AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1458580

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1458580 MtrunA17_Chr8g0370181 90.000 90 9 0 3 92 1 90 8.02e-53 173
Msa1458580 MtrunA17_Chr5g0407381 61.446 83 27 2 10 92 3 80 1.33e-26 101
Msa1458580 MtrunA17_Chr3g0144201 52.727 55 26 0 38 92 9 63 2.61e-14 66.6
Msa1458580 MtrunA17_Chr6g0462051 48.276 58 30 0 34 91 3 60 2.78e-13 63.5
Msa1458580 MtrunA17_Chr2g0317801 39.655 58 35 0 34 91 3 60 6.71e-11 57.0
Msa1458580 MtrunA17_Chr8g0337941 48.077 52 27 0 40 91 12 63 8.04e-11 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1458580 AT5G65970.2 56.452 62 27 0 31 92 25 86 6.16e-19 80.1
Msa1458580 AT5G65970.1 56.452 62 27 0 31 92 25 86 7.48e-19 79.7
Msa1458580 AT2G17480.1 67.925 53 17 0 40 92 39 91 2.74e-18 78.2
Msa1458580 AT1G11310.2 58.491 53 22 0 40 92 8 60 4.37e-16 72.0
Msa1458580 AT1G11310.1 58.491 53 22 0 40 92 8 60 4.76e-16 72.0
Msa1458580 AT2G17430.1 49.206 63 32 0 30 92 21 83 1.23e-15 70.9
Msa1458580 AT2G33670.1 55.556 54 24 0 39 92 14 67 6.04e-15 68.6
Msa1458580 AT1G61560.10 54.717 53 24 0 40 92 8 60 2.07e-14 67.0
Msa1458580 AT1G61560.6 52.727 55 26 0 38 92 6 60 2.24e-14 67.0
Msa1458580 AT1G61560.8 52.727 55 26 0 38 92 6 60 2.24e-14 67.0
Msa1458580 AT1G61560.5 52.727 55 26 0 38 92 6 60 2.24e-14 67.0
Msa1458580 AT1G61560.1 54.717 53 24 0 40 92 8 60 2.30e-14 67.0
Msa1458580 AT1G61560.7 52.727 55 26 0 38 92 6 60 2.31e-14 67.0
Msa1458580 AT1G61560.9 52.727 55 26 0 38 92 6 60 2.31e-14 67.0
Msa1458580 AT1G61560.4 54.717 53 24 0 40 92 8 60 2.39e-14 67.0
Msa1458580 AT2G39200.1 54.717 53 24 0 40 92 6 58 9.64e-14 65.5
Msa1458580 AT1G26700.1 46.667 60 31 1 33 91 2 61 1.59e-12 62.0
Msa1458580 AT1G26700.2 46.667 60 31 1 33 91 2 61 1.59e-12 62.0
Msa1458580 AT5G53760.2 39.344 61 37 0 31 91 7 67 3.40e-11 58.2
Msa1458580 AT5G53760.1 39.344 61 37 0 31 91 7 67 3.40e-11 58.2

Find 33 sgRNAs with CRISPR-Local

Find 103 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGTTTATGGCTTCTGATTA+TGG 0.189589 tig0039676:+851 None:intergenic
AAACAAAGAAAATGATGATA+TGG 0.240891 tig0039676:+689 None:intergenic
CTTTATGCCATAATCTGTTA+TGG 0.269563 tig0039676:+741 None:intergenic
GAGGGCTTTGCTTGAAGCTT+TGG 0.295661 tig0039676:-139 Msa1458580:CDS
AACCAACCCATAACAGATTA+TGG 0.300463 tig0039676:-748 Msa1458580:five_prime_UTR
TTTATGCCATAATCTGTTAT+GGG 0.356105 tig0039676:+742 None:intergenic
ATGGCTTCTGATTATGGTAT+TGG 0.373472 tig0039676:+857 None:intergenic
TTAGCATCAAATCCAACCTT+TGG 0.394625 tig0039676:-924 Msa1458580:five_prime_UTR
GTATTAAATTAAATGAGATT+AGG 0.412480 tig0039676:+815 None:intergenic
AACAAAGAAAATGATGATAT+GGG 0.416179 tig0039676:+690 None:intergenic
GTGTGGCTATGGCTTCTTCA+AGG 0.452448 tig0039676:-580 Msa1458580:CDS
TGCCATAATCTGTTATGGGT+TGG 0.454718 tig0039676:+746 None:intergenic
CCCATGTTGGTGTCTGATCA+AGG 0.506897 tig0039676:+534 None:intergenic
GCTTTGGAGAAAGTCAAATC+TGG 0.508508 tig0039676:-123 None:intergenic
GTACAATGGAAGTGTGGCTA+TGG 0.524539 tig0039676:-591 Msa1458580:CDS
ATGATTAATGTAAGCTCCAA+AGG 0.528486 tig0039676:+908 None:intergenic
TTAATGTAAGCTCCAAAGGT+TGG 0.529759 tig0039676:+912 None:intergenic
GGTATTGGTAGAGTGGTGGC+AGG 0.537132 tig0039676:+872 None:intergenic
TGATTATGGTATTGGTAGAG+TGG 0.579585 tig0039676:+865 None:intergenic
TGTGGCTATGGCTTCTTCAA+GGG 0.581261 tig0039676:-579 Msa1458580:CDS
GGCTGGGAGATAGGCACAAG+AGG 0.584845 tig0039676:-158 Msa1458580:CDS
TTATTTGCATGGTTGTACAA+TGG 0.606123 tig0039676:-605 Msa1458580:CDS
TTATGTCGAAGTACAAGCAA+AGG 0.607346 tig0039676:-646 Msa1458580:CDS
ACAAAGAAAATGATGATATG+GGG 0.622475 tig0039676:+691 None:intergenic
TTCGACATAAACATAAACAT+AGG 0.629977 tig0039676:+659 None:intergenic
CAGACACCAACATGGGCTGT+TGG 0.631951 tig0039676:-527 Msa1458580:CDS
AAGTCTTCACAAAATTGGAA+CGG 0.639934 tig0039676:-459 Msa1458580:intron
ACCTTGATCAGACACCAACA+TGG 0.646672 tig0039676:-535 Msa1458580:CDS
ACACAACCAACAGCCCATGT+TGG 0.661938 tig0039676:+521 None:intergenic
CCTTGATCAGACACCAACAT+GGG 0.673354 tig0039676:-534 Msa1458580:CDS
GCTGGGAGATAGGCACAAGA+GGG 0.683674 tig0039676:-157 Msa1458580:CDS
TTATGGTATTGGTAGAGTGG+TGG 0.715780 tig0039676:+868 None:intergenic
ATGGTTGTACAATGGAAGTG+TGG 0.723974 tig0039676:-597 Msa1458580:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GTATTAAATTAAATGAGATT+AGG + tig0039676:248-267 None:intergenic 15.0%
!!! TTTAGAAATTTTTGAAATTG+AGG - tig0039676:801-820 Msa1458580:five_prime_UTR 15.0%
!!! TTAGAAATTTTTGAAATTGA+GGG - tig0039676:802-821 Msa1458580:five_prime_UTR 15.0%
!! GTATTAAATTAAATGAGATT+AGG + tig0039676:248-267 None:intergenic 15.0%
!!! TTTAGAAATTTTTGAAATTG+AGG - tig0039676:801-820 Msa1458580:five_prime_UTR 15.0%
!!! TTAGAAATTTTTGAAATTGA+GGG - tig0039676:802-821 Msa1458580:five_prime_UTR 15.0%
!! TAAAGAGAAGAAAAAGTTTA+TGG + tig0039676:225-244 None:intergenic 20.0%
!!! TTGGTTTTGAAAATTGAAAA+TGG + tig0039676:298-317 None:intergenic 20.0%
!! AACAAAGAAAATGATGATAT+GGG + tig0039676:373-392 None:intergenic 20.0%
!! AAACAAAGAAAATGATGATA+TGG + tig0039676:374-393 None:intergenic 20.0%
!!! TTTCTTTTGATTTTCAGTTT+AGG - tig0039676:657-676 Msa1458580:CDS 20.0%
!!! TTTTTAGTGTTTTTTTCTGT+TGG - tig0039676:715-734 Msa1458580:five_prime_UTR 20.0%
!!! TAGAAATTTTTGAAATTGAG+GGG - tig0039676:803-822 Msa1458580:five_prime_UTR 20.0%
!! TAAAGAGAAGAAAAAGTTTA+TGG + tig0039676:225-244 None:intergenic 20.0%
!!! TTGGTTTTGAAAATTGAAAA+TGG + tig0039676:298-317 None:intergenic 20.0%
!! AACAAAGAAAATGATGATAT+GGG + tig0039676:373-392 None:intergenic 20.0%
!! AAACAAAGAAAATGATGATA+TGG + tig0039676:374-393 None:intergenic 20.0%
!!! TTTCTTTTGATTTTCAGTTT+AGG - tig0039676:657-676 Msa1458580:CDS 20.0%
!!! TTTTTAGTGTTTTTTTCTGT+TGG - tig0039676:715-734 Msa1458580:five_prime_UTR 20.0%
!!! TAGAAATTTTTGAAATTGAG+GGG - tig0039676:803-822 Msa1458580:five_prime_UTR 20.0%
! TTTATGCCATAATCTGTTAT+GGG + tig0039676:321-340 None:intergenic 25.0%
! ACAAAGAAAATGATGATATG+GGG + tig0039676:372-391 None:intergenic 25.0%
! TTCGACATAAACATAAACAT+AGG + tig0039676:404-423 None:intergenic 25.0%
! GAAAAAAGTCTTCACAAAAT+TGG - tig0039676:596-615 Msa1458580:CDS 25.0%
!!! TTGATTTTCAGTTTAGGTTA+AGG - tig0039676:663-682 Msa1458580:exon 25.0%
!!! GTGTTTTGTATTTTTTTCAG+TGG - tig0039676:881-900 Msa1458580:five_prime_UTR 25.0%
! TTTATGCCATAATCTGTTAT+GGG + tig0039676:321-340 None:intergenic 25.0%
! ACAAAGAAAATGATGATATG+GGG + tig0039676:372-391 None:intergenic 25.0%
! TTCGACATAAACATAAACAT+AGG + tig0039676:404-423 None:intergenic 25.0%
! GAAAAAAGTCTTCACAAAAT+TGG - tig0039676:596-615 Msa1458580:CDS 25.0%
!!! TTGATTTTCAGTTTAGGTTA+AGG - tig0039676:663-682 Msa1458580:exon 25.0%
!!! GTGTTTTGTATTTTTTTCAG+TGG - tig0039676:881-900 Msa1458580:five_prime_UTR 25.0%
ATGATTAATGTAAGCTCCAA+AGG + tig0039676:155-174 None:intergenic 30.0%
AAGTTTATGGCTTCTGATTA+TGG + tig0039676:212-231 None:intergenic 30.0%
CTTTATGCCATAATCTGTTA+TGG + tig0039676:322-341 None:intergenic 30.0%
!!! TATGTCTGGTTTTATTTGCA+TGG - tig0039676:444-463 Msa1458580:intron 30.0%
TTATTTGCATGGTTGTACAA+TGG - tig0039676:455-474 Msa1458580:intron 30.0%
! TGTTTGTACTGTTTTCATCA+TGG - tig0039676:559-578 Msa1458580:CDS 30.0%
AAGTCTTCACAAAATTGGAA+CGG - tig0039676:601-620 Msa1458580:CDS 30.0%
!! TTTTCAGTTTAGGTTAAGGT+TGG - tig0039676:667-686 Msa1458580:exon 30.0%
TTGAAATTGAGGGGTTAATT+TGG - tig0039676:812-831 Msa1458580:five_prime_UTR 30.0%
!!! TTTGTATTTTTTTCAGTGGC+TGG - tig0039676:885-904 Msa1458580:five_prime_UTR 30.0%
!!! TTGTATTTTTTTCAGTGGCT+GGG - tig0039676:886-905 Msa1458580:five_prime_UTR 30.0%
ATGATTAATGTAAGCTCCAA+AGG + tig0039676:155-174 None:intergenic 30.0%
AAGTTTATGGCTTCTGATTA+TGG + tig0039676:212-231 None:intergenic 30.0%
CTTTATGCCATAATCTGTTA+TGG + tig0039676:322-341 None:intergenic 30.0%
!!! TATGTCTGGTTTTATTTGCA+TGG - tig0039676:444-463 Msa1458580:intron 30.0%
TTATTTGCATGGTTGTACAA+TGG - tig0039676:455-474 Msa1458580:intron 30.0%
! TGTTTGTACTGTTTTCATCA+TGG - tig0039676:559-578 Msa1458580:CDS 30.0%
AAGTCTTCACAAAATTGGAA+CGG - tig0039676:601-620 Msa1458580:CDS 30.0%
!! TTTTCAGTTTAGGTTAAGGT+TGG - tig0039676:667-686 Msa1458580:exon 30.0%
TTGAAATTGAGGGGTTAATT+TGG - tig0039676:812-831 Msa1458580:five_prime_UTR 30.0%
!!! TTTGTATTTTTTTCAGTGGC+TGG - tig0039676:885-904 Msa1458580:five_prime_UTR 30.0%
!!! TTGTATTTTTTTCAGTGGCT+GGG - tig0039676:886-905 Msa1458580:five_prime_UTR 30.0%
TTAGCATCAAATCCAACCTT+TGG - tig0039676:136-155 Msa1458580:CDS 35.0%
TTAATGTAAGCTCCAAAGGT+TGG + tig0039676:151-170 None:intergenic 35.0%
!! TGATTATGGTATTGGTAGAG+TGG + tig0039676:198-217 None:intergenic 35.0%
ATGGCTTCTGATTATGGTAT+TGG + tig0039676:206-225 None:intergenic 35.0%
AACCAACCCATAACAGATTA+TGG - tig0039676:312-331 Msa1458580:intron 35.0%
TTATGTCGAAGTACAAGCAA+AGG - tig0039676:414-433 Msa1458580:intron 35.0%
!!! GCAAAGGTTGTTTTTATGTC+TGG - tig0039676:430-449 Msa1458580:intron 35.0%
TTAGCATCAAATCCAACCTT+TGG - tig0039676:136-155 Msa1458580:CDS 35.0%
TTAATGTAAGCTCCAAAGGT+TGG + tig0039676:151-170 None:intergenic 35.0%
!! TGATTATGGTATTGGTAGAG+TGG + tig0039676:198-217 None:intergenic 35.0%
ATGGCTTCTGATTATGGTAT+TGG + tig0039676:206-225 None:intergenic 35.0%
AACCAACCCATAACAGATTA+TGG - tig0039676:312-331 Msa1458580:intron 35.0%
TTATGTCGAAGTACAAGCAA+AGG - tig0039676:414-433 Msa1458580:intron 35.0%
!!! GCAAAGGTTGTTTTTATGTC+TGG - tig0039676:430-449 Msa1458580:intron 35.0%
!! TTATGGTATTGGTAGAGTGG+TGG + tig0039676:195-214 None:intergenic 40.0%
TGCCATAATCTGTTATGGGT+TGG + tig0039676:317-336 None:intergenic 40.0%
ATGGTTGTACAATGGAAGTG+TGG - tig0039676:463-482 Msa1458580:CDS 40.0%
!! GCTTTGGAGAAAGTCAAATC+TGG - tig0039676:937-956 Msa1458580:five_prime_UTR 40.0%
!! TTATGGTATTGGTAGAGTGG+TGG + tig0039676:195-214 None:intergenic 40.0%
TGCCATAATCTGTTATGGGT+TGG + tig0039676:317-336 None:intergenic 40.0%
ATGGTTGTACAATGGAAGTG+TGG - tig0039676:463-482 Msa1458580:CDS 40.0%
! GTACAATGGAAGTGTGGCTA+TGG - tig0039676:469-488 Msa1458580:CDS 45.0%
TGTGGCTATGGCTTCTTCAA+GGG - tig0039676:481-500 Msa1458580:CDS 45.0%
ACCTTGATCAGACACCAACA+TGG - tig0039676:525-544 Msa1458580:CDS 45.0%
CCTTGATCAGACACCAACAT+GGG - tig0039676:526-545 Msa1458580:CDS 45.0%
!! TTTTTCAGTGGCTGGGAGAT+AGG - tig0039676:893-912 Msa1458580:five_prime_UTR 45.0%
! GTACAATGGAAGTGTGGCTA+TGG - tig0039676:469-488 Msa1458580:CDS 45.0%
TGTGGCTATGGCTTCTTCAA+GGG - tig0039676:481-500 Msa1458580:CDS 45.0%
ACCTTGATCAGACACCAACA+TGG - tig0039676:525-544 Msa1458580:CDS 45.0%
CCTTGATCAGACACCAACAT+GGG - tig0039676:526-545 Msa1458580:CDS 45.0%
!! TTTTTCAGTGGCTGGGAGAT+AGG - tig0039676:893-912 Msa1458580:five_prime_UTR 45.0%
!! AAAAAAATAATAAAGATAAA+AGG + tig0039676:749-768 None:intergenic 5.0%
!! AAAAAAATAATAAAGATAAA+AGG + tig0039676:749-768 None:intergenic 5.0%
GTGTGGCTATGGCTTCTTCA+AGG - tig0039676:480-499 Msa1458580:CDS 50.0%
! CCCATGTTGGTGTCTGATCA+AGG + tig0039676:529-548 None:intergenic 50.0%
ACACAACCAACAGCCCATGT+TGG + tig0039676:542-561 None:intergenic 50.0%
GAGGGCTTTGCTTGAAGCTT+TGG - tig0039676:921-940 Msa1458580:five_prime_UTR 50.0%
GTGTGGCTATGGCTTCTTCA+AGG - tig0039676:480-499 Msa1458580:CDS 50.0%
! CCCATGTTGGTGTCTGATCA+AGG + tig0039676:529-548 None:intergenic 50.0%
ACACAACCAACAGCCCATGT+TGG + tig0039676:542-561 None:intergenic 50.0%
GAGGGCTTTGCTTGAAGCTT+TGG - tig0039676:921-940 Msa1458580:five_prime_UTR 50.0%
!! GGTATTGGTAGAGTGGTGGC+AGG + tig0039676:191-210 None:intergenic 55.0%
! CAGACACCAACATGGGCTGT+TGG - tig0039676:533-552 Msa1458580:CDS 55.0%
GCTGGGAGATAGGCACAAGA+GGG - tig0039676:903-922 Msa1458580:five_prime_UTR 55.0%
!! GGTATTGGTAGAGTGGTGGC+AGG + tig0039676:191-210 None:intergenic 55.0%
! CAGACACCAACATGGGCTGT+TGG - tig0039676:533-552 Msa1458580:CDS 55.0%
GCTGGGAGATAGGCACAAGA+GGG - tig0039676:903-922 Msa1458580:five_prime_UTR 55.0%
GGCTGGGAGATAGGCACAAG+AGG - tig0039676:902-921 Msa1458580:five_prime_UTR 60.0%
GGCTGGGAGATAGGCACAAG+AGG - tig0039676:902-921 Msa1458580:five_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
tig0039676 gene 125 957 125 ID=Msa1458580;Name=Msa1458580
tig0039676 mRNA 125 957 125 ID=Msa1458580-mRNA-1;Parent=Msa1458580;Name=Msa1458580-mRNA-1;_AED=0.02;_eAED=0.02;_QI=279|1|0.5|1|1|1|2|0|92
tig0039676 exon 125 181 125 ID=Msa1458580-mRNA-1:exon:21843;Parent=Msa1458580-mRNA-1
tig0039676 exon 460 957 460 ID=Msa1458580-mRNA-1:exon:21842;Parent=Msa1458580-mRNA-1
tig0039676 five_prime_UTR 679 957 679 ID=Msa1458580-mRNA-1:five_prime_utr;Parent=Msa1458580-mRNA-1
tig0039676 CDS 460 678 460 ID=Msa1458580-mRNA-1:cds;Parent=Msa1458580-mRNA-1
tig0039676 CDS 125 181 125 ID=Msa1458580-mRNA-1:cds;Parent=Msa1458580-mRNA-1
Gene Sequence

>Msa1458580

ATGTTTATGTTTATGTCGAAGTACAAGCAAAGGTTGTTTTTATGTCTGGTTTTATTTGCATGGTTGTACAATGGAAGTGTGGCTATGGCTTCTTCAAGGGAAGAAAGTGAAAATTCTAAAGACCTTGATCAGACACCAACATGGGCTGTTGGTTGTGTTTGTACTGTTTTCATCATGGTTTCTATTATTCTTGAAAAAAGTCTTCACAAAATTGGAACGTGGCTGGGAGATAGGCACAAGAGGGCTTTGCTTGAAGCTTTGGAGAAAGTCAAATCT
Protein sequence

>Msa1458580

MFMFMSKYKQRLFLCLVLFAWLYNGSVAMASSREESENSKDLDQTPTWAVGCVCTVFIMVSIILEKSLHKIGTWLGDRHKRALLEALEKVKS