AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0532350


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0532350 MtrunA17_Chr4g0005821 89.552 67 7 0 6 72 534 600 2.50e-37 131
Msa0532350 MtrunA17_Chr7g0241611 70.423 71 20 1 6 75 540 610 2.19e-27 103
Msa0532350 MtrunA17_Chr7g0259681 64.865 74 19 2 2 68 471 544 5.73e-27 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0532350 AT3G09100.2 65.625 64 21 1 6 68 524 587 5.16e-24 94.4
Msa0532350 AT5G01290.1 61.765 68 24 1 6 71 508 575 9.63e-23 90.5
Msa0532350 AT5G28210.1 44.615 65 33 2 6 69 469 531 3.33e-11 57.8

Find 20 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAAGTCAACTGAATTTAAAT+TGG 0.286326 4_1:-6347505 None:intergenic
GAAACTCTTGGATGGGAATA+AGG 0.299659 4_1:+6347690 Msa0532350:CDS
TTCAGTTGACTTTCTGTTTG+AGG 0.348533 4_1:+6347515 Msa0532350:CDS
ATTATATTACTTACCAGGGT+TGG 0.417822 4_1:+6347430 Msa0532350:CDS
TTATATTACTTACCAGGGTT+GGG 0.435094 4_1:+6347431 Msa0532350:CDS
CCCTGGTAAGTAATATAATC+AGG 0.439481 4_1:-6347426 None:intergenic
TGCTTCCATCGGCAGGTTGA+AGG 0.440873 4_1:+6347628 Msa0532350:intron
TCCTGATTATATTACTTACC+AGG 0.458394 4_1:+6347425 Msa0532350:CDS
TCATGAGTACGTGGTACATA+AGG 0.478867 4_1:-6347459 None:intergenic
GGGAATAAGGTTGCTTTCAA+AGG 0.488951 4_1:+6347703 Msa0532350:CDS
ATCGGCAGGTTGAAGGTGAT+CGG 0.499299 4_1:+6347635 Msa0532350:intron
TCGGCAGGTTGAAGGTGATC+GGG 0.508639 4_1:+6347636 Msa0532350:intron
CTCATGAAGGACTCTTAAAG+TGG 0.522723 4_1:+6347475 Msa0532350:CDS
ACGGGGAAAGAAGAAACTCT+TGG 0.528706 4_1:+6347678 Msa0532350:CDS
GGAAAGAAGAAACTCTTGGA+TGG 0.547625 4_1:+6347682 Msa0532350:CDS
CCTGATTATATTACTTACCA+GGG 0.561320 4_1:+6347426 Msa0532350:CDS
TATGTACCACGTACTCATGA+AGG 0.583824 4_1:+6347462 Msa0532350:CDS
GAAAGAAGAAACTCTTGGAT+GGG 0.603849 4_1:+6347683 Msa0532350:CDS
CATAAGGATCGTCCCAACCC+TGG 0.604861 4_1:-6347443 None:intergenic
AAGAGTCCTTCATGAGTACG+TGG 0.699809 4_1:-6347468 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGTCAACTGAATTTAAAT+TGG - chr4_1:6347508-6347527 None:intergenic 20.0%
! TTGGAATTTCTGATATTACA+TGG + chr4_1:6347566-6347585 Msa0532350:intron 25.0%
TCCTGATTATATTACTTACC+AGG + chr4_1:6347425-6347444 Msa0532350:CDS 30.0%
CCTGATTATATTACTTACCA+GGG + chr4_1:6347426-6347445 Msa0532350:CDS 30.0%
ATTATATTACTTACCAGGGT+TGG + chr4_1:6347430-6347449 Msa0532350:CDS 30.0%
TTATATTACTTACCAGGGTT+GGG + chr4_1:6347431-6347450 Msa0532350:CDS 30.0%
! TATCATCACCTTCTTTTGTA+TGG + chr4_1:6347539-6347558 Msa0532350:intron 30.0%
!!! TAATTTTTAGCTGCTTCCAT+CGG + chr4_1:6347617-6347636 Msa0532350:intron 30.0%
!!! AGCTACTTTTTGTGTATGAA+CGG + chr4_1:6347659-6347678 Msa0532350:CDS 30.0%
CCCTGGTAAGTAATATAATC+AGG - chr4_1:6347429-6347448 None:intergenic 35.0%
! TTCAGTTGACTTTCTGTTTG+AGG + chr4_1:6347515-6347534 Msa0532350:CDS 35.0%
CCAAAACACCATACAAAAGA+AGG - chr4_1:6347550-6347569 None:intergenic 35.0%
! CCTTCTTTTGTATGGTGTTT+TGG + chr4_1:6347547-6347566 Msa0532350:intron 35.0%
AGCAGCTAAAAATTAGATGG+CGG - chr4_1:6347612-6347631 None:intergenic 35.0%
GGAAGCAGCTAAAAATTAGA+TGG - chr4_1:6347615-6347634 None:intergenic 35.0%
!!! GCTACTTTTTGTGTATGAAC+GGG + chr4_1:6347660-6347679 Msa0532350:CDS 35.0%
!!! CTACTTTTTGTGTATGAACG+GGG + chr4_1:6347661-6347680 Msa0532350:CDS 35.0%
GAAAGAAGAAACTCTTGGAT+GGG + chr4_1:6347683-6347702 Msa0532350:CDS 35.0%
TCATGAGTACGTGGTACATA+AGG - chr4_1:6347462-6347481 None:intergenic 40.0%
TATGTACCACGTACTCATGA+AGG + chr4_1:6347462-6347481 Msa0532350:CDS 40.0%
CTCATGAAGGACTCTTAAAG+TGG + chr4_1:6347475-6347494 Msa0532350:CDS 40.0%
GGAAAGAAGAAACTCTTGGA+TGG + chr4_1:6347682-6347701 Msa0532350:CDS 40.0%
GAAACTCTTGGATGGGAATA+AGG + chr4_1:6347690-6347709 Msa0532350:CDS 40.0%
! GGGAATAAGGTTGCTTTCAA+AGG + chr4_1:6347703-6347722 Msa0532350:CDS 40.0%
AAGAGTCCTTCATGAGTACG+TGG - chr4_1:6347471-6347490 None:intergenic 45.0%
ACGGGGAAAGAAGAAACTCT+TGG + chr4_1:6347678-6347697 Msa0532350:CDS 45.0%
!! TTTTAGCTGCTTCCATCGGC+AGG + chr4_1:6347621-6347640 Msa0532350:intron 50.0%
! ATCGGCAGGTTGAAGGTGAT+CGG + chr4_1:6347635-6347654 Msa0532350:intron 50.0%
CATAAGGATCGTCCCAACCC+TGG - chr4_1:6347446-6347465 None:intergenic 55.0%
! TGCTTCCATCGGCAGGTTGA+AGG + chr4_1:6347628-6347647 Msa0532350:intron 55.0%
GATCACCTTCAACCTGCCGA+TGG - chr4_1:6347636-6347655 None:intergenic 55.0%
! TCGGCAGGTTGAAGGTGATC+GGG + chr4_1:6347636-6347655 Msa0532350:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 6347414 6347771 6347414 ID=Msa0532350;Name=Msa0532350
chr4_1 mRNA 6347414 6347771 6347414 ID=Msa0532350-mRNA-1;Parent=Msa0532350;Name=Msa0532350-mRNA-1;_AED=0.38;_eAED=0.38;_QI=0|0|0|1|1|1|2|0|83
chr4_1 exon 6347414 6347536 6347414 ID=Msa0532350-mRNA-1:exon:2261;Parent=Msa0532350-mRNA-1
chr4_1 exon 6347643 6347771 6347643 ID=Msa0532350-mRNA-1:exon:2262;Parent=Msa0532350-mRNA-1
chr4_1 CDS 6347414 6347536 6347414 ID=Msa0532350-mRNA-1:cds;Parent=Msa0532350-mRNA-1
chr4_1 CDS 6347643 6347771 6347643 ID=Msa0532350-mRNA-1:cds;Parent=Msa0532350-mRNA-1
Gene Sequence

>Msa0532350

ATGAAGTTTGTTCCTGATTATATTACTTACCAGGGTTGGGACGATCCTTATGTACCACGTACTCATGAAGGACTCTTAAAGTGGAAATACGCCAATTTAAATTCAGTTGACTTTCTGTTTGAGGTTGAAGGTGATCGGGAGCTACTTTTTGTGTATGAACGGGGAAAGAAGAAACTCTTGGATGGGAATAAGGTTGCTTTCAAAGGTCAGACAAAGTTCATTTATTTTATATGTCCAACTTTGTTTTTATAA

Protein sequence

>Msa0532350

MKFVPDYITYQGWDDPYVPRTHEGLLKWKYANLNSVDFLFEVEGDRELLFVYERGKKKLLDGNKVAFKGQTKFIYFICPTLFL*