AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0476440


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0476440 MtrunA17_Chr3g0136171 96.667 120 4 0 1 120 24 143 5.84e-79 229
Msa0476440 MtrunA17_Chr1g0150841 66.129 124 37 2 1 119 1 124 4.40e-48 150
Msa0476440 MtrunA17_Chr4g0070691 57.851 121 44 5 1 119 1 116 3.95e-35 117
Msa0476440 MtrunA17_Chr2g0300351 55.738 122 48 3 1 119 1 119 2.00e-24 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0476440 AT2G06520.1 52.427 103 46 1 20 119 13 115 2.48e-24 90.1

Find 22 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATACTTGGAGCTGTTAT+TGG 0.192002 3_3:+80270861 Msa0476440:CDS
TTTGACTGTGTGATCCTCTT+TGG 0.259959 3_3:-80270663 None:intergenic
CTATACTTGGAGCTGTTATT+GGG 0.283981 3_3:+80270862 Msa0476440:CDS
ATTAATTAAGCTCTCTTAAC+CGG 0.332183 3_3:-80270900 None:intergenic
TTTGGTTGTGCGATGGGTAA+TGG 0.371937 3_3:-80270645 None:intergenic
AGATGCATTAATTTCAACCT+TGG 0.419109 3_3:-80270688 None:intergenic
TAATGCATCTTTGAAAGAAA+AGG 0.433518 3_3:+80270701 Msa0476440:CDS
CCTGATGTGGCTCATGCAGC+TGG 0.437171 3_3:+80270771 Msa0476440:CDS
ATCCTCTTTGGTTGTGCGAT+GGG 0.483107 3_3:-80270651 None:intergenic
TGGGGTTTCCAACTTTGATC+CGG 0.483190 3_3:+80270881 Msa0476440:CDS
CCAGCTGCATGAGCCACATC+AGG 0.505992 3_3:-80270771 None:intergenic
GATCCTCTTTGGTTGTGCGA+TGG 0.509446 3_3:-80270652 None:intergenic
CTCCATGGTTATACCTGATG+TGG 0.524546 3_3:+80270758 Msa0476440:CDS
TCTCTTAACCGGATCAAAGT+TGG 0.532912 3_3:-80270889 None:intergenic
TGCATCCTTGACAGCCTCCA+TGG 0.539158 3_3:+80270743 Msa0476440:CDS
GCTGTGCTAACAGCTATACT+TGG 0.540967 3_3:+80270849 Msa0476440:CDS
TATACTTGGAGCTGTTATTG+GGG 0.562747 3_3:+80270863 Msa0476440:CDS
TATAACCATGGAGGCTGTCA+AGG 0.564152 3_3:-80270748 None:intergenic
TACCCATCGCACAACCAAAG+AGG 0.604798 3_3:+80270649 Msa0476440:CDS
GATCACACAGTCAAAATCCA+AGG 0.634917 3_3:+80270671 Msa0476440:CDS
AGCCACATCAGGTATAACCA+TGG 0.670542 3_3:-80270760 None:intergenic
CACATCAGGTATAACCATGG+AGG 0.712255 3_3:-80270757 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGCATCTTTGAAAGAAA+AGG + chr3_3:80270701-80270720 Msa0476440:CDS 25.0%
!! TGGATTTTTCAGCTTGTTTT+GGG - chr3_3:80270604-80270623 None:intergenic 30.0%
!! ATGGATTTTTCAGCTTGTTT+TGG - chr3_3:80270605-80270624 None:intergenic 30.0%
AGATGCATTAATTTCAACCT+TGG - chr3_3:80270691-80270710 None:intergenic 30.0%
AAATGCTTAGCAAAAAGTTC+TGG - chr3_3:80270818-80270837 None:intergenic 30.0%
! TTTTTGCTAAGCATTTTTGC+TGG + chr3_3:80270822-80270841 Msa0476440:CDS 30.0%
TAATGGCCTGAAAAATGACT+CGG - chr3_3:80270631-80270650 None:intergenic 35.0%
CTATACTTGGAGCTGTTATT+GGG + chr3_3:80270862-80270881 Msa0476440:CDS 35.0%
TATACTTGGAGCTGTTATTG+GGG + chr3_3:80270863-80270882 Msa0476440:CDS 35.0%
TTTGACTGTGTGATCCTCTT+TGG - chr3_3:80270666-80270685 None:intergenic 40.0%
GATCACACAGTCAAAATCCA+AGG + chr3_3:80270671-80270690 Msa0476440:CDS 40.0%
!! AGCAAAAAGTTCTGGAGAGA+TGG - chr3_3:80270810-80270829 None:intergenic 40.0%
! TTGCTAAGCATTTTTGCTGG+TGG + chr3_3:80270825-80270844 Msa0476440:CDS 40.0%
GCTATACTTGGAGCTGTTAT+TGG + chr3_3:80270861-80270880 Msa0476440:CDS 40.0%
TCTCTTAACCGGATCAAAGT+TGG - chr3_3:80270892-80270911 None:intergenic 40.0%
!! TTTTGGGTAGCAGAACTCAG+TGG - chr3_3:80270588-80270607 None:intergenic 45.0%
! CTGAAAAATGACTCGGAGGA+TGG - chr3_3:80270624-80270643 None:intergenic 45.0%
!!! CATCCTCCGAGTCATTTTTC+AGG + chr3_3:80270622-80270641 Msa0476440:CDS 45.0%
TTTGGTTGTGCGATGGGTAA+TGG - chr3_3:80270648-80270667 None:intergenic 45.0%
ATCCTCTTTGGTTGTGCGAT+GGG - chr3_3:80270654-80270673 None:intergenic 45.0%
TATAACCATGGAGGCTGTCA+AGG - chr3_3:80270751-80270770 None:intergenic 45.0%
CACATCAGGTATAACCATGG+AGG - chr3_3:80270760-80270779 None:intergenic 45.0%
CTCCATGGTTATACCTGATG+TGG + chr3_3:80270758-80270777 Msa0476440:CDS 45.0%
AGCCACATCAGGTATAACCA+TGG - chr3_3:80270763-80270782 None:intergenic 45.0%
GCTGTGCTAACAGCTATACT+TGG + chr3_3:80270849-80270868 Msa0476440:CDS 45.0%
TGGGGTTTCCAACTTTGATC+CGG + chr3_3:80270881-80270900 Msa0476440:CDS 45.0%
! TGGCCTGAAAAATGACTCGG+AGG - chr3_3:80270628-80270647 None:intergenic 50.0%
TACCCATCGCACAACCAAAG+AGG + chr3_3:80270649-80270668 Msa0476440:CDS 50.0%
GATCCTCTTTGGTTGTGCGA+TGG - chr3_3:80270655-80270674 None:intergenic 50.0%
TGCATCCTTGACAGCCTCCA+TGG + chr3_3:80270743-80270762 Msa0476440:CDS 55.0%
CCAGCTGCATGAGCCACATC+AGG - chr3_3:80270774-80270793 None:intergenic 60.0%
CCTGATGTGGCTCATGCAGC+TGG + chr3_3:80270771-80270790 Msa0476440:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 80270555 80270917 80270555 ID=Msa0476440;Name=Msa0476440
chr3_3 mRNA 80270555 80270917 80270555 ID=Msa0476440-mRNA-1;Parent=Msa0476440;Name=Msa0476440-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|120
chr3_3 exon 80270555 80270917 80270555 ID=Msa0476440-mRNA-1:exon:21922;Parent=Msa0476440-mRNA-1
chr3_3 CDS 80270555 80270917 80270555 ID=Msa0476440-mRNA-1:cds;Parent=Msa0476440-mRNA-1
Gene Sequence

>Msa0476440

ATGGCTTCTGCTTCTGTTGCAACAGCTTTGCCACTGAGTTCTGCTACCCAAAACAAGCTGAAAAATCCATCCTCCGAGTCATTTTTCAGGCCATTACCCATCGCACAACCAAAGAGGATCACACAGTCAAAATCCAAGGTTGAAATTAATGCATCTTTGAAAGAAAAGGCAGTGACAGCACTTACAGCTGCATCCTTGACAGCCTCCATGGTTATACCTGATGTGGCTCATGCAGCTGGATCTGATCTCTCACCATCTCTCCAGAACTTTTTGCTAAGCATTTTTGCTGGTGGAGCTGTGCTAACAGCTATACTTGGAGCTGTTATTGGGGTTTCCAACTTTGATCCGGTTAAGAGAGCTTAA

Protein sequence

>Msa0476440

MASASVATALPLSSATQNKLKNPSSESFFRPLPIAQPKRITQSKSKVEINASLKEKAVTALTAASLTASMVIPDVAHAAGSDLSPSLQNFLLSIFAGGAVLTAILGAVIGVSNFDPVKRA*