AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1440880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1440880 MtrunA17_Chr4g0072411 100.000 103 0 0 1 103 59 161 5.39e-69 203
Msa1440880 MtrunA17_Chr5g0425951 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr4g0030431 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0100121 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0113681 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr2g0327641 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0103351 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr8g0352791 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0103821 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0104031 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr7g0225731 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0103801 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr3g0103881 100.000 103 0 0 1 103 1 103 2.26e-68 199
Msa1440880 MtrunA17_Chr7g0262791 100.000 103 0 0 1 103 1 103 2.26e-68 199
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1440880 AT3G53730.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT1G07820.2 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT1G07820.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT5G59690.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT3G46320.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT2G28740.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT1G07660.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT3G45930.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT5G59970.1 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT5G59970.2 100.000 103 0 0 1 103 1 103 3.11e-68 199
Msa1440880 AT1G07660.2 83.495 103 0 1 1 103 1 86 4.52e-51 155

Find 39 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGCACCTTCCTATGCCTTT+TGG 0.317118 tig0029131:+3734 None:intergenic
TTTCATCTCTTGAAAATGTC+TGG 0.354834 tig0029131:-3795 None:intergenic
AGGCAGGGAAGAACCCTCTA+TGG 0.361242 tig0029131:-3504 Msa1440880:CDS
TAAGCCTGCGATTCGTCGTT+TGG 0.371129 tig0029131:-3688 Msa1440880:CDS
GGAAGAACCCTCTATGGGTT+TGG 0.426577 tig0029131:-3498 Msa1440880:CDS
GGAGGTAAGGGACTAGGAAA+GGG 0.443358 tig0029131:-3762 Msa1440880:CDS
ATCAACCTCCAAACCCATAG+AGG 0.443645 tig0029131:+3490 None:intergenic
GGGAGGTAAGGGACTAGGAA+AGG 0.449480 tig0029131:-3763 Msa1440880:CDS
TGGTCGTGGTAAGGGAGGTA+AGG 0.462120 tig0029131:-3775 Msa1440880:CDS
GAAAATGTCTGGTCGTGGTA+AGG 0.478730 tig0029131:-3784 None:intergenic
TGTCTATGCTTTGAAGAGGC+AGG 0.485721 tig0029131:-3520 Msa1440880:CDS
AAAGATCTTCAACACACCTC+TGG 0.488735 tig0029131:+3617 None:intergenic
AGAACCCTCTATGGGTTTGG+AGG 0.501382 tig0029131:-3495 Msa1440880:CDS
GGTGCTTCGCGATAACATCC+AGG 0.510741 tig0029131:-3718 Msa1440880:CDS
CTCGCCAAACGACGAATCGC+AGG 0.516571 tig0029131:+3684 None:intergenic
ATTCGTCGTTTGGCGAGAAG+AGG 0.517863 tig0029131:-3678 Msa1440880:CDS
GGTAAGGGAGGTAAGGGACT+AGG 0.518213 tig0029131:-3768 Msa1440880:CDS
TTCGTCGTTTGGCGAGAAGA+GGG 0.520355 tig0029131:-3677 Msa1440880:CDS
AAAATGTCTGGTCGTGGTAA+GGG 0.526072 tig0029131:-3783 Msa1440880:CDS
GTCTATGCTTTGAAGAGGCA+GGG 0.532756 tig0029131:-3519 Msa1440880:CDS
CGTCGTTTGGCGAGAAGAGG+GGG 0.550836 tig0029131:-3675 Msa1440880:CDS
CTCTTGAAAATGTCTGGTCG+TGG 0.562247 tig0029131:-3789 None:intergenic
GGTAAGGGACTAGGAAAGGG+AGG 0.563878 tig0029131:-3759 Msa1440880:CDS
TAGGAAAGGGAGGTGCCAAA+AGG 0.574680 tig0029131:-3749 Msa1440880:CDS
AGGGAGGTGCCAAAAGGCAT+AGG 0.583251 tig0029131:-3743 Msa1440880:CDS
TCGTCGTTTGGCGAGAAGAG+GGG 0.586238 tig0029131:-3676 Msa1440880:CDS
TTACATACACTGAGCATGCA+AGG 0.586915 tig0029131:-3569 Msa1440880:CDS
TCGCAGGCTTAGTGATACCC+TGG 0.594313 tig0029131:+3700 None:intergenic
GGCAGGGAAGAACCCTCTAT+GGG 0.597151 tig0029131:-3503 Msa1440880:CDS
GGTCGTGGTAAGGGAGGTAA+GGG 0.613033 tig0029131:-3774 Msa1440880:CDS
GAGGAAGACAGTTACCGCAA+TGG 0.617710 tig0029131:-3547 Msa1440880:CDS
AGGTGCCAAAAGGCATAGGA+AGG 0.632227 tig0029131:-3739 Msa1440880:CDS
TCAACCTCCAAACCCATAGA+GGG 0.633837 tig0029131:+3491 None:intergenic
ATGTCTGGTCGTGGTAAGGG+AGG 0.640958 tig0029131:-3780 Msa1440880:CDS
GTGCTTCGCGATAACATCCA+GGG 0.673472 tig0029131:-3717 Msa1440880:CDS
AGCATAGACAACATCCATTG+CGG 0.679983 tig0029131:+3533 None:intergenic
ATGTTGTCTATGCTTTGAAG+AGG 0.684273 tig0029131:-3524 Msa1440880:CDS
TTGATCTATGAAGAAACCAG+AGG 0.704889 tig0029131:-3633 Msa1440880:CDS
CATACACTGAGCATGCAAGG+AGG 0.758591 tig0029131:-3566 Msa1440880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TTGATCTATGAAGAAACCAG+AGG - tig0029131:3638-3657 Msa1440880:CDS 35.0%
! AGGTGTGTTGAAGATCTTTT+TGG - tig0029131:3658-3677 Msa1440880:CDS 35.0%
!! ATGTTGTCTATGCTTTGAAG+AGG - tig0029131:3747-3766 Msa1440880:CDS 35.0%
AAAGATCTTCAACACACCTC+TGG + tig0029131:3657-3676 None:intergenic 40.0%
TTACATACACTGAGCATGCA+AGG - tig0029131:3702-3721 Msa1440880:CDS 40.0%
AGCATAGACAACATCCATTG+CGG + tig0029131:3741-3760 None:intergenic 40.0%
! AAGCACCTTCCTATGCCTTT+TGG + tig0029131:3540-3559 None:intergenic 45.0%
!! TGTCTATGCTTTGAAGAGGC+AGG - tig0029131:3751-3770 Msa1440880:CDS 45.0%
!! GTCTATGCTTTGAAGAGGCA+GGG - tig0029131:3752-3771 Msa1440880:CDS 45.0%
TCAACCTCCAAACCCATAGA+GGG + tig0029131:3783-3802 None:intergenic 45.0%
GGAGGTAAGGGACTAGGAAA+GGG - tig0029131:3509-3528 Msa1440880:CDS 50.0%
!! TAGGAAAGGGAGGTGCCAAA+AGG - tig0029131:3522-3541 Msa1440880:CDS 50.0%
! AGGTGCCAAAAGGCATAGGA+AGG - tig0029131:3532-3551 Msa1440880:CDS 50.0%
GTGCTTCGCGATAACATCCA+GGG - tig0029131:3554-3573 Msa1440880:CDS 50.0%
TAAGCCTGCGATTCGTCGTT+TGG - tig0029131:3583-3602 Msa1440880:CDS 50.0%
ATTCGTCGTTTGGCGAGAAG+AGG - tig0029131:3593-3612 Msa1440880:CDS 50.0%
TTCGTCGTTTGGCGAGAAGA+GGG - tig0029131:3594-3613 Msa1440880:CDS 50.0%
CATACACTGAGCATGCAAGG+AGG - tig0029131:3705-3724 Msa1440880:CDS 50.0%
GAGGAAGACAGTTACCGCAA+TGG - tig0029131:3724-3743 Msa1440880:CDS 50.0%
GGAAGAACCCTCTATGGGTT+TGG - tig0029131:3773-3792 Msa1440880:CDS 50.0%
AGAACCCTCTATGGGTTTGG+AGG - tig0029131:3776-3795 Msa1440880:CDS 50.0%
ATGTCTGGTCGTGGTAAGGG+AGG - tig0029131:3491-3510 Msa1440880:CDS 55.0%
TGGTCGTGGTAAGGGAGGTA+AGG - tig0029131:3496-3515 Msa1440880:CDS 55.0%
GGTCGTGGTAAGGGAGGTAA+GGG - tig0029131:3497-3516 Msa1440880:CDS 55.0%
GGTAAGGGAGGTAAGGGACT+AGG - tig0029131:3503-3522 Msa1440880:CDS 55.0%
GGGAGGTAAGGGACTAGGAA+AGG - tig0029131:3508-3527 Msa1440880:CDS 55.0%
GGTAAGGGACTAGGAAAGGG+AGG - tig0029131:3512-3531 Msa1440880:CDS 55.0%
!! AGGGAGGTGCCAAAAGGCAT+AGG - tig0029131:3528-3547 Msa1440880:CDS 55.0%
GGTGCTTCGCGATAACATCC+AGG - tig0029131:3553-3572 Msa1440880:CDS 55.0%
TCGCAGGCTTAGTGATACCC+TGG + tig0029131:3574-3593 None:intergenic 55.0%
TCGTCGTTTGGCGAGAAGAG+GGG - tig0029131:3595-3614 Msa1440880:CDS 55.0%
AGGCAGGGAAGAACCCTCTA+TGG - tig0029131:3767-3786 Msa1440880:CDS 55.0%
GGCAGGGAAGAACCCTCTAT+GGG - tig0029131:3768-3787 Msa1440880:CDS 55.0%
CTCGCCAAACGACGAATCGC+AGG + tig0029131:3590-3609 None:intergenic 60.0%
CGTCGTTTGGCGAGAAGAGG+GGG - tig0029131:3596-3615 Msa1440880:CDS 60.0%
! CGAGAAGAGGGGGTGTGAAG+AGG - tig0029131:3606-3625 Msa1440880:CDS 60.0%
! GGGGGTGTGAAGAGGATCAG+TGG - tig0029131:3614-3633 Msa1440880:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0029131 gene 3491 3802 3491 ID=Msa1440880;Name=Msa1440880
tig0029131 mRNA 3491 3802 3491 ID=Msa1440880-mRNA-1;Parent=Msa1440880;Name=Msa1440880-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|103
tig0029131 exon 3491 3802 3491 ID=Msa1440880-mRNA-1:exon:12510;Parent=Msa1440880-mRNA-1
tig0029131 CDS 3491 3802 3491 ID=Msa1440880-mRNA-1:cds;Parent=Msa1440880-mRNA-1
Gene Sequence

>Msa1440880

ATGTCTGGTCGTGGTAAGGGAGGTAAGGGACTAGGAAAGGGAGGTGCCAAAAGGCATAGGAAGGTGCTTCGCGATAACATCCAGGGTATCACTAAGCCTGCGATTCGTCGTTTGGCGAGAAGAGGGGGTGTGAAGAGGATCAGTGGTTTGATCTATGAAGAAACCAGAGGTGTGTTGAAGATCTTTTTGGAGAATGTCATTCGTGATGCAGTTACATACACTGAGCATGCAAGGAGGAAGACAGTTACCGCAATGGATGTTGTCTATGCTTTGAAGAGGCAGGGAAGAACCCTCTATGGGTTTGGAGGTTGA

Protein sequence

>Msa1440880

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGFGG*