AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0646020

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0646020 MtrunA17_Chr4g0034761 92.708 96 5 1 1 96 11 104 2.09e-61 182
Msa0646020 MtrunA17_Chr5g0446661 60.215 93 30 2 1 87 1 92 1.01e-25 91.7
Msa0646020 MtrunA17_Chr3g0078771 61.538 78 24 1 1 72 1 78 2.44e-22 83.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0646020 AT1G49310.1 42.254 71 37 2 8 74 12 82 7.49e-13 58.9

Find 29 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTTTCTTCTTCTGCTTCT+TGG 0.153872 4_3:+51548670 None:intergenic
TTAATATCTTATATGTTATA+TGG 0.245081 4_3:-51548580 Msa0646020:three_prime_UTR
GAAAAGACTTGGGAGATTAT+TGG 0.261061 4_3:-51548826 Msa0646020:CDS
AATTAGATTTGTTAGTTTGA+TGG 0.285742 4_3:+51549077 None:intergenic
CTCCCCAGATGTATTGTGTT+TGG 0.312718 4_3:-51548337 Msa0646020:three_prime_UTR
ACAAGTTCTTTGATTGCTTC+AGG 0.324229 4_3:+51548776 None:intergenic
TTGTTGGCACCAGTTGAAAT+TGG 0.331468 4_3:-51549169 None:intergenic
AAATACATCTATAGATAAAA+AGG 0.351346 4_3:+51548479 None:intergenic
AACTCTGAACAAGAGCTTCA+TGG 0.354626 4_3:-51548632 Msa0646020:CDS
AATACCAAACACAATACATC+TGG 0.373946 4_3:+51548333 None:intergenic
GATACATCAATCAAATCTAT+TGG 0.418852 4_3:+51548401 None:intergenic
CTCTTATGCAAGAAAAGACT+TGG 0.442343 4_3:-51548837 Msa0646020:CDS
GAGTATGAGAGAAGCAAAGA+TGG 0.451907 4_3:+51549020 None:intergenic
GATTTGTTAGTTTGATGGCT+AGG 0.457950 4_3:+51549082 None:intergenic
TCTTTGATTGCTTCAGGCAT+AGG 0.472850 4_3:+51548782 None:intergenic
ACGGTTGTACCAATTTCAAC+TGG 0.472939 4_3:+51549160 None:intergenic
AGTCAAAAGACAGTGAAACT+TGG 0.478801 4_3:-51548303 Msa0646020:three_prime_UTR
GTGTGATATAATATGACATT+AGG 0.480243 4_3:+51548704 None:intergenic
TGATTGCTTCAGGCATAGGT+TGG 0.514568 4_3:+51548786 None:intergenic
TGGTACAACCGTGTATAAAG+TGG 0.539054 4_3:-51549149 Msa0646020:five_prime_UTR
AGAACTTGTTCAAAATCAAG+AGG 0.539159 4_3:-51548762 Msa0646020:CDS
TTTGATTGATGTATCTAGTG+TGG 0.552142 4_3:-51548393 Msa0646020:three_prime_UTR
ATACCAAACACAATACATCT+GGG 0.600413 4_3:+51548334 None:intergenic
AAAAGACAGTGAAACTTGGA+TGG 0.605833 4_3:-51548299 Msa0646020:three_prime_UTR
TCTTATGCAAGAAAAGACTT+GGG 0.611202 4_3:-51548836 Msa0646020:CDS
TAAAAGTCCACATCTTAGCA+AGG 0.615141 4_3:-51549055 Msa0646020:five_prime_UTR
GGTACAACCGTGTATAAAGT+GGG 0.640534 4_3:-51549148 Msa0646020:five_prime_UTR
AAAGGGGCCCACTTTATACA+CGG 0.655601 4_3:+51549141 None:intergenic
TACCAAACACAATACATCTG+GGG 0.678240 4_3:+51548335 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAATATCTTATATGTTATA+TGG - chr4_3:51548867-51548886 Msa0646020:intron 10.0%
!! TTAATATCTTATATGTTATA+TGG - chr4_3:51548867-51548886 Msa0646020:intron 10.0%
!! ACAATATAGTATAAATTGAT+TGG + chr4_3:51548545-51548564 None:intergenic 15.0%
!!! AATTTTCTTTGTACTAAAAT+AGG - chr4_3:51548577-51548596 Msa0646020:three_prime_UTR 15.0%
!!! TATTTAAGGTTTATTTTGTA+GGG - chr4_3:51548901-51548920 Msa0646020:intron 15.0%
!! AAATACATCTATAGATAAAA+AGG + chr4_3:51548971-51548990 None:intergenic 15.0%
!!! TATCTATAGATGTATTTTTA+TGG - chr4_3:51548974-51548993 Msa0646020:intron 15.0%
!! ACAATATAGTATAAATTGAT+TGG + chr4_3:51548545-51548564 None:intergenic 15.0%
!!! AATTTTCTTTGTACTAAAAT+AGG - chr4_3:51548577-51548596 Msa0646020:three_prime_UTR 15.0%
!!! TATTTAAGGTTTATTTTGTA+GGG - chr4_3:51548901-51548920 Msa0646020:intron 15.0%
!! AAATACATCTATAGATAAAA+AGG + chr4_3:51548971-51548990 None:intergenic 15.0%
!!! TATCTATAGATGTATTTTTA+TGG - chr4_3:51548974-51548993 Msa0646020:intron 15.0%
!!! AATTAGATTTGTTAGTTTGA+TGG + chr4_3:51548373-51548392 None:intergenic 20.0%
!! TTAGTACAAAGAAAATTGAA+AGG + chr4_3:51548574-51548593 None:intergenic 20.0%
!! TGGAAAAAGATTAGTATTTA+AGG - chr4_3:51548887-51548906 Msa0646020:intron 20.0%
!!! GTATTTAAGGTTTATTTTGT+AGG - chr4_3:51548900-51548919 Msa0646020:intron 20.0%
!!! TAAAGTTGTATTTTTGTTGA+TGG - chr4_3:51548939-51548958 Msa0646020:intron 20.0%
!!! AATTAGATTTGTTAGTTTGA+TGG + chr4_3:51548373-51548392 None:intergenic 20.0%
!! TTAGTACAAAGAAAATTGAA+AGG + chr4_3:51548574-51548593 None:intergenic 20.0%
!! TGGAAAAAGATTAGTATTTA+AGG - chr4_3:51548887-51548906 Msa0646020:intron 20.0%
!!! GTATTTAAGGTTTATTTTGT+AGG - chr4_3:51548900-51548919 Msa0646020:intron 20.0%
!!! TAAAGTTGTATTTTTGTTGA+TGG - chr4_3:51548939-51548958 Msa0646020:intron 20.0%
!! TTCTTTTTATAGGCCAAAAA+GGG + chr4_3:51548326-51548345 None:intergenic 25.0%
!! TTTCTTTTTATAGGCCAAAA+AGG + chr4_3:51548327-51548346 None:intergenic 25.0%
!!! CTCTGACTATTTCTTTTTAT+AGG + chr4_3:51548336-51548355 None:intergenic 25.0%
! CTATAAAAAGAAATAGTCAG+AGG - chr4_3:51548334-51548353 Msa0646020:three_prime_UTR 25.0%
! GTGTGATATAATATGACATT+AGG + chr4_3:51548746-51548765 None:intergenic 25.0%
!!! TTTTTTGCTGCATCTATTTT+TGG - chr4_3:51549005-51549024 Msa0646020:CDS 25.0%
!!! TTTTTGCTGCATCTATTTTT+GGG - chr4_3:51549006-51549025 Msa0646020:CDS 25.0%
! GATACATCAATCAAATCTAT+TGG + chr4_3:51549049-51549068 None:intergenic 25.0%
!! TTCTTTTTATAGGCCAAAAA+GGG + chr4_3:51548326-51548345 None:intergenic 25.0%
!! TTTCTTTTTATAGGCCAAAA+AGG + chr4_3:51548327-51548346 None:intergenic 25.0%
!!! CTCTGACTATTTCTTTTTAT+AGG + chr4_3:51548336-51548355 None:intergenic 25.0%
! CTATAAAAAGAAATAGTCAG+AGG - chr4_3:51548334-51548353 Msa0646020:three_prime_UTR 25.0%
! GTGTGATATAATATGACATT+AGG + chr4_3:51548746-51548765 None:intergenic 25.0%
!!! TTTTTTGCTGCATCTATTTT+TGG - chr4_3:51549005-51549024 Msa0646020:CDS 25.0%
!!! TTTTTGCTGCATCTATTTTT+GGG - chr4_3:51549006-51549025 Msa0646020:CDS 25.0%
! GATACATCAATCAAATCTAT+TGG + chr4_3:51549049-51549068 None:intergenic 25.0%
! TCTTTTTATAGGCCAAAAAG+GGG + chr4_3:51548325-51548344 None:intergenic 30.0%
!!! ATTTTTTCCTTGCTAAGATG+TGG + chr4_3:51548402-51548421 None:intergenic 30.0%
TCTTATGCAAGAAAAGACTT+GGG - chr4_3:51548611-51548630 Msa0646020:exon 30.0%
! AGAACTTGTTCAAAATCAAG+AGG - chr4_3:51548685-51548704 Msa0646020:CDS 30.0%
CTTCATGGAACATAAAAACA+TGG - chr4_3:51548830-51548849 Msa0646020:CDS 30.0%
ATGGAACATAAAAACATGGT+TGG - chr4_3:51548834-51548853 Msa0646020:CDS 30.0%
TTTGATTGATGTATCTAGTG+TGG - chr4_3:51549054-51549073 Msa0646020:five_prime_UTR 30.0%
ATACCAAACACAATACATCT+GGG + chr4_3:51549116-51549135 None:intergenic 30.0%
AATACCAAACACAATACATC+TGG + chr4_3:51549117-51549136 None:intergenic 30.0%
! TCTTTTTATAGGCCAAAAAG+GGG + chr4_3:51548325-51548344 None:intergenic 30.0%
!!! ATTTTTTCCTTGCTAAGATG+TGG + chr4_3:51548402-51548421 None:intergenic 30.0%
TCTTATGCAAGAAAAGACTT+GGG - chr4_3:51548611-51548630 Msa0646020:exon 30.0%
! AGAACTTGTTCAAAATCAAG+AGG - chr4_3:51548685-51548704 Msa0646020:CDS 30.0%
CTTCATGGAACATAAAAACA+TGG - chr4_3:51548830-51548849 Msa0646020:CDS 30.0%
ATGGAACATAAAAACATGGT+TGG - chr4_3:51548834-51548853 Msa0646020:CDS 30.0%
TTTGATTGATGTATCTAGTG+TGG - chr4_3:51549054-51549073 Msa0646020:five_prime_UTR 30.0%
ATACCAAACACAATACATCT+GGG + chr4_3:51549116-51549135 None:intergenic 30.0%
AATACCAAACACAATACATC+TGG + chr4_3:51549117-51549136 None:intergenic 30.0%
!! GATTTGTTAGTTTGATGGCT+AGG + chr4_3:51548368-51548387 None:intergenic 35.0%
TAAAAGTCCACATCTTAGCA+AGG - chr4_3:51548392-51548411 Msa0646020:three_prime_UTR 35.0%
! CATACTCTTTTCTCTTCTTC+TGG - chr4_3:51548443-51548462 Msa0646020:three_prime_UTR 35.0%
! AGTCTTTTCTTGCATAAGAG+AGG + chr4_3:51548610-51548629 None:intergenic 35.0%
CTCTTATGCAAGAAAAGACT+TGG - chr4_3:51548610-51548629 Msa0646020:exon 35.0%
GAAAAGACTTGGGAGATTAT+TGG - chr4_3:51548621-51548640 Msa0646020:exon 35.0%
ACAAGTTCTTTGATTGCTTC+AGG + chr4_3:51548674-51548693 None:intergenic 35.0%
! TTGTTTCTTCTTCTGCTTCT+TGG + chr4_3:51548780-51548799 None:intergenic 35.0%
TACCAAACACAATACATCTG+GGG + chr4_3:51549115-51549134 None:intergenic 35.0%
AGTCAAAAGACAGTGAAACT+TGG - chr4_3:51549144-51549163 Msa0646020:five_prime_UTR 35.0%
AAAAGACAGTGAAACTTGGA+TGG - chr4_3:51549148-51549167 Msa0646020:five_prime_UTR 35.0%
GAAACTTGGATGGTATTTGA+TGG - chr4_3:51549158-51549177 Msa0646020:five_prime_UTR 35.0%
!! GATTTGTTAGTTTGATGGCT+AGG + chr4_3:51548368-51548387 None:intergenic 35.0%
TAAAAGTCCACATCTTAGCA+AGG - chr4_3:51548392-51548411 Msa0646020:three_prime_UTR 35.0%
! CATACTCTTTTCTCTTCTTC+TGG - chr4_3:51548443-51548462 Msa0646020:three_prime_UTR 35.0%
! AGTCTTTTCTTGCATAAGAG+AGG + chr4_3:51548610-51548629 None:intergenic 35.0%
CTCTTATGCAAGAAAAGACT+TGG - chr4_3:51548610-51548629 Msa0646020:exon 35.0%
GAAAAGACTTGGGAGATTAT+TGG - chr4_3:51548621-51548640 Msa0646020:exon 35.0%
ACAAGTTCTTTGATTGCTTC+AGG + chr4_3:51548674-51548693 None:intergenic 35.0%
! TTGTTTCTTCTTCTGCTTCT+TGG + chr4_3:51548780-51548799 None:intergenic 35.0%
TACCAAACACAATACATCTG+GGG + chr4_3:51549115-51549134 None:intergenic 35.0%
AGTCAAAAGACAGTGAAACT+TGG - chr4_3:51549144-51549163 Msa0646020:five_prime_UTR 35.0%
AAAAGACAGTGAAACTTGGA+TGG - chr4_3:51549148-51549167 Msa0646020:five_prime_UTR 35.0%
TGGTACAACCGTGTATAAAG+TGG - chr4_3:51548298-51548317 Msa0646020:three_prime_UTR 40.0%
GGTACAACCGTGTATAAAGT+GGG - chr4_3:51548299-51548318 Msa0646020:three_prime_UTR 40.0%
GAGTATGAGAGAAGCAAAGA+TGG + chr4_3:51548430-51548449 None:intergenic 40.0%
TCTTTGATTGCTTCAGGCAT+AGG + chr4_3:51548668-51548687 None:intergenic 40.0%
AACTCTGAACAAGAGCTTCA+TGG - chr4_3:51548815-51548834 Msa0646020:CDS 40.0%
TGGTACAACCGTGTATAAAG+TGG - chr4_3:51548298-51548317 Msa0646020:three_prime_UTR 40.0%
GGTACAACCGTGTATAAAGT+GGG - chr4_3:51548299-51548318 Msa0646020:three_prime_UTR 40.0%
GAGTATGAGAGAAGCAAAGA+TGG + chr4_3:51548430-51548449 None:intergenic 40.0%
TCTTTGATTGCTTCAGGCAT+AGG + chr4_3:51548668-51548687 None:intergenic 40.0%
AACTCTGAACAAGAGCTTCA+TGG - chr4_3:51548815-51548834 Msa0646020:CDS 40.0%
AAAGGGGCCCACTTTATACA+CGG + chr4_3:51548309-51548328 None:intergenic 45.0%
! GTATAAAGTGGGCCCCTTTT+TGG - chr4_3:51548310-51548329 Msa0646020:three_prime_UTR 45.0%
TGATTGCTTCAGGCATAGGT+TGG + chr4_3:51548664-51548683 None:intergenic 45.0%
CTCCCCAGATGTATTGTGTT+TGG - chr4_3:51549110-51549129 Msa0646020:five_prime_UTR 45.0%
AAAGGGGCCCACTTTATACA+CGG + chr4_3:51548309-51548328 None:intergenic 45.0%
! GTATAAAGTGGGCCCCTTTT+TGG - chr4_3:51548310-51548329 Msa0646020:three_prime_UTR 45.0%
TGATTGCTTCAGGCATAGGT+TGG + chr4_3:51548664-51548683 None:intergenic 45.0%
CTCCCCAGATGTATTGTGTT+TGG - chr4_3:51549110-51549129 Msa0646020:five_prime_UTR 45.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 51548290 51549179 51548290 ID=Msa0646020;Name=Msa0646020
chr4_3 mRNA 51548290 51549179 51548290 ID=Msa0646020-mRNA-1;Parent=Msa0646020;Name=Msa0646020-mRNA-1;_AED=0.01;_eAED=0.01;_QI=130|1|1|1|1|1|2|335|96
chr4_3 exon 51548290 51548870 51548290 ID=Msa0646020-mRNA-1:exon:12545;Parent=Msa0646020-mRNA-1
chr4_3 exon 51549005 51549179 51549005 ID=Msa0646020-mRNA-1:exon:12544;Parent=Msa0646020-mRNA-1
chr4_3 five_prime_UTR 51549050 51549179 51549050 ID=Msa0646020-mRNA-1:five_prime_utr;Parent=Msa0646020-mRNA-1
chr4_3 CDS 51549005 51549049 51549005 ID=Msa0646020-mRNA-1:cds;Parent=Msa0646020-mRNA-1
chr4_3 CDS 51548625 51548870 51548625 ID=Msa0646020-mRNA-1:cds;Parent=Msa0646020-mRNA-1
chr4_3 three_prime_UTR 51548290 51548624 51548290 ID=Msa0646020-mRNA-1:three_prime_utr;Parent=Msa0646020-mRNA-1
Gene Sequence

>Msa0646020

ATGAAGTCCATCTTTGCTTCTCTCATACTCTTTTCTCTTCTTCTGGTTGCTGACCTCTCTTATGCAAGAAAAGACTTGGGAGATTATTGGAAGAATATGATGAATGACCAACCTATGCCTGAAGCAATCAAAGAACTTGTTCAAAATCAAGAGGTTTCAGATGACTTTATTAGAGACTTTGATGTAAAGCCTAATGTCATATTATATCACACACATGCTGAATCCAAGAAGCAGAAGAAGAAACAACATGTCTTTGTGAAAAACTCTGAACAAGAGCTTCATGGAACATAA
Protein sequence

>Msa0646020

MKSIFASLILFSLLLVADLSYARKDLGDYWKNMMNDQPMPEAIKELVQNQEVSDDFIRDFDVKPNVILYHTHAESKKQKKKQHVFVKNSEQELHGT*