AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0641730


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0641730 MtrunA17_Chr4g0026421 94.444 90 3 1 1 88 1 90 1.12e-52 168
Msa0641730 MtrunA17_Chr2g0321351 62.857 70 21 2 19 88 28 92 2.53e-20 83.6
Msa0641730 MtrunA17_Chr2g0321341 39.773 88 49 1 1 88 1 84 9.54e-18 76.3
Msa0641730 MtrunA17_Chr3g0136021 62.069 58 18 1 33 90 122 175 5.35e-17 74.7
Msa0641730 MtrunA17_Chr1g0178741 50.685 73 32 1 8 80 65 133 2.89e-15 69.7
Msa0641730 MtrunA17_Chr1g0178721 47.945 73 34 1 8 80 40 108 3.60e-14 66.6
Msa0641730 MtrunA17_Chr1g0171181 38.750 80 45 1 1 80 1 76 2.42e-13 63.9
Msa0641730 MtrunA17_Chr2g0321361 43.836 73 32 2 16 88 89 152 9.90e-12 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0641730 AT5G22460.2 43.333 90 47 1 1 90 1 86 2.60e-19 80.9
Msa0641730 AT5G22460.3 43.333 90 47 1 1 90 1 86 2.60e-19 80.9
Msa0641730 AT5G22460.1 43.333 90 47 1 1 90 1 86 2.60e-19 80.9
Msa0641730 AT1G08310.1 69.565 46 14 0 43 88 8 53 9.79e-17 73.6
Msa0641730 AT1G08310.2 69.565 46 14 0 43 88 8 53 1.00e-16 73.6
Msa0641730 AT1G08310.3 69.565 46 14 0 43 88 8 53 1.26e-16 72.4
Msa0641730 AT3G44510.3 68.182 44 14 0 45 88 8 51 6.36e-15 67.8
Msa0641730 AT3G44510.2 68.182 44 14 0 45 88 8 51 2.42e-14 67.0
Msa0641730 AT3G03240.1 55.769 52 23 0 37 88 29 80 9.45e-13 62.8
Msa0641730 AT3G03230.1 58.333 48 20 0 37 84 29 76 7.62e-12 60.1
Msa0641730 AT3G48410.1 40.217 92 47 2 6 93 37 124 7.71e-11 57.4
Msa0641730 AT3G48410.2 40.217 92 47 2 6 93 79 166 7.87e-11 57.4

Find 14 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCATTGTTGTTCATGGTTT+TGG 0.249695 4_3:-42455514 Msa0641730:CDS
CATAGCATCATTGTTGTTCA+TGG 0.265095 4_3:-42455520 Msa0641730:CDS
GTGTTAATCATAGGTCTTCT+AGG 0.323591 4_3:-42455700 Msa0641730:CDS
TCAAATGAATCATTACTCTT+TGG 0.340365 4_3:+42455646 None:intergenic
TTTCTTGCTTATAGAGAAAG+TGG 0.467006 4_3:-42455565 Msa0641730:CDS
GAATCATTACTCTTTGGTGC+TGG 0.470717 4_3:+42455652 None:intergenic
AAGAACAATACTTGTGGTGC+AGG 0.474769 4_3:+42455469 None:intergenic
GCAGTAATAGTGTTAATCAT+AGG 0.496651 4_3:-42455709 Msa0641730:CDS
AATCATAGGTCTTCTAGGAA+TGG 0.507432 4_3:-42455695 Msa0641730:CDS
GTGTAGAGCTGTCAATATCA+TGG 0.511749 4_3:-42455343 Msa0641730:CDS
TGTAGAGCTGTCAATATCAT+GGG 0.525164 4_3:-42455342 Msa0641730:CDS
ACAAGAATTCAACTCAGTGA+TGG 0.568319 4_3:-42455592 Msa0641730:CDS
TAGAGAAAGTGGTGTTACAA+AGG 0.595237 4_3:-42455554 Msa0641730:CDS
GTAGAGCTGTCAATATCATG+GGG 0.686879 4_3:-42455341 Msa0641730:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATTTCATTATATTGATC+TGG - chr4_3:42455625-42455644 Msa0641730:CDS 15.0%
!! TAATTTCATTATATTGATCT+GGG - chr4_3:42455626-42455645 Msa0641730:CDS 15.0%
!!! TGATGAAGAAAATGATTTTA+TGG - chr4_3:42455436-42455455 Msa0641730:intron 20.0%
!! TGTATGATGTGTTTAATTAA+TGG - chr4_3:42455656-42455675 Msa0641730:CDS 20.0%
!! GTATGATGTGTTTAATTAAT+GGG - chr4_3:42455657-42455676 Msa0641730:CDS 20.0%
!!! GGTTTTGATCTAAATTTTAA+GGG - chr4_3:42455678-42455697 Msa0641730:CDS 20.0%
! TCAAATGAATCATTACTCTT+TGG + chr4_3:42455413-42455432 None:intergenic 25.0%
!!! GGGTTTTGATCTAAATTTTA+AGG - chr4_3:42455677-42455696 Msa0641730:CDS 25.0%
GCAGTAATAGTGTTAATCAT+AGG - chr4_3:42455347-42455366 Msa0641730:CDS 30.0%
TTTCTTGCTTATAGAGAAAG+TGG - chr4_3:42455491-42455510 Msa0641730:CDS 30.0%
!! ATCATTGTTGTTCATGGTTT+TGG - chr4_3:42455542-42455561 Msa0641730:CDS 30.0%
GAAATCAAGAACAATACTTG+TGG + chr4_3:42455596-42455615 None:intergenic 30.0%
GTGTTAATCATAGGTCTTCT+AGG - chr4_3:42455356-42455375 Msa0641730:CDS 35.0%
! AATCATAGGTCTTCTAGGAA+TGG - chr4_3:42455361-42455380 Msa0641730:intron 35.0%
ACAAGAATTCAACTCAGTGA+TGG - chr4_3:42455464-42455483 Msa0641730:intron 35.0%
!! TAGAGAAAGTGGTGTTACAA+AGG - chr4_3:42455502-42455521 Msa0641730:CDS 35.0%
! CATAGCATCATTGTTGTTCA+TGG - chr4_3:42455536-42455555 Msa0641730:CDS 35.0%
TGTAGAGCTGTCAATATCAT+GGG - chr4_3:42455714-42455733 Msa0641730:CDS 35.0%
! GAATCATTACTCTTTGGTGC+TGG + chr4_3:42455407-42455426 None:intergenic 40.0%
AAGAACAATACTTGTGGTGC+AGG + chr4_3:42455590-42455609 None:intergenic 40.0%
GTGTAGAGCTGTCAATATCA+TGG - chr4_3:42455713-42455732 Msa0641730:CDS 40.0%
GTAGAGCTGTCAATATCATG+GGG - chr4_3:42455715-42455734 Msa0641730:CDS 40.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 42455335 42455743 42455335 ID=Msa0641730;Name=Msa0641730
chr4_3 mRNA 42455335 42455743 42455335 ID=Msa0641730-mRNA-1;Parent=Msa0641730;Name=Msa0641730-mRNA-1;_AED=0.23;_eAED=0.23;_QI=0|0|0|0.5|1|1|2|0|102
chr4_3 exon 42455480 42455743 42455480 ID=Msa0641730-mRNA-1:exon:9604;Parent=Msa0641730-mRNA-1
chr4_3 exon 42455335 42455379 42455335 ID=Msa0641730-mRNA-1:exon:9603;Parent=Msa0641730-mRNA-1
chr4_3 CDS 42455480 42455743 42455480 ID=Msa0641730-mRNA-1:cds;Parent=Msa0641730-mRNA-1
chr4_3 CDS 42455335 42455379 42455335 ID=Msa0641730-mRNA-1:cds;Parent=Msa0641730-mRNA-1
Gene Sequence

>Msa0641730

ATGGTTTCAAAAGCAGTAATAGTGTTAATCATAGGTCTTCTAGGAATGGTTTATCAAGCAACTCAACTTCCAGCACCAAAGAGTAATGATTCATTTGATGATGATGAAGAAAATGATTTTATGGTTTCAACAAGAATTCAACTCAGTGATGGAAGATTTCTTGCTTATAGAGAAAGTGGTGTTACAAAGGATAAAGCAAAACATAGCATCATTGTTGTTCATGGTTTTGGAAGCTCTAAAGATATGAACTTTCCTGCACCACAAGGAGTTGACATGCTGTGTAGAGCTGTCAATATCATGGGGCCTTGA

Protein sequence

>Msa0641730

MVSKAVIVLIIGLLGMVYQATQLPAPKSNDSFDDDEENDFMVSTRIQLSDGRFLAYRESGVTKDKAKHSIIVVHGFGSSKDMNFPAPQGVDMLCRAVNIMGP*