msa0899760:intron 40.0%
! TGATTGATGCTTGTTACGGA+GGG - chr6_1:95122867-95122886 Msa0899760:intron 40.0%
GAACAGAACAACTTTGTGGT+GGG + chr6_1:95122909-95122928 None:intergenic 40.0%
TGAACAGAACAACTTTGTGG+TGG + chr6_1:95122910-95122929 None:intergenic 40.0%
TCATCAGTGGCATAAAGGTT+GGG + chr6_1:95123091-95123110 None:intergenic 40.0%
AGTTACCTTGTTGCAGCCAA+TGG - chr6_1:95122670-95122689 Msa0899760:CDS 45.0%
GCCAATGGAACTCCTTTACA+TGG - chr6_1:95122685-95122704 Msa0899760:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG - chr6_1:95122788-95122807 Msa0899760:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG - chr6_1:95122827-95122846 Msa0899760:intron 45.0%
! GATTGATGCTTGTTACGGAG+GGG - chr6_1:95122868-95122887 Msa0899760:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG - chr6_1:95122869-95122888 Msa0899760:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG + chr6_1:95122939-95122958 None:intergenic 45.0%
! GAGTCAGTCAGAGGTTCTTT+TGG - chr6_1:95122950-95122969 Msa0899760:CDS 45.0%
CTCATCAGTGGCATAAAGGT+TGG + chr6_1:95123092-95123111 None:intergenic 45.0%
AGTTACCTTGTTGCAGCCAA+TGG - chr6_1:95122670-95122689 Msa0899760:CDS 45.0%
GCCAATGGAACTCCTTTACA+TGG - chr6_1:95122685-95122704 Msa0899760:CDS 45.0%
! ATTTGCTACGTGACTTGTGC+AGG - chr6_1:95122788-95122807 Msa0899760:intron 45.0%
GTGTTAGACCAAATGGCTGA+CGG - chr6_1:95122827-95122846 Msa0899760:intron 45.0%
! GATTGATGCTTGTTACGGAG+GGG - chr6_1:95122868-95122887 Msa0899760:CDS 45.0%
! ATTGATGCTTGTTACGGAGG+GGG - chr6_1:95122869-95122888 Msa0899760:CDS 45.0%
!! GACTGACTCTTCATCCCTTT+TGG + chr6_1:95122939-95122958 None:intergenic 45.0%
! GAGTCAGTCAGAGGTTCTTT+TGG - chr6_1:95122950-95122969 Msa0899760:CDS 45.0%
CTCATCAGTGGCATAAAGGT+TGG + chr6_1:95123092-95123111 None:intergenic 45.0%
TGGCAAGACAGAAACGATGG+AGG - chr6_1:95122520-95122539 Msa0899760:CDS 50.0%
! GAGTTCCATTGGCTGCAACA+AGG + chr6_1:95122678-95122697 None:intergenic 50.0%
TCTTGACACCGTCAGCCATT+TGG + chr6_1:95122838-95122857 None:intergenic 50.0%
! TTGATGCTTGTTACGGAGGG+GGG - chr6_1:95122870-95122889 Msa0899760:CDS 50.0%
AGGGATGAAGAGTCAGTCAG+AGG - chr6_1:95122941-95122960 Msa0899760:CDS 50.0%
GTGGCATAAAGGTTGGGTAG+TGG + chr6_1:95123085-95123104 None:intergenic 50.0%
TGGCAAGACAGAAACGATGG+AGG - chr6_1:95122520-95122539 Msa0899760:CDS 50.0%
! GAGTTCCATTGGCTGCAACA+AGG + chr6_1:95122678-95122697 None:intergenic 50.0%
TCTTGACACCGTCAGCCATT+TGG + chr6_1:95122838-95122857 None:intergenic 50.0%
! TTGATGCTTGTTACGGAGGG+GGG - chr6_1:95122870-95122889 Msa0899760:CDS 50.0%
AGGGATGAAGAGTCAGTCAG+AGG - chr6_1:95122941-95122960 Msa0899760:CDS 50.0%
GTGGCATAAAGGTTGGGTAG+TGG + chr6_1:95123085-95123104 None:intergenic 50.0%
GACAGAAACGATGGAGGACC+TGG - chr6_1:95122526-95122545 Msa0899760:CDS 55.0%
GACAGAAACGATGGAGGACC+TGG - chr6_1:95122526-95122545 Msa0899760:CDS 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 95122376 95123198 95122376 ID=Msa0899760;Name=Msa0899760
chr6_1 mRNA 95122376 95123198 95122376 ID=Msa0899760-mRNA-1;Parent=Msa0899760;Name=Msa0899760-mRNA-1;_AED=0.05;_eAED=0.05;_QI=0|1|0.5|1|1|1|2|60|219
chr6_1 exon 95122376 95122764 95122376 ID=Msa0899760-mRNA-1:exon:16338;Parent=Msa0899760-mRNA-1
chr6_1 exon 95122868 95123198 95122868 ID=Msa0899760-mRNA-1:exon:16337;Parent=Msa0899760-mRNA-1
chr6_1 CDS 95122868 95123198 95122868 ID=Msa0899760-mRNA-1:cds;Parent=Msa0899760-mRNA-1
chr6_1 CDS 95122436 95122764 95122436 ID=Msa0899760-mRNA-1:cds;Parent=Msa0899760-mRNA-1
chr6_1 three_prime_UTR 95122376 95122435 95122376 ID=Msa0899760-mRNA-1:three_prime_utr;Parent=Msa0899760-mRNA-1
Gene Sequence

>Msa0899760

TTGTACAGCAACAATTCTCCTACAAAGAGAGCTTTAATAGTCAATTTACAATTTCGAGAACCTACACTCAATACATATTCCGATGGTGCGAAGATAAAAAGTTTGCTAATAAACCGTGGATTTAAAGATGAAAATATTGATTATTGGCAAGACAGAAACGATGGAGGACCTGGTTTCCTTATTGATGCTGACAAAATACGTAATAGATTACATGATTTAATTACCATATCAAAGCCAGGTGATACTTTATTTTTTCATTTCAGTGGACATGGTAACTATCAACAAAGAGGGAGAAGTTACCTTGTTGCAGCCAATGGAACTCCTTTACATGGTTATGAATTTAAAAAAGTGTTAGACCAAATGGCTGACGGTGTCAAGATAATTTTCATGATTGATGCTTGTTACGGAGGGGGGTTTATTGAACTAGCCCACCACAAAGTTGTTCTGTTCACATCTTCCAAAAGGGATGAAGAGTCAGTCAGAGGTTCTTTTGGTTCTGTGTTTACGAATGCGTTTGTTGATTGTGTTAATGATTACACTGGAATAACGCATGATGAATTGATACAAAGAATCCAAATATTATATGGTCAGCATGGAAGCAAACCACTACCCAACCTTTATGCCACTGATGAGATAAAAAATTCTATTTTTATTCTATAG

Protein sequence

>Msa0899760

LYSNNSPTKRALIVNLQFREPTLNTYSDGAKIKSLLINRGFKDENIDYWQDRNDGGPGFLIDADKIRNRLHDLITISKPGDTLFFHFSGHGNYQQRGRSYLVAANGTPLHGYEFKKVLDQMADGVKIIFMIDACYGGGFIELAHHKVVLFTSSKRDEESVRGSFGSVFTNAFVDCVNDYTGITHDELIQRIQILYGQHGSKPLPNLYATDEIKNSIFIL*