AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0520450


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0520450 MtrunA17_Chr3g0136171 95.833 120 5 0 1 120 24 143 1.62e-78 228
Msa0520450 MtrunA17_Chr1g0150841 65.323 124 38 2 1 119 1 124 1.48e-47 149
Msa0520450 MtrunA17_Chr4g0070691 57.025 121 45 5 1 119 1 116 1.47e-34 115
Msa0520450 MtrunA17_Chr2g0300351 54.918 122 49 3 1 119 1 119 6.61e-24 89.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0520450 AT2G06520.1 52.427 103 46 1 20 119 13 115 2.40e-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_4:+72996813 Msa0520450:CDS
TTTGACTGTGTGATCCTCTT+TGG 0.259959 3_4:-72996615 None:intergenic
CTATACTTGGAGCTGTTATT+GGG 0.283981 3_4:+72996814 Msa0520450:CDS
ATTAATTAAGCTCTCTTAAC+CGG 0.332183 3_4:-72996852 None:intergenic
TTTGGTTGTGCGATGGGTAA+TGG 0.371937 3_4:-72996597 None:intergenic
AGATGCATTAATTTCAACCT+TGG 0.419109 3_4:-72996640 None:intergenic
TAATGCATCTTTGAAAGAAA+AGG 0.433518 3_4:+72996653 Msa0520450:CDS
CCTGATGTGGCTCATGCAGC+TGG 0.437171 3_4:+72996723 Msa0520450:CDS
ATCCTCTTTGGTTGTGCGAT+GGG 0.483107 3_4:-72996603 None:intergenic
TGGGGTTTCCAACTTTGATC+CGG 0.483190 3_4:+72996833 Msa0520450:CDS
CCAGCTGCATGAGCCACATC+AGG 0.505992 3_4:-72996723 None:intergenic
GATCCTCTTTGGTTGTGCGA+TGG 0.509446 3_4:-72996604 None:intergenic
CTCCATGGTTATACCTGATG+TGG 0.524546 3_4:+72996710 Msa0520450:CDS
TCTCTTAACCGGATCAAAGT+TGG 0.532912 3_4:-72996841 None:intergenic
TGCATCCTTGACAGCCTCCA+TGG 0.539158 3_4:+72996695 Msa0520450:CDS
GCTGTGCTAACAGCTATACT+TGG 0.540967 3_4:+72996801 Msa0520450:CDS
TATACTTGGAGCTGTTATTG+GGG 0.562747 3_4:+72996815 Msa0520450:CDS
TATAACCATGGAGGCTGTCA+AGG 0.564152 3_4:-72996700 None:intergenic
TACCCATCGCACAACCAAAG+AGG 0.604798 3_4:+72996601 Msa0520450:CDS
GATCACACAGTCAAAATCCA+AGG 0.634917 3_4:+72996623 Msa0520450:CDS
AGCCACATCAGGTATAACCA+TGG 0.670542 3_4:-72996712 None:intergenic
CACATCAGGTATAACCATGG+AGG 0.712255 3_4:-72996709 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGCATCTTTGAAAGAAA+AGG + chr3_4:72996653-72996672 Msa0520450:CDS 25.0%
!! TGGATTTTTCAGCTTGTTTT+GGG - chr3_4:72996556-72996575 None:intergenic 30.0%
!! ATGGATTTTTCAGCTTGTTT+TGG - chr3_4:72996557-72996576 None:intergenic 30.0%
TAATGGCCTGAAAAATGATT+CGG - chr3_4:72996583-72996602 None:intergenic 30.0%
AGATGCATTAATTTCAACCT+TGG - chr3_4:72996643-72996662 None:intergenic 30.0%
AAATGCTTAGCAAAAAGTTC+TGG - chr3_4:72996770-72996789 None:intergenic 30.0%
! TTTTTGCTAAGCATTTTTGC+TGG + chr3_4:72996774-72996793 Msa0520450:CDS 30.0%
CTATACTTGGAGCTGTTATT+GGG + chr3_4:72996814-72996833 Msa0520450:CDS 35.0%
TATACTTGGAGCTGTTATTG+GGG + chr3_4:72996815-72996834 Msa0520450:CDS 35.0%
! CTGAAAAATGATTCGGAGGA+TGG - chr3_4:72996576-72996595 None:intergenic 40.0%
!! CATCCTCCGAATCATTTTTC+AGG + chr3_4:72996574-72996593 Msa0520450:CDS 40.0%
TTTGACTGTGTGATCCTCTT+TGG - chr3_4:72996618-72996637 None:intergenic 40.0%
GATCACACAGTCAAAATCCA+AGG + chr3_4:72996623-72996642 Msa0520450:CDS 40.0%
!! AGCAAAAAGTTCTGGAGAGA+TGG - chr3_4:72996762-72996781 None:intergenic 40.0%
! TTGCTAAGCATTTTTGCTGG+TGG + chr3_4:72996777-72996796 Msa0520450:CDS 40.0%
GCTATACTTGGAGCTGTTAT+TGG + chr3_4:72996813-72996832 Msa0520450:CDS 40.0%
TCTCTTAACCGGATCAAAGT+TGG - chr3_4:72996844-72996863 None:intergenic 40.0%
!! TTTTGGGTAGCAGAACTCAC+TGG - chr3_4:72996540-72996559 None:intergenic 45.0%
! TGGCCTGAAAAATGATTCGG+AGG - chr3_4:72996580-72996599 None:intergenic 45.0%
TTTGGTTGTGCGATGGGTAA+TGG - chr3_4:72996600-72996619 None:intergenic 45.0%
ATCCTCTTTGGTTGTGCGAT+GGG - chr3_4:72996606-72996625 None:intergenic 45.0%
TATAACCATGGAGGCTGTCA+AGG - chr3_4:72996703-72996722 None:intergenic 45.0%
CACATCAGGTATAACCATGG+AGG - chr3_4:72996712-72996731 None:intergenic 45.0%
CTCCATGGTTATACCTGATG+TGG + chr3_4:72996710-72996729 Msa0520450:CDS 45.0%
AGCCACATCAGGTATAACCA+TGG - chr3_4:72996715-72996734 None:intergenic 45.0%
GCTGTGCTAACAGCTATACT+TGG + chr3_4:72996801-72996820 Msa0520450:CDS 45.0%
TGGGGTTTCCAACTTTGATC+CGG + chr3_4:72996833-72996852 Msa0520450:CDS 45.0%
TACCCATCGCACAACCAAAG+AGG + chr3_4:72996601-72996620 Msa0520450:CDS 50.0%
GATCCTCTTTGGTTGTGCGA+TGG - chr3_4:72996607-72996626 None:intergenic 50.0%
TGCATCCTTGACAGCCTCCA+TGG + chr3_4:72996695-72996714 Msa0520450:CDS 55.0%
CCAGCTGCATGAGCCACATC+AGG - chr3_4:72996726-72996745 None:intergenic 60.0%
CCTGATGTGGCTCATGCAGC+TGG + chr3_4:72996723-72996742 Msa0520450:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 72996507 72996869 72996507 ID=Msa0520450;Name=Msa0520450
chr3_4 mRNA 72996507 72996869 72996507 ID=Msa0520450-mRNA-1;Parent=Msa0520450;Name=Msa0520450-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|120
chr3_4 exon 72996507 72996869 72996507 ID=Msa0520450-mRNA-1:exon:20327;Parent=Msa0520450-mRNA-1
chr3_4 CDS 72996507 72996869 72996507 ID=Msa0520450-mRNA-1:cds;Parent=Msa0520450-mRNA-1
Gene Sequence

>Msa0520450

ATGGCTTCTGCTTCTGTTGCAACAGCTTTGCCAGTGAGTTCTGCTACCCAAAACAAGCTGAAAAATCCATCCTCCGAATCATTTTTCAGGCCATTACCCATCGCACAACCAAAGAGGATCACACAGTCAAAATCCAAGGTTGAAATTAATGCATCTTTGAAAGAAAAGGCAGTGACAGCACTTACAGCTGCATCCTTGACAGCCTCCATGGTTATACCTGATGTGGCTCATGCAGCTGGATCTGATCTCTCGCCATCTCTCCAGAACTTTTTGCTAAGCATTTTTGCTGGTGGAGCTGTGCTAACAGCTATACTTGGAGCTGTTATTGGGGTTTCCAACTTTGATCCGGTTAAGAGAGCTTAA

Protein sequence

>Msa0520450

MASASVATALPVSSATQNKLKNPSSESFFRPLPIAQPKRITQSKSKVEINASLKEKAVTALTAASLTASMVIPDVAHAAGSDLSPSLQNFLLSIFAGGAVLTAILGAVIGVSNFDPVKRA*