AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0189520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0189520 MtrunA17_Chr2g0278531 92.063 63 5 0 25 87 11 73 4.71e-38 121
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0189520 AT1G25275.3 50.000 70 31 1 20 85 2 71 1.30e-17 70.9
Msa0189520 AT1G25275.1 50.000 70 31 1 20 85 2 71 1.59e-17 70.1
Msa0189520 AT1G25275.2 48.571 70 32 1 20 85 2 71 1.43e-16 67.8

Find 22 sgRNAs with CRISPR-Local

Find 105 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GATGCTTCTGATTGCCTTGA+TGG 0.154913 2_1:-4904785 Msa0189520:CDS
CTCTTTGAACGCAGGCAGTT+TGG 0.316423 2_1:+4904759 None:intergenic
AACAACCAAGTTTAATTAGA+AGG 0.335558 2_1:+4904081 None:intergenic
GCTACCTATTGAATGTTTGC+TGG 0.357659 2_1:-4904118 Msa0189520:three_prime_UTR
ACAACCAGCAAACATTCAAT+AGG 0.448858 2_1:+4904114 None:intergenic
ATTGTGATAGCTAGCAGAAT+TGG 0.459069 2_1:+4903960 None:intergenic
ATGTAGCAAGTAATTGCTTA+AGG 0.470851 2_1:-4903993 Msa0189520:three_prime_UTR
TGCTCGATTAGATGCGGTCC+AGG 0.477134 2_1:-4904524 Msa0189520:intron
TATTACCTTCTAATTAAACT+TGG 0.478187 2_1:-4904086 Msa0189520:three_prime_UTR
TGCAGATTCTATGGTGGAGA+AGG 0.494670 2_1:-4904247 Msa0189520:intron
TGAGACAGTTGACAAGTTGT+TGG 0.503043 2_1:+4904178 None:intergenic
TCAAGGCAATCAGAAGCATC+AGG 0.516390 2_1:+4904788 None:intergenic
GTGACATGCAGCAAGGCTTA+CGG 0.519988 2_1:-4904564 Msa0189520:intron
GCAGATTCTATGGTGGAGAA+GGG 0.551697 2_1:-4904246 Msa0189520:intron
AGGCAGTTTGGCAACCATCA+AGG 0.564306 2_1:+4904771 None:intergenic
GCATGCACTTCCACATGGAT+AGG 0.569600 2_1:-4905044 None:intergenic
TTCTATGGTGGAGAAGGGCA+TGG 0.592128 2_1:-4904241 Msa0189520:CDS
ATGCAGCAAGGCTTACGGCA+AGG 0.642528 2_1:-4904559 Msa0189520:intron
CGCAAGTGCTCGATTAGATG+CGG 0.643345 2_1:-4904530 Msa0189520:CDS
CTAACAGTCTCTTTGAACGC+AGG 0.676017 2_1:+4904751 None:intergenic
GAAGATGATGAAGAAGACGA+CGG 0.724386 2_1:-4904864 Msa0189520:CDS
GATGATGAAGAAGACGACGG+TGG 0.786514 2_1:-4904861 Msa0189520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! GAATTATTAAGAAAAGTAAA+AGG + chr2_1:4904231-4904250 None:intergenic 15.0%
!!! AAAGAAATGGTATTATTTTT+GGG + chr2_1:4904453-4904472 None:intergenic 15.0%
!!! AAAAGAAATGGTATTATTTT+TGG + chr2_1:4904454-4904473 None:intergenic 15.0%
!! CATTAAAAAAGAAAAAGAAA+TGG + chr2_1:4904466-4904485 None:intergenic 15.0%
!!! TCTTTTTCTTTTTTAATGAA+AGG - chr2_1:4904468-4904487 Msa0189520:intron 15.0%
!! GAATTATTAAGAAAAGTAAA+AGG + chr2_1:4904231-4904250 None:intergenic 15.0%
!!! AAAGAAATGGTATTATTTTT+GGG + chr2_1:4904453-4904472 None:intergenic 15.0%
!!! AAAAGAAATGGTATTATTTT+TGG + chr2_1:4904454-4904473 None:intergenic 15.0%
!! CATTAAAAAAGAAAAAGAAA+TGG + chr2_1:4904466-4904485 None:intergenic 15.0%
!!! TCTTTTTCTTTTTTAATGAA+AGG - chr2_1:4904468-4904487 Msa0189520:intron 15.0%
!! ATAATAATCTTGAGAAACTA+CGG + chr2_1:4903945-4903964 None:intergenic 20.0%
!! GAATCATAAAAAAAACATCT+AGG + chr2_1:4904007-4904026 None:intergenic 20.0%
!!! ATTTGTGATATTTTCTCAAA+TGG - chr2_1:4904117-4904136 Msa0189520:three_prime_UTR 20.0%
!!! CATTGTCTTCTTTTAATTTA+AGG - chr2_1:4904250-4904269 Msa0189520:intron 20.0%
!! CAAGAAATTTAATTAAACCT+CGG + chr2_1:4904536-4904555 None:intergenic 20.0%
!!! ATTTAATTTTGCAGATTCTA+TGG - chr2_1:4904683-4904702 Msa0189520:intron 20.0%
!! TATTACCTTCTAATTAAACT+TGG - chr2_1:4904853-4904872 Msa0189520:CDS 20.0%
!!! TTTTTAAGTTAAAAAGCTCA+AGG - chr2_1:4905027-4905046 Msa0189520:intron 20.0%
!! ATAATAATCTTGAGAAACTA+CGG + chr2_1:4903945-4903964 None:intergenic 20.0%
!! GAATCATAAAAAAAACATCT+AGG + chr2_1:4904007-4904026 None:intergenic 20.0%
!!! ATTTGTGATATTTTCTCAAA+TGG - chr2_1:4904117-4904136 Msa0189520:three_prime_UTR 20.0%
!!! CATTGTCTTCTTTTAATTTA+AGG - chr2_1:4904250-4904269 Msa0189520:intron 20.0%
!! CAAGAAATTTAATTAAACCT+CGG + chr2_1:4904536-4904555 None:intergenic 20.0%
!!! ATTTAATTTTGCAGATTCTA+TGG - chr2_1:4904683-4904702 Msa0189520:intron 20.0%
!! TATTACCTTCTAATTAAACT+TGG - chr2_1:4904853-4904872 Msa0189520:CDS 20.0%
!!! TTTTTAAGTTAAAAAGCTCA+AGG - chr2_1:4905027-4905046 Msa0189520:intron 20.0%
! GTAGTTTCTCAAGATTATTA+TGG - chr2_1:4903944-4903963 Msa0189520:three_prime_UTR 25.0%
! AACAACCAAGTTTAATTAGA+AGG + chr2_1:4904861-4904880 None:intergenic 25.0%
! GTAGTTTCTCAAGATTATTA+TGG - chr2_1:4903944-4903963 Msa0189520:three_prime_UTR 25.0%
! AACAACCAAGTTTAATTAGA+AGG + chr2_1:4904861-4904880 None:intergenic 25.0%
TTTGGGTAATGTTAATTACC+TGG + chr2_1:4904436-4904455 None:intergenic 30.0%
! TAATTTTGCAGATTCTATGG+TGG - chr2_1:4904686-4904705 Msa0189520:intron 30.0%
ATGTAGCAAGTAATTGCTTA+AGG - chr2_1:4904946-4904965 Msa0189520:intron 30.0%
TTTGGGTAATGTTAATTACC+TGG + chr2_1:4904436-4904455 None:intergenic 30.0%
! TAATTTTGCAGATTCTATGG+TGG - chr2_1:4904686-4904705 Msa0189520:intron 30.0%
ATGTAGCAAGTAATTGCTTA+AGG - chr2_1:4904946-4904965 Msa0189520:intron 30.0%
TAGGTGTGCATTTATGACTT+TGG - chr2_1:4903914-4903933 Msa0189520:three_prime_UTR 35.0%
! CTCTTTTCTCTTTGATCGTT+TGG + chr2_1:4904041-4904060 None:intergenic 35.0%
CTTGAATGATCGATAACAAC+AGG - chr2_1:4904552-4904571 Msa0189520:CDS 35.0%
ATAATATATTGTCTGAGCCC+AGG + chr2_1:4904637-4904656 None:intergenic 35.0%
ACAACCAGCAAACATTCAAT+AGG + chr2_1:4904828-4904847 None:intergenic 35.0%
ATTGTGATAGCTAGCAGAAT+TGG + chr2_1:4904982-4905001 None:intergenic 35.0%
ATAAATGCACACCTATCCAT+AGG + chr2_1:4903909-4903928 None:intergenic 35.0%
TAGGTGTGCATTTATGACTT+TGG - chr2_1:4903914-4903933 Msa0189520:three_prime_UTR 35.0%
! CTCTTTTCTCTTTGATCGTT+TGG + chr2_1:4904041-4904060 None:intergenic 35.0%
CTTGAATGATCGATAACAAC+AGG - chr2_1:4904552-4904571 Msa0189520:CDS 35.0%
ATAATATATTGTCTGAGCCC+AGG + chr2_1:4904637-4904656 None:intergenic 35.0%
ACAACCAGCAAACATTCAAT+AGG + chr2_1:4904828-4904847 None:intergenic 35.0%
ATTGTGATAGCTAGCAGAAT+TGG + chr2_1:4904982-4905001 None:intergenic 35.0%
GAAGATGATGAAGAAGACGA+CGG - chr2_1:4904075-4904094 Msa0189520:three_prime_UTR 40.0%
TATGTATGTGACATGCAGCA+AGG - chr2_1:4904368-4904387 Msa0189520:intron 40.0%
! TTAGTGCTGAAAAGATACCG+AGG - chr2_1:4904516-4904535 Msa0189520:intron 40.0%
ATGATCGATAACAACAGGTC+TGG - chr2_1:4904557-4904576 Msa0189520:intron 40.0%
TGATCGATAACAACAGGTCT+GGG - chr2_1:4904558-4904577 Msa0189520:intron 40.0%
TGAGACAGTTGACAAGTTGT+TGG + chr2_1:4904764-4904783 None:intergenic 40.0%
GCTACCTATTGAATGTTTGC+TGG - chr2_1:4904821-4904840 Msa0189520:CDS 40.0%
GAAGATGATGAAGAAGACGA+CGG - chr2_1:4904075-4904094 Msa0189520:three_prime_UTR 40.0%
TATGTATGTGACATGCAGCA+AGG - chr2_1:4904368-4904387 Msa0189520:intron 40.0%
! TTAGTGCTGAAAAGATACCG+AGG - chr2_1:4904516-4904535 Msa0189520:intron 40.0%
ATGATCGATAACAACAGGTC+TGG - chr2_1:4904557-4904576 Msa0189520:intron 40.0%
TGATCGATAACAACAGGTCT+GGG - chr2_1:4904558-4904577 Msa0189520:intron 40.0%
TGAGACAGTTGACAAGTTGT+TGG + chr2_1:4904764-4904783 None:intergenic 40.0%
GCTACCTATTGAATGTTTGC+TGG - chr2_1:4904821-4904840 Msa0189520:CDS 40.0%
!! TCAAGGCAATCAGAAGCATC+AGG + chr2_1:4904154-4904173 None:intergenic 45.0%
GATGCTTCTGATTGCCTTGA+TGG - chr2_1:4904154-4904173 Msa0189520:three_prime_UTR 45.0%
CTAACAGTCTCTTTGAACGC+AGG + chr2_1:4904191-4904210 None:intergenic 45.0%
! TGCAGATTCTATGGTGGAGA+AGG - chr2_1:4904692-4904711 Msa0189520:intron 45.0%
! GCAGATTCTATGGTGGAGAA+GGG - chr2_1:4904693-4904712 Msa0189520:intron 45.0%
!! TCAAGGCAATCAGAAGCATC+AGG + chr2_1:4904154-4904173 None:intergenic 45.0%
GATGCTTCTGATTGCCTTGA+TGG - chr2_1:4904154-4904173 Msa0189520:three_prime_UTR 45.0%
CTAACAGTCTCTTTGAACGC+AGG + chr2_1:4904191-4904210 None:intergenic 45.0%
! TGCAGATTCTATGGTGGAGA+AGG - chr2_1:4904692-4904711 Msa0189520:intron 45.0%
! GCAGATTCTATGGTGGAGAA+GGG - chr2_1:4904693-4904712 Msa0189520:intron 45.0%
GATGATGAAGAAGACGACGG+TGG - chr2_1:4904078-4904097 Msa0189520:three_prime_UTR 50.0%
AGGCAGTTTGGCAACCATCA+AGG + chr2_1:4904171-4904190 None:intergenic 50.0%
CTCTTTGAACGCAGGCAGTT+TGG + chr2_1:4904183-4904202 None:intergenic 50.0%
GTGACATGCAGCAAGGCTTA+CGG - chr2_1:4904375-4904394 Msa0189520:intron 50.0%
CGCAAGTGCTCGATTAGATG+CGG - chr2_1:4904409-4904428 Msa0189520:intron 50.0%
TCGATAACAACAGGTCTGGG+TGG - chr2_1:4904561-4904580 Msa0189520:intron 50.0%
! ACGCTAGTCTCACACACTAG+AGG - chr2_1:4904598-4904617 Msa0189520:intron 50.0%
! TTCTATGGTGGAGAAGGGCA+TGG - chr2_1:4904698-4904717 Msa0189520:intron 50.0%
GATGATGAAGAAGACGACGG+TGG - chr2_1:4904078-4904097 Msa0189520:three_prime_UTR 50.0%
AGGCAGTTTGGCAACCATCA+AGG + chr2_1:4904171-4904190 None:intergenic 50.0%
CTCTTTGAACGCAGGCAGTT+TGG + chr2_1:4904183-4904202 None:intergenic 50.0%
GTGACATGCAGCAAGGCTTA+CGG - chr2_1:4904375-4904394 Msa0189520:intron 50.0%
CGCAAGTGCTCGATTAGATG+CGG - chr2_1:4904409-4904428 Msa0189520:intron 50.0%
TCGATAACAACAGGTCTGGG+TGG - chr2_1:4904561-4904580 Msa0189520:intron 50.0%
! ACGCTAGTCTCACACACTAG+AGG - chr2_1:4904598-4904617 Msa0189520:intron 50.0%
! TTCTATGGTGGAGAAGGGCA+TGG - chr2_1:4904698-4904717 Msa0189520:intron 50.0%
ATGCAGCAAGGCTTACGGCA+AGG - chr2_1:4904380-4904399 Msa0189520:intron 55.0%
TGCTCGATTAGATGCGGTCC+AGG - chr2_1:4904415-4904434 Msa0189520:intron 55.0%
ACAGGTCTGGGTGGTGTAGT+CGG - chr2_1:4904570-4904589 Msa0189520:intron 55.0%
TCTGAGCCCAGGTTCGAACT+GGG + chr2_1:4904626-4904645 None:intergenic 55.0%
ATGCAGCAAGGCTTACGGCA+AGG - chr2_1:4904380-4904399 Msa0189520:intron 55.0%
TGCTCGATTAGATGCGGTCC+AGG - chr2_1:4904415-4904434 Msa0189520:intron 55.0%
ACAGGTCTGGGTGGTGTAGT+CGG - chr2_1:4904570-4904589 Msa0189520:intron 55.0%
TCTGAGCCCAGGTTCGAACT+GGG + chr2_1:4904626-4904645 None:intergenic 55.0%
AGAGGTCCCCAGTTCGAACC+TGG - chr2_1:4904616-4904635 Msa0189520:intron 60.0%
GAGGTCCCCAGTTCGAACCT+GGG - chr2_1:4904617-4904636 Msa0189520:intron 60.0%
CTGAGCCCAGGTTCGAACTG+GGG + chr2_1:4904625-4904644 None:intergenic 60.0%
GTCTGAGCCCAGGTTCGAAC+TGG + chr2_1:4904627-4904646 None:intergenic 60.0%
AGAGGTCCCCAGTTCGAACC+TGG - chr2_1:4904616-4904635 Msa0189520:intron 60.0%
GAGGTCCCCAGTTCGAACCT+GGG - chr2_1:4904617-4904636 Msa0189520:intron 60.0%
CTGAGCCCAGGTTCGAACTG+GGG + chr2_1:4904625-4904644 None:intergenic 60.0%
GTCTGAGCCCAGGTTCGAAC+TGG + chr2_1:4904627-4904646 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_1 gene 4903909 4905052 4903909 ID=Msa0189520;Name=Msa0189520
chr2_1 mRNA 4903909 4905052 4903909 ID=Msa0189520-mRNA-1;Parent=Msa0189520;Name=Msa0189520-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0.66|0.5|1|0.33|0.5|4|327|87
chr2_1 exon 4903909 4904264 4903909 ID=Msa0189520-mRNA-1:exon:2214;Parent=Msa0189520-mRNA-1
chr2_1 exon 4904525 4904575 4904525 ID=Msa0189520-mRNA-1:exon:2213;Parent=Msa0189520-mRNA-1
chr2_1 exon 4904756 4904931 4904756 ID=Msa0189520-mRNA-1:exon:2212;Parent=Msa0189520-mRNA-1
chr2_1 exon 4905045 4905052 4905045 ID=Msa0189520-mRNA-1:exon:2211;Parent=Msa0189520-mRNA-1
chr2_1 CDS 4905045 4905052 4905045 ID=Msa0189520-mRNA-1:cds;Parent=Msa0189520-mRNA-1
chr2_1 CDS 4904756 4904931 4904756 ID=Msa0189520-mRNA-1:cds;Parent=Msa0189520-mRNA-1
chr2_1 CDS 4904525 4904575 4904525 ID=Msa0189520-mRNA-1:cds;Parent=Msa0189520-mRNA-1
chr2_1 CDS 4904236 4904264 4904236 ID=Msa0189520-mRNA-1:cds;Parent=Msa0189520-mRNA-1
chr2_1 three_prime_UTR 4903909 4904235 4903909 ID=Msa0189520-mRNA-1:three_prime_utr;Parent=Msa0189520-mRNA-1
Gene Sequence

>Msa0189520

ATGGATAGAGAATCTACCAAACGATCAAAGAGAAAAGAGAAAGTAAAGTTAGTGAAGATGATGAAGAAGACGACGGTGGTTGCTATGATGCTTTTATTTGTGATATTTTCTCAAATGGATAGCGTTGTTCCTGATGCTTCTGATTGCCTTGATGGTTGCCAAACTGCCTGCGTTCAAAGAGACTCAAGGCTTACGGCAAGGTGTGAGCGCAAGTGCTCGATTAGATGCGGTCCAGATTCTATGGTGGAGAAGGGCATGGATTGA

Protein sequence

>Msa0189520

MDRESTKRSKRKEKVKLVKMMKKTTVVAMMLLFVIFSQMDSVVPDASDCLDGCQTACVQRDSRLTARCERKCSIRCGPDSMVEKGMD*