AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0385840


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0385840 MtrunA17_Chr8g0350831 100.000 78 0 0 1 78 1 78 3.36e-50 164
Msa0385840 MtrunA17_Chr1g0199481 50.980 51 25 0 21 71 82 132 3.71e-12 62.4
Msa0385840 MtrunA17_Chr4g0028631 49.020 51 26 0 21 71 62 112 6.75e-12 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0385840 AT1G01910.3 89.041 73 8 0 6 78 5 77 6.02e-30 110
Msa0385840 AT1G01910.1 89.041 73 8 0 6 78 5 77 1.11e-29 110
Msa0385840 AT1G01910.4 89.041 73 8 0 6 78 5 77 1.11e-29 110
Msa0385840 AT1G01910.2 89.041 73 8 0 6 78 5 77 1.11e-29 110
Msa0385840 AT3G10350.1 50.980 51 25 0 21 71 88 138 4.28e-12 62.8
Msa0385840 AT3G10350.2 50.980 51 25 0 21 71 119 169 6.48e-12 62.4

Find 33 sgRNAs with CRISPR-Local

Find 118 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACCAACGAAAACCCACTTTA+AGG 0.186644 3_1:-89560944 None:intergenic
AAAACCCCTACTTTGGTTAA+TGG 0.187000 3_1:+89561102 Msa0385840:CDS
CTGCCGCAAAAGAATGTTTC+TGG 0.208035 3_1:+89561621 Msa0385840:three_prime_UTR
GGTGTTGAGATGAATGTTTC+TGG 0.222340 3_1:+89561532 Msa0385840:CDS
TGCGGCAGTAACCATTTCTT+TGG 0.282598 3_1:-89561606 None:intergenic
ACTTTAAGGTTTCTTGTTCT+AGG 0.289287 3_1:-89560930 None:intergenic
TGTAATGTTCCTTCTGGTAA+TGG 0.356987 3_1:-89560901 None:intergenic
TGTGAGGAAGGAAATGAAAA+TGG 0.357426 3_1:+89561471 Msa0385840:CDS
TGGAGGTCGTATGGTTTGAA+TGG 0.385540 3_1:+89561491 Msa0385840:CDS
TGCTGGATTTGTGAACTTTG+TGG 0.399664 3_1:+89561439 Msa0385840:CDS
TGGATTTGTGTTGTGAAGAT+TGG 0.419456 3_1:+89561511 Msa0385840:CDS
GCTGGATTTGTGAACTTTGT+GGG 0.421956 3_1:+89561440 Msa0385840:CDS
TGGGAGAGATATTGTGAGGA+AGG 0.428937 3_1:+89561459 Msa0385840:CDS
TAGAACAAGAAACCTTAAAG+TGG 0.452112 3_1:+89560932 Msa0385840:CDS
AGGGATTTGATCCAAAGAAA+TGG 0.461576 3_1:+89561595 Msa0385840:three_prime_UTR
GAGAAACCATTAACCAAAGT+AGG 0.484214 3_1:-89561108 None:intergenic
AGAAACCATTAACCAAAGTA+GGG 0.499369 3_1:-89561107 None:intergenic
TGGTAATGGTTGATCTTCCA+TGG 0.510241 3_1:-89560887 None:intergenic
AAATGAAAATGGAGGTCGTA+TGG 0.532532 3_1:+89561482 Msa0385840:CDS
AAATTGGTTTAGTGTTCTTG+AGG 0.543875 3_1:+89561559 Msa0385840:exon
GTTGGTGGCAAAGGTGGTGT+TGG 0.544218 3_1:+89560961 Msa0385840:CDS
ACAAAGTTCACAAATCCAGC+AGG 0.583190 3_1:-89561437 None:intergenic
AGAACAAGAAACCTTAAAGT+GGG 0.586075 3_1:+89560933 Msa0385840:CDS
GCATCGCTAAGATTATGAGC+AGG 0.586661 3_1:-89561060 None:intergenic
GATCTATGTTGTGTGCGTGT+TGG 0.599575 3_1:+89561387 Msa0385840:CDS
GCTAAGATTATGAGCAGGAT+CGG 0.605307 3_1:-89561055 None:intergenic
TTTGTGGGAGAGATATTGTG+AGG 0.612058 3_1:+89561455 Msa0385840:CDS
AAGAACGAACAGAAGCGAGA+AGG 0.622461 3_1:-89561014 None:intergenic
GAAACCATTAACCAAAGTAG+GGG 0.628988 3_1:-89561106 None:intergenic
ATCACAGCACAACATTCTGT+CGG 0.629252 3_1:-89561367 None:intergenic
GAAGATCAACCATTACCAGA+AGG 0.651887 3_1:+89560892 Msa0385840:CDS
GAGGAAGGAAATGAAAATGG+AGG 0.668970 3_1:+89561474 Msa0385840:CDS
TGCGTGTTGGTAAATCACTG+TGG 0.798281 3_1:+89561400 Msa0385840:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATAGAAAATTTCAAAAA+GGG - chr3_1:89561177-89561196 None:intergenic 10.0%
!! AAAAATAGAAAATTTCAAAA+AGG - chr3_1:89561178-89561197 None:intergenic 10.0%
!! AAATTCATAAATTAACAAAA+GGG - chr3_1:89561248-89561267 None:intergenic 10.0%
!! AAAATAGAAAATTTCAAAAA+GGG - chr3_1:89561177-89561196 None:intergenic 10.0%
!! AAAAATAGAAAATTTCAAAA+AGG - chr3_1:89561178-89561197 None:intergenic 10.0%
!! AAATTCATAAATTAACAAAA+GGG - chr3_1:89561248-89561267 None:intergenic 10.0%
!! AATTCATAAATTAACAAAAG+GGG - chr3_1:89561247-89561266 None:intergenic 15.0%
!! GAAATTCATAAATTAACAAA+AGG - chr3_1:89561249-89561268 None:intergenic 15.0%
!! AAAATCAAAAATTGACAAAA+GGG - chr3_1:89561279-89561298 None:intergenic 15.0%
!! AAAAATCAAAAATTGACAAA+AGG - chr3_1:89561280-89561299 None:intergenic 15.0%
!! TTAACAAAATTTAACAGTTT+AGG - chr3_1:89561308-89561327 None:intergenic 15.0%
!! AATTCATAAATTAACAAAAG+GGG - chr3_1:89561247-89561266 None:intergenic 15.0%
!! GAAATTCATAAATTAACAAA+AGG - chr3_1:89561249-89561268 None:intergenic 15.0%
!! AAAATCAAAAATTGACAAAA+GGG - chr3_1:89561279-89561298 None:intergenic 15.0%
!! AAAAATCAAAAATTGACAAA+AGG - chr3_1:89561280-89561299 None:intergenic 15.0%
!! TTAACAAAATTTAACAGTTT+AGG - chr3_1:89561308-89561327 None:intergenic 15.0%
!!! CTGTTAAATTTTGTTAATTG+TGG + chr3_1:89561311-89561330 Msa0385840:intron 20.0%
!!! CTGTTAAATTTTGTTAATTG+TGG + chr3_1:89561311-89561330 Msa0385840:intron 20.0%
!!! GAATGTTTCTGGAAAAAAAT+TGG + chr3_1:89561543-89561562 Msa0385840:CDS 25.0%
!!! TTGAGGTTTTGAAAGAAAAA+GGG + chr3_1:89561576-89561595 Msa0385840:three_prime_UTR 25.0%
!!! GAATGTTTCTGGAAAAAAAT+TGG + chr3_1:89561543-89561562 Msa0385840:CDS 25.0%
!!! GAATGTTTCTGGAAAAAAAT+TGG + chr3_1:89561543-89561562 Msa0385840:CDS 25.0%
!!! TTGAGGTTTTGAAAGAAAAA+GGG + chr3_1:89561576-89561595 Msa0385840:three_prime_UTR 25.0%
!!! GAATGTTTCTGGAAAAAAAT+TGG + chr3_1:89561543-89561562 Msa0385840:CDS 25.0%
! ATGTTTTGTAATGTTCCTTC+TGG - chr3_1:89560910-89560929 None:intergenic 30.0%
!! ACTTTAAGGTTTCTTGTTCT+AGG - chr3_1:89560933-89560952 None:intergenic 30.0%
TAGAACAAGAAACCTTAAAG+TGG + chr3_1:89560932-89560951 Msa0385840:CDS 30.0%
AGAACAAGAAACCTTAAAGT+GGG + chr3_1:89560933-89560952 Msa0385840:CDS 30.0%
AGAAACCATTAACCAAAGTA+GGG - chr3_1:89561110-89561129 None:intergenic 30.0%
GGATCTGTCAATAATAAAAG+GGG - chr3_1:89561349-89561368 None:intergenic 30.0%
CGGATCTGTCAATAATAAAA+GGG - chr3_1:89561350-89561369 None:intergenic 30.0%
TCGGATCTGTCAATAATAAA+AGG - chr3_1:89561351-89561370 None:intergenic 30.0%
! AAATTGGTTTAGTGTTCTTG+AGG + chr3_1:89561559-89561578 Msa0385840:exon 30.0%
!!! CTTGAGGTTTTGAAAGAAAA+AGG + chr3_1:89561575-89561594 Msa0385840:three_prime_UTR 30.0%
! TTTCCAGAAACATTCTTTTG+CGG - chr3_1:89561627-89561646 None:intergenic 30.0%
! ATGTTTTGTAATGTTCCTTC+TGG - chr3_1:89560910-89560929 None:intergenic 30.0%
!! ACTTTAAGGTTTCTTGTTCT+AGG - chr3_1:89560933-89560952 None:intergenic 30.0%
TAGAACAAGAAACCTTAAAG+TGG + chr3_1:89560932-89560951 Msa0385840:CDS 30.0%
AGAACAAGAAACCTTAAAGT+GGG + chr3_1:89560933-89560952 Msa0385840:CDS 30.0%
AGAAACCATTAACCAAAGTA+GGG - chr3_1:89561110-89561129 None:intergenic 30.0%
GGATCTGTCAATAATAAAAG+GGG - chr3_1:89561349-89561368 None:intergenic 30.0%
CGGATCTGTCAATAATAAAA+GGG - chr3_1:89561350-89561369 None:intergenic 30.0%
TCGGATCTGTCAATAATAAA+AGG - chr3_1:89561351-89561370 None:intergenic 30.0%
! AAATTGGTTTAGTGTTCTTG+AGG + chr3_1:89561559-89561578 Msa0385840:exon 30.0%
!!! CTTGAGGTTTTGAAAGAAAA+AGG + chr3_1:89561575-89561594 Msa0385840:three_prime_UTR 30.0%
! TTTCCAGAAACATTCTTTTG+CGG - chr3_1:89561627-89561646 None:intergenic 30.0%
TGTAATGTTCCTTCTGGTAA+TGG - chr3_1:89560904-89560923 None:intergenic 35.0%
ATTCACAAAAACCCCTACTT+TGG + chr3_1:89561095-89561114 Msa0385840:CDS 35.0%
AAAACCCCTACTTTGGTTAA+TGG + chr3_1:89561102-89561121 Msa0385840:CDS 35.0%
GAAACCATTAACCAAAGTAG+GGG - chr3_1:89561109-89561128 None:intergenic 35.0%
GAGAAACCATTAACCAAAGT+AGG - chr3_1:89561111-89561130 None:intergenic 35.0%
TTTCTCCAATCTCTATGCTA+TGG + chr3_1:89561125-89561144 Msa0385840:intron 35.0%
ACAAACCATAGCATAGAGAT+TGG - chr3_1:89561133-89561152 None:intergenic 35.0%
! GTGTTGAATTTTGCTTCTTG+TGG + chr3_1:89561209-89561228 Msa0385840:intron 35.0%
TGTGAGGAAGGAAATGAAAA+TGG + chr3_1:89561471-89561490 Msa0385840:CDS 35.0%
AAATGAAAATGGAGGTCGTA+TGG + chr3_1:89561482-89561501 Msa0385840:CDS 35.0%
TGGATTTGTGTTGTGAAGAT+TGG + chr3_1:89561511-89561530 Msa0385840:CDS 35.0%
AGGGATTTGATCCAAAGAAA+TGG + chr3_1:89561595-89561614 Msa0385840:three_prime_UTR 35.0%
TGTAATGTTCCTTCTGGTAA+TGG - chr3_1:89560904-89560923 None:intergenic 35.0%
ATTCACAAAAACCCCTACTT+TGG + chr3_1:89561095-89561114 Msa0385840:CDS 35.0%
AAAACCCCTACTTTGGTTAA+TGG + chr3_1:89561102-89561121 Msa0385840:CDS 35.0%
GAAACCATTAACCAAAGTAG+GGG - chr3_1:89561109-89561128 None:intergenic 35.0%
GAGAAACCATTAACCAAAGT+AGG - chr3_1:89561111-89561130 None:intergenic 35.0%
TTTCTCCAATCTCTATGCTA+TGG + chr3_1:89561125-89561144 Msa0385840:intron 35.0%
ACAAACCATAGCATAGAGAT+TGG - chr3_1:89561133-89561152 None:intergenic 35.0%
! GTGTTGAATTTTGCTTCTTG+TGG + chr3_1:89561209-89561228 Msa0385840:intron 35.0%
TGTGAGGAAGGAAATGAAAA+TGG + chr3_1:89561471-89561490 Msa0385840:CDS 35.0%
AAATGAAAATGGAGGTCGTA+TGG + chr3_1:89561482-89561501 Msa0385840:CDS 35.0%
TGGATTTGTGTTGTGAAGAT+TGG + chr3_1:89561511-89561530 Msa0385840:CDS 35.0%
AGGGATTTGATCCAAAGAAA+TGG + chr3_1:89561595-89561614 Msa0385840:three_prime_UTR 35.0%
GAAGATCAACCATTACCAGA+AGG + chr3_1:89560892-89560911 Msa0385840:CDS 40.0%
!! ACCTTAAAGTGGGTTTTCGT+TGG + chr3_1:89560943-89560962 Msa0385840:CDS 40.0%
ACCAACGAAAACCCACTTTA+AGG - chr3_1:89560947-89560966 None:intergenic 40.0%
!! TTAAAGTGGGTTTTCGTTGG+TGG + chr3_1:89560946-89560965 Msa0385840:CDS 40.0%
GCTAAGATTATGAGCAGGAT+CGG - chr3_1:89561058-89561077 None:intergenic 40.0%
ATCACAGCACAACATTCTGT+CGG - chr3_1:89561370-89561389 None:intergenic 40.0%
ACAAAGTTCACAAATCCAGC+AGG - chr3_1:89561440-89561459 None:intergenic 40.0%
TGCTGGATTTGTGAACTTTG+TGG + chr3_1:89561439-89561458 Msa0385840:CDS 40.0%
GCTGGATTTGTGAACTTTGT+GGG + chr3_1:89561440-89561459 Msa0385840:CDS 40.0%
TTTGTGGGAGAGATATTGTG+AGG + chr3_1:89561455-89561474 Msa0385840:CDS 40.0%
GAGGAAGGAAATGAAAATGG+AGG + chr3_1:89561474-89561493 Msa0385840:CDS 40.0%
! GGTGTTGAGATGAATGTTTC+TGG + chr3_1:89561532-89561551 Msa0385840:CDS 40.0%
GAAGATCAACCATTACCAGA+AGG + chr3_1:89560892-89560911 Msa0385840:CDS 40.0%
!! ACCTTAAAGTGGGTTTTCGT+TGG + chr3_1:89560943-89560962 Msa0385840:CDS 40.0%
ACCAACGAAAACCCACTTTA+AGG - chr3_1:89560947-89560966 None:intergenic 40.0%
!! TTAAAGTGGGTTTTCGTTGG+TGG + chr3_1:89560946-89560965 Msa0385840:CDS 40.0%
GCTAAGATTATGAGCAGGAT+CGG - chr3_1:89561058-89561077 None:intergenic 40.0%
ATCACAGCACAACATTCTGT+CGG - chr3_1:89561370-89561389 None:intergenic 40.0%
ACAAAGTTCACAAATCCAGC+AGG - chr3_1:89561440-89561459 None:intergenic 40.0%
TGCTGGATTTGTGAACTTTG+TGG + chr3_1:89561439-89561458 Msa0385840:CDS 40.0%
GCTGGATTTGTGAACTTTGT+GGG + chr3_1:89561440-89561459 Msa0385840:CDS 40.0%
TTTGTGGGAGAGATATTGTG+AGG + chr3_1:89561455-89561474 Msa0385840:CDS 40.0%
GAGGAAGGAAATGAAAATGG+AGG + chr3_1:89561474-89561493 Msa0385840:CDS 40.0%
! GGTGTTGAGATGAATGTTTC+TGG + chr3_1:89561532-89561551 Msa0385840:CDS 40.0%
AAGAACGAACAGAAGCGAGA+AGG - chr3_1:89561017-89561036 None:intergenic 45.0%
GCATCGCTAAGATTATGAGC+AGG - chr3_1:89561063-89561082 None:intergenic 45.0%
GATCTATGTTGTGTGCGTGT+TGG + chr3_1:89561387-89561406 Msa0385840:CDS 45.0%
! TGCGTGTTGGTAAATCACTG+TGG + chr3_1:89561400-89561419 Msa0385840:CDS 45.0%
!!! GTAGTCGTTTTTTAGCCTGC+TGG + chr3_1:89561422-89561441 Msa0385840:CDS 45.0%
TGGGAGAGATATTGTGAGGA+AGG + chr3_1:89561459-89561478 Msa0385840:CDS 45.0%
TGGAGGTCGTATGGTTTGAA+TGG + chr3_1:89561491-89561510 Msa0385840:CDS 45.0%
TGCGGCAGTAACCATTTCTT+TGG - chr3_1:89561609-89561628 None:intergenic 45.0%
CTGCCGCAAAAGAATGTTTC+TGG + chr3_1:89561621-89561640 Msa0385840:three_prime_UTR 45.0%
AAGAACGAACAGAAGCGAGA+AGG - chr3_1:89561017-89561036 None:intergenic 45.0%
GCATCGCTAAGATTATGAGC+AGG - chr3_1:89561063-89561082 None:intergenic 45.0%
GATCTATGTTGTGTGCGTGT+TGG + chr3_1:89561387-89561406 Msa0385840:CDS 45.0%
! TGCGTGTTGGTAAATCACTG+TGG + chr3_1:89561400-89561419 Msa0385840:CDS 45.0%
!!! GTAGTCGTTTTTTAGCCTGC+TGG + chr3_1:89561422-89561441 Msa0385840:CDS 45.0%
TGGGAGAGATATTGTGAGGA+AGG + chr3_1:89561459-89561478 Msa0385840:CDS 45.0%
TGGAGGTCGTATGGTTTGAA+TGG + chr3_1:89561491-89561510 Msa0385840:CDS 45.0%
TGCGGCAGTAACCATTTCTT+TGG - chr3_1:89561609-89561628 None:intergenic 45.0%
CTGCCGCAAAAGAATGTTTC+TGG + chr3_1:89561621-89561640 Msa0385840:three_prime_UTR 45.0%
!!! TGGGTTTTCGTTGGTGGCAA+AGG + chr3_1:89560952-89560971 Msa0385840:CDS 50.0%
!!! GTTTTCGTTGGTGGCAAAGG+TGG + chr3_1:89560955-89560974 Msa0385840:CDS 50.0%
!!! TGGGTTTTCGTTGGTGGCAA+AGG + chr3_1:89560952-89560971 Msa0385840:CDS 50.0%
!!! GTTTTCGTTGGTGGCAAAGG+TGG + chr3_1:89560955-89560974 Msa0385840:CDS 50.0%
!! GTTGGTGGCAAAGGTGGTGT+TGG + chr3_1:89560961-89560980 Msa0385840:CDS 55.0%
!! GTTGGTGGCAAAGGTGGTGT+TGG + chr3_1:89560961-89560980 Msa0385840:CDS 55.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 89560889 89561671 89560889 ID=Msa0385840;Name=Msa0385840
chr3_1 mRNA 89560889 89561671 89560889 ID=Msa0385840-mRNA-1;Parent=Msa0385840;Name=Msa0385840-mRNA-1;_AED=0.16;_eAED=0.19;_QI=0|0|0.5|1|1|1|2|101|146
chr3_1 exon 89560889 89561123 89560889 ID=Msa0385840-mRNA-1:exon:24396;Parent=Msa0385840-mRNA-1
chr3_1 exon 89561365 89561671 89561365 ID=Msa0385840-mRNA-1:exon:24397;Parent=Msa0385840-mRNA-1
chr3_1 CDS 89560889 89561123 89560889 ID=Msa0385840-mRNA-1:cds;Parent=Msa0385840-mRNA-1
chr3_1 CDS 89561365 89561570 89561365 ID=Msa0385840-mRNA-1:cds;Parent=Msa0385840-mRNA-1
chr3_1 three_prime_UTR 89561571 89561671 89561571 ID=Msa0385840-mRNA-1:three_prime_utr;Parent=Msa0385840-mRNA-1
Gene Sequence

>Msa0385840

ATGGAAGATCAACCATTACCAGAAGGAACATTACAAAACATCCTAGAACAAGAAACCTTAAAGTGGGTTTTCGTTGGTGGCAAAGGTGGTGTTGGAAAAACAACATGCAGTTCAATTCTCTCTATCCTTCTCGCTTCTGTTCGTTCTTCTGTTCTCATCATTTCAACCGATCCTGCTCATAATCTTAGCGATGCTTTTCAACAACGATTCACAAAAACCCCTACTTTGGTTAATGATCCGACAGAATGTTGTGCTGTGATCTATGTTGTGTGCGTGTTGGTAAATCACTGTGGTAGTCGTTTTTTAGCCTGCTGGATTTGTGAACTTTGTGGGAGAGATATTGTGAGGAAGGAAATGAAAATGGAGGTCGTATGGTTTGAATGGATTTGTGTTGTGAAGATTGGTGTTGAGATGAATGTTTCTGGAAAAAAATTGGTTTAG

Protein sequence

>Msa0385840

MEDQPLPEGTLQNILEQETLKWVFVGGKGGVGKTTCSSILSILLASVRSSVLIISTDPAHNLSDAFQQRFTKTPTLVNDPTECCAVIYVVCVLVNHCGSRFLACWICELCGRDIVRKEMKMEVVWFEWICVVKIGVEMNVSGKKLV*