AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0212310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0212310 MtrunA17_Chr2g0299991 98.148 54 1 0 1 54 1 54 1.32e-30 109
Msa0212310 MtrunA17_Chr4g0070851 67.925 53 17 0 1 53 1 53 4.40e-19 78.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0212310 AT4G29810.1 62.500 56 21 0 1 56 1 56 3.64e-17 73.6
Msa0212310 AT4G29810.2 53.846 65 21 1 1 56 1 65 2.48e-14 65.9
Msa0212310 AT4G29810.3 53.846 65 21 1 1 56 1 65 2.50e-14 65.9

Find 9 sgRNAs with CRISPR-Local

Find 13 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCCTTTCTTCATGATTATT+TGG 0.138975 2_1:+54351766 None:intergenic
AGTATTTAATTTGCAATGTT+TGG 0.312418 2_1:+54351907 None:intergenic
GGAACATTGAGTTTGAGATT+TGG 0.333485 2_1:+54351735 None:intergenic
AACTTGCTTGTTAATAAAGA+TGG 0.423601 2_1:-54351553 Msa0212310:CDS
TAGCTCTCACATGAGAGCTT+AGG 0.494342 2_1:-54351791 Msa0212310:five_prime_UTR
TTTAATTTGCAATGTTTGGT+TGG 0.502390 2_1:+54351911 None:intergenic
AACCAAATAATCATGAAGAA+AGG 0.514356 2_1:-54351768 Msa0212310:exon
AAAGAAGCTTCATTAGATGA+AGG 0.524926 2_1:+54351714 None:intergenic
TTTATTTGTAGGACTCAAAG+TGG 0.592348 2_1:-54351592 Msa0212310:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTATTTAATTTGCAATGTT+TGG + chr2_1:54351482-54351501 None:intergenic 20.0%
!! AGTAATTGAGATTTATTTGT+AGG - chr2_1:54351783-54351802 Msa0212310:five_prime_UTR 20.0%
!!! TTTAATTTGCAATGTTTGGT+TGG + chr2_1:54351478-54351497 None:intergenic 25.0%
! AACCAAATAATCATGAAGAA+AGG - chr2_1:54351618-54351637 Msa0212310:intron 25.0%
! ATCCTTTCTTCATGATTATT+TGG + chr2_1:54351623-54351642 None:intergenic 25.0%
!!! ATTGTTTTGTTTTGTGTGTA+TGG - chr2_1:54351751-54351770 Msa0212310:CDS 25.0%
!!! AAAGTGGTACTTTTAAAGAA+GGG - chr2_1:54351810-54351829 Msa0212310:five_prime_UTR 25.0%
!! AACTTGCTTGTTAATAAAGA+TGG - chr2_1:54351833-54351852 Msa0212310:five_prime_UTR 25.0%
AAAGAAGCTTCATTAGATGA+AGG + chr2_1:54351675-54351694 None:intergenic 30.0%
TTTATTTGTAGGACTCAAAG+TGG - chr2_1:54351794-54351813 Msa0212310:five_prime_UTR 30.0%
!! CAAAGTGGTACTTTTAAAGA+AGG - chr2_1:54351809-54351828 Msa0212310:five_prime_UTR 30.0%
! GGAACATTGAGTTTGAGATT+TGG + chr2_1:54351654-54351673 None:intergenic 35.0%
TAGCTCTCACATGAGAGCTT+AGG - chr2_1:54351595-54351614 Msa0212310:intron 45.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 54351468 54351940 54351468 ID=Msa0212310;Name=Msa0212310
chr2_1 mRNA 54351468 54351940 54351468 ID=Msa0212310-mRNA-1;Parent=Msa0212310;Name=Msa0212310-mRNA-1;_AED=0.06;_eAED=0.06;_QI=162|1|0.5|1|1|1|2|0|70
chr2_1 exon 54351468 54351603 54351468 ID=Msa0212310-mRNA-1:exon:15048;Parent=Msa0212310-mRNA-1
chr2_1 exon 54351702 54351940 54351702 ID=Msa0212310-mRNA-1:exon:15047;Parent=Msa0212310-mRNA-1
chr2_1 five_prime_UTR 54351779 54351940 54351779 ID=Msa0212310-mRNA-1:five_prime_utr;Parent=Msa0212310-mRNA-1
chr2_1 CDS 54351702 54351778 54351702 ID=Msa0212310-mRNA-1:cds;Parent=Msa0212310-mRNA-1
chr2_1 CDS 54351468 54351603 54351468 ID=Msa0212310-mRNA-1:cds;Parent=Msa0212310-mRNA-1
Gene Sequence

>Msa0212310

ATGAAGAAAGGATGTTTAGCTCCAAATCTCAAACTCAATGTTCCTTCATCTAATGAAGCTTCTTTTGCAAAGTTTCTGACTCAAAGTGGTACTTTTAAAGAAGGGAACTTGCTTGTTAATAAAGATGGAGTTAGAATTGTTTCTCAAAGTGAAGTTGAAACTGTAACATATTTCTCTCTCTCTCAACTTTTATCTTGCATTTGTTTATTTTGA

Protein sequence

>Msa0212310

MKKGCLAPNLKLNVPSSNEASFAKFLTQSGTFKEGNLLVNKDGVRIVSQSEVETVTYFSLSQLLSCICLF*