AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0197660


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0197660 MtrunA17_Chr2g0290831 94.805 77 4 0 12 88 1 77 1.74e-46 143
Msa0197660 MtrunA17_Chr3g0120541 49.315 73 37 0 13 85 3 75 8.22e-19 74.3
Msa0197660 MtrunA17_Chr6g0483521 57.143 70 30 0 12 81 1 70 2.83e-18 75.5
Msa0197660 MtrunA17_Chr6g0483581 52.703 74 35 0 12 85 1 74 7.63e-18 74.7
Msa0197660 MtrunA17_Chr6g0483561 52.113 71 34 0 12 82 1 71 5.12e-17 72.4
Msa0197660 MtrunA17_Chr6g0483511 54.286 70 32 0 12 81 1 70 5.42e-17 71.6
Msa0197660 MtrunA17_Chr3g0120551 47.945 73 38 0 13 85 3 75 7.45e-17 69.3
Msa0197660 MtrunA17_Chr3g0120531 48.611 72 36 1 13 83 3 74 2.66e-15 65.5
Msa0197660 MtrunA17_Chr5g0445581 40.000 65 39 0 12 76 1 65 5.65e-12 55.8
Msa0197660 MtrunA17_Chr5g0438551 43.421 76 42 1 14 88 2 77 1.23e-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
Msa0197660 AT4G05030.2 60.811 74 29 0 12 85 1 74 1.86e-24 87.8
Msa0197660 AT4G05030.1 61.111 72 28 0 14 85 36 107 2.14e-23 86.3
Msa0197660 AT3G20180.3 45.333 75 41 0 12 86 1 75 1.22e-16 69.3
Msa0197660 AT3G20180.2 43.421 76 43 0 11 86 19 94 2.29e-16 69.3
Msa0197660 AT3G20180.4 43.056 72 41 0 15 86 2 73 2.81e-14 63.2
Msa0197660 AT3G20180.1 43.478 69 39 0 18 86 3 71 5.31e-14 62.4
Msa0197660 AT3G07600.1 42.857 77 44 0 12 88 1 77 2.62e-13 61.6
Msa0197660 AT5G48290.1 41.558 77 45 0 12 88 1 77 5.83e-11 55.8

Find 21 sgRNAs with CRISPR-Local

Find 73 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCAAAATATCATTACTTAAT+TGG 0.106114 2_1:-15848750 None:intergenic
CAAATTTAATGTTTAGCTTT+AGG 0.204714 2_1:+15848975 Msa0197660:three_prime_UTR
TTAGGAATATAATATATATT+TGG 0.223892 2_1:+15848993 Msa0197660:three_prime_UTR
AAAGACAAGATAGTAGTTAT+TGG 0.241019 2_1:+15848582 Msa0197660:CDS
AAAGCAATGGAGAGAGAAAA+AGG 0.349934 2_1:+15848830 Msa0197660:three_prime_UTR
ATATTTGGATTGGTATGTAA+TGG 0.411614 2_1:+15849008 Msa0197660:three_prime_UTR
TCAACAAAGTTGTCATCAAA+TGG 0.417779 2_1:-15848776 None:intergenic
AGCTACAACCTTGAGTGCCT+TGG 0.451895 2_1:-15848276 None:intergenic
TGGTATGTAATGGAATGAAA+TGG 0.466169 2_1:+15849018 Msa0197660:three_prime_UTR
CAAACTGAAATTGTCAGCTT+AGG 0.480321 2_1:+15848657 Msa0197660:CDS
ACTTAATTGGAAAATACAAA+AGG 0.486207 2_1:-15848737 None:intergenic
AAGGCACTCAAGGTTGTAGC+TGG 0.487303 2_1:+15848278 Msa0197660:CDS
AATATAATATATATTTGGAT+TGG 0.491812 2_1:+15848998 Msa0197660:three_prime_UTR
TTCTTATTGGTCAAAAGCAA+TGG 0.519411 2_1:+15848817 Msa0197660:three_prime_UTR
AAGATAGTAGTTATTGGAGA+TGG 0.521542 2_1:+15848588 Msa0197660:CDS
GCAGCAAAAGATTGTGATGA+GGG 0.535212 2_1:+15848226 Msa0197660:intron
GTGTCGCACCAAGGCACTCA+AGG 0.539664 2_1:+15848268 Msa0197660:CDS
AAGGTTGTAGCTGGAGCAAA+CGG 0.547469 2_1:+15848287 Msa0197660:CDS
TTTCATCTCTGAAAACATGA+AGG 0.581141 2_1:+15848058 Msa0197660:CDS
TGCAGCAAAAGATTGTGATG+AGG 0.660386 2_1:+15848225 Msa0197660:intron
ATGTCAAAAGTGTCGCACCA+AGG 0.695558 2_1:+15848259 Msa0197660:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAGGAATATAATATATATT+TGG + chr2_1:15848993-15849012 Msa0197660:three_prime_UTR 10.0%
!! AATATAATATATATTTGGAT+TGG + chr2_1:15848998-15849017 Msa0197660:three_prime_UTR 10.0%
!! TTAGGAATATAATATATATT+TGG + chr2_1:15848993-15849012 Msa0197660:three_prime_UTR 10.0%
!! AATATAATATATATTTGGAT+TGG + chr2_1:15848998-15849017 Msa0197660:three_prime_UTR 10.0%
!! TCAAAATATCATTACTTAAT+TGG - chr2_1:15848753-15848772 None:intergenic 15.0%
!! TCAAAATATCATTACTTAAT+TGG - chr2_1:15848753-15848772 None:intergenic 15.0%
!!! GTTACTAAAATTTTGTGATT+TGG + chr2_1:15848518-15848537 Msa0197660:intron 20.0%
!! AATTGTTTGAGAAAAAAAGT+TGG + chr2_1:15848633-15848652 Msa0197660:CDS 20.0%
!!! TTTTATTTCAGTTTTTCAAC+TGG - chr2_1:15848694-15848713 None:intergenic 20.0%
!! ACTTAATTGGAAAATACAAA+AGG - chr2_1:15848740-15848759 None:intergenic 20.0%
!! TCAAAAAGAAGAAGAAAAAT+TGG - chr2_1:15848946-15848965 None:intergenic 20.0%
!!! CAAATTTAATGTTTAGCTTT+AGG + chr2_1:15848975-15848994 Msa0197660:three_prime_UTR 20.0%
!!! GTTACTAAAATTTTGTGATT+TGG + chr2_1:15848518-15848537 Msa0197660:intron 20.0%
!! AATTGTTTGAGAAAAAAAGT+TGG + chr2_1:15848633-15848652 Msa0197660:CDS 20.0%
!!! TTTTATTTCAGTTTTTCAAC+TGG - chr2_1:15848694-15848713 None:intergenic 20.0%
!! ACTTAATTGGAAAATACAAA+AGG - chr2_1:15848740-15848759 None:intergenic 20.0%
!! TCAAAAAGAAGAAGAAAAAT+TGG - chr2_1:15848946-15848965 None:intergenic 20.0%
!!! CAAATTTAATGTTTAGCTTT+AGG + chr2_1:15848975-15848994 Msa0197660:three_prime_UTR 20.0%
! TTAACGATTGAAATTAGTGA+CGG + chr2_1:15848383-15848402 Msa0197660:intron 25.0%
! AAAGACAAGATAGTAGTTAT+TGG + chr2_1:15848582-15848601 Msa0197660:CDS 25.0%
! AATAAGAAGTGAGAAAAACA+AGG - chr2_1:15848805-15848824 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG + chr2_1:15848804-15848823 Msa0197660:three_prime_UTR 25.0%
!!! ATATTTGGATTGGTATGTAA+TGG + chr2_1:15849008-15849027 Msa0197660:three_prime_UTR 25.0%
! TTAACGATTGAAATTAGTGA+CGG + chr2_1:15848383-15848402 Msa0197660:intron 25.0%
! AAAGACAAGATAGTAGTTAT+TGG + chr2_1:15848582-15848601 Msa0197660:CDS 25.0%
! AATAAGAAGTGAGAAAAACA+AGG - chr2_1:15848805-15848824 None:intergenic 25.0%
!!! TTGTTTTTCTCACTTCTTAT+TGG + chr2_1:15848804-15848823 Msa0197660:three_prime_UTR 25.0%
!!! ATATTTGGATTGGTATGTAA+TGG + chr2_1:15849008-15849027 Msa0197660:three_prime_UTR 25.0%
! TTTCATCTCTGAAAACATGA+AGG + chr2_1:15848058-15848077 Msa0197660:CDS 30.0%
AAGATAGTAGTTATTGGAGA+TGG + chr2_1:15848588-15848607 Msa0197660:CDS 30.0%
TCAACAAAGTTGTCATCAAA+TGG - chr2_1:15848779-15848798 None:intergenic 30.0%
TTCTTATTGGTCAAAAGCAA+TGG + chr2_1:15848817-15848836 Msa0197660:three_prime_UTR 30.0%
!!! AACCACTTTTTGACAACTTT+TGG - chr2_1:15848902-15848921 None:intergenic 30.0%
! TGGTATGTAATGGAATGAAA+TGG + chr2_1:15849018-15849037 Msa0197660:three_prime_UTR 30.0%
! TTTCATCTCTGAAAACATGA+AGG + chr2_1:15848058-15848077 Msa0197660:CDS 30.0%
AAGATAGTAGTTATTGGAGA+TGG + chr2_1:15848588-15848607 Msa0197660:CDS 30.0%
TCAACAAAGTTGTCATCAAA+TGG - chr2_1:15848779-15848798 None:intergenic 30.0%
TTCTTATTGGTCAAAAGCAA+TGG + chr2_1:15848817-15848836 Msa0197660:three_prime_UTR 30.0%
!!! AACCACTTTTTGACAACTTT+TGG - chr2_1:15848902-15848921 None:intergenic 30.0%
! TGGTATGTAATGGAATGAAA+TGG + chr2_1:15849018-15849037 Msa0197660:three_prime_UTR 30.0%
!! TTTTGTGATTTGGCAAATGC+AGG + chr2_1:15848528-15848547 Msa0197660:intron 35.0%
! AAATGCAGGTGTGAATTTTG+TGG + chr2_1:15848542-15848561 Msa0197660:intron 35.0%
! AATGCAGGTGTGAATTTTGT+GGG + chr2_1:15848543-15848562 Msa0197660:intron 35.0%
! TGTGAATTTTGTGGGATTAG+AGG + chr2_1:15848551-15848570 Msa0197660:CDS 35.0%
! GTGAATTTTGTGGGATTAGA+GGG + chr2_1:15848552-15848571 Msa0197660:CDS 35.0%
CAAACTGAAATTGTCAGCTT+AGG + chr2_1:15848657-15848676 Msa0197660:CDS 35.0%
AAAGCAATGGAGAGAGAAAA+AGG + chr2_1:15848830-15848849 Msa0197660:three_prime_UTR 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG + chr2_1:15848897-15848916 Msa0197660:three_prime_UTR 35.0%
!! TTTTGTGATTTGGCAAATGC+AGG + chr2_1:15848528-15848547 Msa0197660:intron 35.0%
! AAATGCAGGTGTGAATTTTG+TGG + chr2_1:15848542-15848561 Msa0197660:intron 35.0%
! AATGCAGGTGTGAATTTTGT+GGG + chr2_1:15848543-15848562 Msa0197660:intron 35.0%
! TGTGAATTTTGTGGGATTAG+AGG + chr2_1:15848551-15848570 Msa0197660:CDS 35.0%
! GTGAATTTTGTGGGATTAGA+GGG + chr2_1:15848552-15848571 Msa0197660:CDS 35.0%
CAAACTGAAATTGTCAGCTT+AGG + chr2_1:15848657-15848676 Msa0197660:CDS 35.0%
AAAGCAATGGAGAGAGAAAA+AGG + chr2_1:15848830-15848849 Msa0197660:three_prime_UTR 35.0%
GTCCAAAAGTTGTCAAAAAG+TGG + chr2_1:15848897-15848916 Msa0197660:three_prime_UTR 35.0%
TGCAGCAAAAGATTGTGATG+AGG + chr2_1:15848225-15848244 Msa0197660:intron 40.0%
GCAGCAAAAGATTGTGATGA+GGG + chr2_1:15848226-15848245 Msa0197660:intron 40.0%
AGAGAGAAAAAGGAAGAGAG+AGG + chr2_1:15848840-15848859 Msa0197660:three_prime_UTR 40.0%
ATAGAATCAGCAGAGTTGAG+TGG + chr2_1:15849052-15849071 Msa0197660:three_prime_UTR 40.0%
TGCAGCAAAAGATTGTGATG+AGG + chr2_1:15848225-15848244 Msa0197660:intron 40.0%
GCAGCAAAAGATTGTGATGA+GGG + chr2_1:15848226-15848245 Msa0197660:intron 40.0%
AGAGAGAAAAAGGAAGAGAG+AGG + chr2_1:15848840-15848859 Msa0197660:three_prime_UTR 40.0%
!! ATGTCAAAAGTGTCGCACCA+AGG + chr2_1:15848259-15848278 Msa0197660:CDS 45.0%
AAGGTTGTAGCTGGAGCAAA+CGG + chr2_1:15848287-15848306 Msa0197660:CDS 45.0%
!! ATGTCAAAAGTGTCGCACCA+AGG + chr2_1:15848259-15848278 Msa0197660:CDS 45.0%
AAGGTTGTAGCTGGAGCAAA+CGG + chr2_1:15848287-15848306 Msa0197660:CDS 45.0%
AGCTACAACCTTGAGTGCCT+TGG - chr2_1:15848279-15848298 None:intergenic 50.0%
! AAGGCACTCAAGGTTGTAGC+TGG + chr2_1:15848278-15848297 Msa0197660:CDS 50.0%
AGCTACAACCTTGAGTGCCT+TGG - chr2_1:15848279-15848298 None:intergenic 50.0%
! AAGGCACTCAAGGTTGTAGC+TGG + chr2_1:15848278-15848297 Msa0197660:CDS 50.0%
! GTGTCGCACCAAGGCACTCA+AGG + chr2_1:15848268-15848287 Msa0197660:CDS 60.0%
! GTGTCGCACCAAGGCACTCA+AGG + chr2_1:15848268-15848287 Msa0197660:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 15848041 15849073 15848041 ID=Msa0197660;Name=Msa0197660
chr2_1 mRNA 15848041 15849073 15848041 ID=Msa0197660-mRNA-1;Parent=Msa0197660;Name=Msa0197660-mRNA-1;_AED=0.02;_eAED=0.02;_QI=0|1|0.66|1|1|1|3|375|88
chr2_1 exon 15848041 15848079 15848041 ID=Msa0197660-mRNA-1:exon:6593;Parent=Msa0197660-mRNA-1
chr2_1 exon 15848230 15848308 15848230 ID=Msa0197660-mRNA-1:exon:6594;Parent=Msa0197660-mRNA-1
chr2_1 exon 15848550 15849073 15848550 ID=Msa0197660-mRNA-1:exon:6595;Parent=Msa0197660-mRNA-1
chr2_1 CDS 15848041 15848079 15848041 ID=Msa0197660-mRNA-1:cds;Parent=Msa0197660-mRNA-1
chr2_1 CDS 15848230 15848308 15848230 ID=Msa0197660-mRNA-1:cds;Parent=Msa0197660-mRNA-1
chr2_1 CDS 15848550 15848698 15848550 ID=Msa0197660-mRNA-1:cds;Parent=Msa0197660-mRNA-1
chr2_1 three_prime_UTR 15848699 15849073 15848699 ID=Msa0197660-mRNA-1:three_prime_utr;Parent=Msa0197660-mRNA-1
Gene Sequence

>Msa0197660

GTTAAGTTTCTTAAGAATTTCATCTCTGAAAACATGAAGCAAAAGATTGTGATGAGGGTTAGCATGAGATGTCAAAAGTGTCGCACCAAGGCACTCAAGGTTGTAGCTGGAGCAAACGGTGTGAATTTTGTGGGATTAGAGGGAGATGAGAAAGACAAGATAGTAGTTATTGGAGATGGTGTAGATGCTGTCAAGTTGACAAATTGTTTGAGAAAAAAAGTTGGACAAACTGAAATTGTCAGCTTAGGAGAAGTTAAAGCCAGTTGA

Protein sequence

>Msa0197660

VKFLKNFISENMKQKIVMRVSMRCQKCRTKALKVVAGANGVNFVGLEGDEKDKIVVIGDGVDAVKLTNCLRKKVGQTEIVSLGEVKAS*