AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1257590


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1257590 MtrunA17_Chr3g0128201 97.778 135 3 0 1 135 59 193 6.03e-94 269
Msa1257590 MtrunA17_Chr5g0428861 85.075 134 20 0 1 134 59 192 3.11e-85 247
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1257590 AT1G33140.1 86.667 135 18 0 1 135 60 194 5.46e-85 247
Msa1257590 AT1G33120.1 86.667 135 18 0 1 135 60 194 5.46e-85 247
Msa1257590 AT4G10450.1 84.444 135 21 0 1 135 60 194 5.82e-83 241
Msa1257590 AT4G10450.2 84.112 107 17 0 1 107 60 166 4.35e-64 193

Find 34 sgRNAs with CRISPR-Local

Find 110 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTGAGATCCGAAACTTTAT+TGG 0.213194 8_2:+58226959 Msa1257590:CDS
TCGATGCTTGGTTTGGTTCC+AGG 0.300629 8_2:+58226795 Msa1257590:CDS
GGTGAAGGATGAGGTTGTTT+TGG 0.319250 8_2:+58227413 Msa1257590:CDS
CTCAAGATCGATGCTTGGTT+TGG 0.321969 8_2:+58226788 None:intergenic
ATGACATTGAGCTTGTTTCT+AGG 0.326351 8_2:+58227442 Msa1257590:CDS
TCTTCTCTCCAATAAAGTTT+CGG 0.368690 8_2:-58226967 None:intergenic
CTCAATCGACTTGTTGTCAT+TGG 0.397158 8_2:-58226942 None:intergenic
GGTATTTATGTTAGTGAGAA+GGG 0.433044 8_2:+58227624 Msa1257590:CDS
ATTGGTGATGCTAGCGTTGA+TGG 0.438976 8_2:-58226924 None:intergenic
GATATCAGGAAGTTTCTTGA+TGG 0.450730 8_2:+58227603 Msa1257590:CDS
AGGAAAGTAGATTTGCTTGA+TGG 0.454716 8_2:+58227366 Msa1257590:CDS
AGCAGTTCTGATGGCGGCGG+AGG 0.457127 8_2:-58226822 None:intergenic
TTCTTCTCAAGATCGATGCT+TGG 0.472069 8_2:+58226783 None:intergenic
AAACTTTATTGGAGAGAAGA+AGG 0.475592 8_2:+58226970 Msa1257590:CDS
TTCAATTGTTCGATCTGAGA+AGG 0.526562 8_2:+58227392 Msa1257590:CDS
TGGTATTTATGTTAGTGAGA+AGG 0.531892 8_2:+58227623 Msa1257590:CDS
TTGGTGATGCTAGCGTTGAT+GGG 0.543746 8_2:-58226923 None:intergenic
TTATGTTAGTGAGAAGGGAT+CGG 0.552761 8_2:+58227629 Msa1257590:CDS
CACGTTGAGAATCTCATCAC+TGG 0.554104 8_2:+58226851 Msa1257590:CDS
CATCTTGTAGCGGAAACCCT+TGG 0.558729 8_2:-58226879 None:intergenic
AGGGTTTCCGCTACAAGATG+AGG 0.564650 8_2:+58226882 Msa1257590:CDS
ATCTGAGAAGGTGAAGGATG+AGG 0.567425 8_2:+58227404 Msa1257590:CDS
CTCATCACTGGTGTTACCAA+GGG 0.573994 8_2:+58226863 Msa1257590:CDS
GAGAGCAGTTCTGATGGCGG+CGG 0.574544 8_2:-58226825 None:intergenic
GTGGCTGAGAGCAGTTCTGA+TGG 0.581831 8_2:-58226831 None:intergenic
TCTCATCACTGGTGTTACCA+AGG 0.595050 8_2:+58226862 Msa1257590:CDS
GTCATGTGCACTTATTAACC+AGG 0.625933 8_2:+58227464 Msa1257590:CDS
TGTTCGATCTGAGAAGGTGA+AGG 0.628133 8_2:+58227398 Msa1257590:CDS
GGTGGTATCTGAAGAATAGA+CGG 0.636082 8_2:+58227650 Msa1257590:exon
TGTTAGTGAGAAGGGATCGG+TGG 0.651106 8_2:+58227632 Msa1257590:CDS
TGGTGATGCTAGCGTTGATG+GGG 0.676063 8_2:-58226922 None:intergenic
GCTGAGAGCAGTTCTGATGG+CGG 0.677632 8_2:-58226828 None:intergenic
ACACAAACCTCATCTTGTAG+CGG 0.691692 8_2:-58226889 None:intergenic
CAGTGATGAGATTCTCAACG+TGG 0.725921 8_2:-58226850 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTTAATTTCTTCAATTTT+AGG + chr8_2:58227024-58227043 Msa1257590:intron 10.0%
!! TATAAATTAGATTAAAACTA+GGG - chr8_2:58227091-58227110 None:intergenic 10.0%
!! TTATAAATTAGATTAAAACT+AGG - chr8_2:58227092-58227111 None:intergenic 10.0%
!!! ATGAGTTAATTTTTTTATTT+TGG + chr8_2:58227234-58227253 Msa1257590:intron 10.0%
!!! ATTTTAATTTCTTCAATTTT+AGG + chr8_2:58227024-58227043 Msa1257590:intron 10.0%
!! TATAAATTAGATTAAAACTA+GGG - chr8_2:58227091-58227110 None:intergenic 10.0%
!! TTATAAATTAGATTAAAACT+AGG - chr8_2:58227092-58227111 None:intergenic 10.0%
!!! ATGAGTTAATTTTTTTATTT+TGG + chr8_2:58227234-58227253 Msa1257590:intron 10.0%
!!! AAATAAGTTAATCTTTTATC+TGG + chr8_2:58227202-58227221 Msa1257590:intron 15.0%
!!! AAATAAGTTAATCTTTTATC+TGG + chr8_2:58227202-58227221 Msa1257590:intron 15.0%
!! TAAAATTGCATAAAACAACA+AGG - chr8_2:58227058-58227077 None:intergenic 20.0%
!! TAAAATTGCATAAAACAACA+AGG - chr8_2:58227058-58227077 None:intergenic 20.0%
! GAGATAATGTCTGATTTATT+TGG + chr8_2:58227268-58227287 Msa1257590:intron 25.0%
! GAATCGAATAATGTTGTATT+AGG + chr8_2:58227341-58227360 Msa1257590:intron 25.0%
! ACAAAAATAAAGCATGTTCA+TGG - chr8_2:58227508-58227527 None:intergenic 25.0%
!! GAATGTTATTGTTGTGTTTT+TGG + chr8_2:58227554-58227573 Msa1257590:intron 25.0%
!! TGATATCCTTCTTTTTAACA+TGG - chr8_2:58227590-58227609 None:intergenic 25.0%
! ATGTTAAAAAGAAGGATATC+AGG + chr8_2:58227589-58227608 Msa1257590:CDS 25.0%
! GAGATAATGTCTGATTTATT+TGG + chr8_2:58227268-58227287 Msa1257590:intron 25.0%
! GAATCGAATAATGTTGTATT+AGG + chr8_2:58227341-58227360 Msa1257590:intron 25.0%
! ACAAAAATAAAGCATGTTCA+TGG - chr8_2:58227508-58227527 None:intergenic 25.0%
!! GAATGTTATTGTTGTGTTTT+TGG + chr8_2:58227554-58227573 Msa1257590:intron 25.0%
!! TGATATCCTTCTTTTTAACA+TGG - chr8_2:58227590-58227609 None:intergenic 25.0%
! ATGTTAAAAAGAAGGATATC+AGG + chr8_2:58227589-58227608 Msa1257590:CDS 25.0%
ATTGAGATCCGAAACTTTAT+TGG + chr8_2:58226959-58226978 Msa1257590:CDS 30.0%
TCTTCTCTCCAATAAAGTTT+CGG - chr8_2:58226970-58226989 None:intergenic 30.0%
AAACTTTATTGGAGAGAAGA+AGG + chr8_2:58226970-58226989 Msa1257590:CDS 30.0%
GTCTGATTTATTTGGTTATC+TGG + chr8_2:58227276-58227295 Msa1257590:intron 30.0%
! TTTACTAGTTTGAGAATCTG+TGG + chr8_2:58227314-58227333 Msa1257590:intron 30.0%
GAATAATGTTGTATTAGGTG+AGG + chr8_2:58227346-58227365 Msa1257590:intron 30.0%
GAAATGCCATGTTAAAAAGA+AGG + chr8_2:58227581-58227600 Msa1257590:intron 30.0%
TGGTATTTATGTTAGTGAGA+AGG + chr8_2:58227623-58227642 Msa1257590:CDS 30.0%
GGTATTTATGTTAGTGAGAA+GGG + chr8_2:58227624-58227643 Msa1257590:CDS 30.0%
ATTGAGATCCGAAACTTTAT+TGG + chr8_2:58226959-58226978 Msa1257590:CDS 30.0%
TCTTCTCTCCAATAAAGTTT+CGG - chr8_2:58226970-58226989 None:intergenic 30.0%
AAACTTTATTGGAGAGAAGA+AGG + chr8_2:58226970-58226989 Msa1257590:CDS 30.0%
GTCTGATTTATTTGGTTATC+TGG + chr8_2:58227276-58227295 Msa1257590:intron 30.0%
! TTTACTAGTTTGAGAATCTG+TGG + chr8_2:58227314-58227333 Msa1257590:intron 30.0%
GAATAATGTTGTATTAGGTG+AGG + chr8_2:58227346-58227365 Msa1257590:intron 30.0%
GAAATGCCATGTTAAAAAGA+AGG + chr8_2:58227581-58227600 Msa1257590:intron 30.0%
TGGTATTTATGTTAGTGAGA+AGG + chr8_2:58227623-58227642 Msa1257590:CDS 30.0%
GGTATTTATGTTAGTGAGAA+GGG + chr8_2:58227624-58227643 Msa1257590:CDS 30.0%
! AGGAAAGTAGATTTGCTTGA+TGG + chr8_2:58227366-58227385 Msa1257590:CDS 35.0%
TTCAATTGTTCGATCTGAGA+AGG + chr8_2:58227392-58227411 Msa1257590:CDS 35.0%
! ATGACATTGAGCTTGTTTCT+AGG + chr8_2:58227442-58227461 Msa1257590:CDS 35.0%
ATGTTCATGGACCATGTTAA+GGG - chr8_2:58227495-58227514 None:intergenic 35.0%
GATATCAGGAAGTTTCTTGA+TGG + chr8_2:58227603-58227622 Msa1257590:CDS 35.0%
TTATGTTAGTGAGAAGGGAT+CGG + chr8_2:58227629-58227648 Msa1257590:CDS 35.0%
! AGGAAAGTAGATTTGCTTGA+TGG + chr8_2:58227366-58227385 Msa1257590:CDS 35.0%
TTCAATTGTTCGATCTGAGA+AGG + chr8_2:58227392-58227411 Msa1257590:CDS 35.0%
! ATGACATTGAGCTTGTTTCT+AGG + chr8_2:58227442-58227461 Msa1257590:CDS 35.0%
ATGTTCATGGACCATGTTAA+GGG - chr8_2:58227495-58227514 None:intergenic 35.0%
GATATCAGGAAGTTTCTTGA+TGG + chr8_2:58227603-58227622 Msa1257590:CDS 35.0%
TTATGTTAGTGAGAAGGGAT+CGG + chr8_2:58227629-58227648 Msa1257590:CDS 35.0%
ACACAAACCTCATCTTGTAG+CGG - chr8_2:58226892-58226911 None:intergenic 40.0%
!! CTCAATCGACTTGTTGTCAT+TGG - chr8_2:58226945-58226964 None:intergenic 40.0%
!!! AAGGATGAGGTTGTTTTGGA+TGG + chr8_2:58227417-58227436 Msa1257590:CDS 40.0%
GTCATGTGCACTTATTAACC+AGG + chr8_2:58227464-58227483 Msa1257590:CDS 40.0%
TGTTCATGGACCATGTTAAG+GGG - chr8_2:58227494-58227513 None:intergenic 40.0%
CATGTTCATGGACCATGTTA+AGG - chr8_2:58227496-58227515 None:intergenic 40.0%
GGTGGTATCTGAAGAATAGA+CGG + chr8_2:58227650-58227669 Msa1257590:exon 40.0%
ACACAAACCTCATCTTGTAG+CGG - chr8_2:58226892-58226911 None:intergenic 40.0%
!! CTCAATCGACTTGTTGTCAT+TGG - chr8_2:58226945-58226964 None:intergenic 40.0%
!!! AAGGATGAGGTTGTTTTGGA+TGG + chr8_2:58227417-58227436 Msa1257590:CDS 40.0%
GTCATGTGCACTTATTAACC+AGG + chr8_2:58227464-58227483 Msa1257590:CDS 40.0%
TGTTCATGGACCATGTTAAG+GGG - chr8_2:58227494-58227513 None:intergenic 40.0%
CATGTTCATGGACCATGTTA+AGG - chr8_2:58227496-58227515 None:intergenic 40.0%
GGTGGTATCTGAAGAATAGA+CGG + chr8_2:58227650-58227669 Msa1257590:exon 40.0%
CAGTGATGAGATTCTCAACG+TGG - chr8_2:58226853-58226872 None:intergenic 45.0%
CACGTTGAGAATCTCATCAC+TGG + chr8_2:58226851-58226870 Msa1257590:CDS 45.0%
!! TCTCATCACTGGTGTTACCA+AGG + chr8_2:58226862-58226881 Msa1257590:CDS 45.0%
!! CTCATCACTGGTGTTACCAA+GGG + chr8_2:58226863-58226882 Msa1257590:CDS 45.0%
!! TTGGTGATGCTAGCGTTGAT+GGG - chr8_2:58226926-58226945 None:intergenic 45.0%
!! ATTGGTGATGCTAGCGTTGA+TGG - chr8_2:58226927-58226946 None:intergenic 45.0%
TGTTCGATCTGAGAAGGTGA+AGG + chr8_2:58227398-58227417 Msa1257590:CDS 45.0%
ATCTGAGAAGGTGAAGGATG+AGG + chr8_2:58227404-58227423 Msa1257590:CDS 45.0%
! GGTGAAGGATGAGGTTGTTT+TGG + chr8_2:58227413-58227432 Msa1257590:CDS 45.0%
CAGTGATGAGATTCTCAACG+TGG - chr8_2:58226853-58226872 None:intergenic 45.0%
CACGTTGAGAATCTCATCAC+TGG + chr8_2:58226851-58226870 Msa1257590:CDS 45.0%
!! TCTCATCACTGGTGTTACCA+AGG + chr8_2:58226862-58226881 Msa1257590:CDS 45.0%
!! CTCATCACTGGTGTTACCAA+GGG + chr8_2:58226863-58226882 Msa1257590:CDS 45.0%
!! TTGGTGATGCTAGCGTTGAT+GGG - chr8_2:58226926-58226945 None:intergenic 45.0%
!! ATTGGTGATGCTAGCGTTGA+TGG - chr8_2:58226927-58226946 None:intergenic 45.0%
TGTTCGATCTGAGAAGGTGA+AGG + chr8_2:58227398-58227417 Msa1257590:CDS 45.0%
ATCTGAGAAGGTGAAGGATG+AGG + chr8_2:58227404-58227423 Msa1257590:CDS 45.0%
! GGTGAAGGATGAGGTTGTTT+TGG + chr8_2:58227413-58227432 Msa1257590:CDS 45.0%
!! TCGATGCTTGGTTTGGTTCC+AGG + chr8_2:58226795-58226814 Msa1257590:CDS 50.0%
! CATCTTGTAGCGGAAACCCT+TGG - chr8_2:58226882-58226901 None:intergenic 50.0%
AGGGTTTCCGCTACAAGATG+AGG + chr8_2:58226882-58226901 Msa1257590:CDS 50.0%
!! TGGTGATGCTAGCGTTGATG+GGG - chr8_2:58226925-58226944 None:intergenic 50.0%
ACCAGGTACACCCCTTAACA+TGG + chr8_2:58227481-58227500 Msa1257590:intron 50.0%
! ACCATGTTAAGGGGTGTACC+TGG - chr8_2:58227485-58227504 None:intergenic 50.0%
TGTTAGTGAGAAGGGATCGG+TGG + chr8_2:58227632-58227651 Msa1257590:CDS 50.0%
!! TCGATGCTTGGTTTGGTTCC+AGG + chr8_2:58226795-58226814 Msa1257590:CDS 50.0%
! CATCTTGTAGCGGAAACCCT+TGG - chr8_2:58226882-58226901 None:intergenic 50.0%
AGGGTTTCCGCTACAAGATG+AGG + chr8_2:58226882-58226901 Msa1257590:CDS 50.0%
!! TGGTGATGCTAGCGTTGATG+GGG - chr8_2:58226925-58226944 None:intergenic 50.0%
ACCAGGTACACCCCTTAACA+TGG + chr8_2:58227481-58227500 Msa1257590:intron 50.0%
! ACCATGTTAAGGGGTGTACC+TGG - chr8_2:58227485-58227504 None:intergenic 50.0%
TGTTAGTGAGAAGGGATCGG+TGG + chr8_2:58227632-58227651 Msa1257590:CDS 50.0%
! GCTGAGAGCAGTTCTGATGG+CGG - chr8_2:58226831-58226850 None:intergenic 55.0%
! GTGGCTGAGAGCAGTTCTGA+TGG - chr8_2:58226834-58226853 None:intergenic 55.0%
! GCTGAGAGCAGTTCTGATGG+CGG - chr8_2:58226831-58226850 None:intergenic 55.0%
! GTGGCTGAGAGCAGTTCTGA+TGG - chr8_2:58226834-58226853 None:intergenic 55.0%
!! GAGAGCAGTTCTGATGGCGG+CGG - chr8_2:58226828-58226847 None:intergenic 60.0%
!! GAGAGCAGTTCTGATGGCGG+CGG - chr8_2:58226828-58226847 None:intergenic 60.0%
!! GATGGCGGCGGAGGTTTTCC+TGG - chr8_2:58226816-58226835 None:intergenic 65.0%
!! AGCAGTTCTGATGGCGGCGG+AGG - chr8_2:58226825-58226844 None:intergenic 65.0%
!! GATGGCGGCGGAGGTTTTCC+TGG - chr8_2:58226816-58226835 None:intergenic 65.0%
!! AGCAGTTCTGATGGCGGCGG+AGG - chr8_2:58226825-58226844 None:intergenic 65.0%
Chromosome Type Strat End Strand Name
chr8_2 gene 58226794 58227677 58226794 ID=Msa1257590;Name=Msa1257590
chr8_2 mRNA 58226794 58227677 58226794 ID=Msa1257590-mRNA-1;Parent=Msa1257590;Name=Msa1257590-mRNA-1;_AED=0.10;_eAED=0.10;_QI=0|1|0.66|1|1|1|3|9|135
chr8_2 exon 58226794 58226991 58226794 ID=Msa1257590-mRNA-1:exon:18053;Parent=Msa1257590-mRNA-1
chr8_2 exon 58227363 58227485 58227363 ID=Msa1257590-mRNA-1:exon:18054;Parent=Msa1257590-mRNA-1
chr8_2 exon 58227582 58227677 58227582 ID=Msa1257590-mRNA-1:exon:18055;Parent=Msa1257590-mRNA-1
chr8_2 CDS 58226794 58226991 58226794 ID=Msa1257590-mRNA-1:cds;Parent=Msa1257590-mRNA-1
chr8_2 CDS 58227363 58227485 58227363 ID=Msa1257590-mRNA-1:cds;Parent=Msa1257590-mRNA-1
chr8_2 CDS 58227582 58227668 58227582 ID=Msa1257590-mRNA-1:cds;Parent=Msa1257590-mRNA-1
chr8_2 three_prime_UTR 58227669 58227677 58227669 ID=Msa1257590-mRNA-1:three_prime_utr;Parent=Msa1257590-mRNA-1
Gene Sequence

>Msa1257590

ATCGATGCTTGGTTTGGTTCCAGGAAAACCTCCGCCGCCATCAGAACTGCTCTCAGCCACGTTGAGAATCTCATCACTGGTGTTACCAAGGGTTTCCGCTACAAGATGAGGTTTGTGTATGCTCATTTCCCCATCAACGCTAGCATCACCAATGACAACAAGTCGATTGAGATCCGAAACTTTATTGGAGAGAAGAAGGTGAGGAAAGTAGATTTGCTTGATGGAGTTTCAATTGTTCGATCTGAGAAGGTGAAGGATGAGGTTGTTTTGGATGGAAATGACATTGAGCTTGTTTCTAGGTCATGTGCACTTATTAACCAGAAATGCCATGTTAAAAAGAAGGATATCAGGAAGTTTCTTGATGGTATTTATGTTAGTGAGAAGGGATCGGTGGTATCTGAAGAATAG

Protein sequence

>Msa1257590

IDAWFGSRKTSAAIRTALSHVENLITGVTKGFRYKMRFVYAHFPINASITNDNKSIEIRNFIGEKKVRKVDLLDGVSIVRSEKVKDEVVLDGNDIELVSRSCALINQKCHVKKKDIRKFLDGIYVSEKGSVVSEE*