AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0562740


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0562740 MtrunA17_Chr8g0376171 97.458 118 3 0 4 121 79 196 4.20e-82 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0562740 AT1G70760.1 62.393 117 42 2 5 121 75 189 1.03e-47 152

Find 44 sgRNAs with CRISPR-Local

Find 125 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAGAACTTTGGTGGATTT+TGG 0.186030 4_1:-62822394 Msa0562740:CDS
TTACTCCTAAACTATATTAT+TGG 0.192300 4_1:-62821848 Msa0562740:three_prime_UTR
CAAAGCCAGAACAAGATTAT+TGG 0.194951 4_1:+62822239 None:intergenic
CTGTCTGTATCAATCTTGTT+AGG 0.260132 4_1:+62821671 None:intergenic
TGCAGCCAATAATCTTGTTC+TGG 0.318687 4_1:-62822244 Msa0562740:intron
CAATAATCTTGTTCTGGCTT+TGG 0.325939 4_1:-62822238 Msa0562740:CDS
TGTGATGTAGGCTCATTGTT+TGG 0.328228 4_1:-62822039 Msa0562740:intron
GGGTACCGTTTCTAAACTTC+AGG 0.341388 4_1:-62822018 Msa0562740:CDS
CATCACCAATAATATAGTTT+AGG 0.363519 4_1:+62821843 None:intergenic
AAATGAAGACAAACATGAAT+TGG 0.365498 4_1:+62822177 None:intergenic
GATGGCTAGTCATAATCTTC+AGG 0.365633 4_1:+62821899 None:intergenic
GTGATGTAGGCTCATTGTTT+GGG 0.399295 4_1:-62822038 Msa0562740:intron
ATAATAATCCGCAAGAACTT+TGG 0.423897 4_1:-62822404 Msa0562740:CDS
AAATGATACATATGATTTGT+TGG 0.424912 4_1:+62821870 None:intergenic
CAAAAGGTGATTATTTGAAC+AGG 0.427722 4_1:-62822463 None:intergenic
AATGATACATATGATTTGTT+GGG 0.430071 4_1:+62821871 None:intergenic
TGTTCTGGCTTTGGAAAAGA+TGG 0.430184 4_1:-62822229 Msa0562740:CDS
CAACGTTGAAAGTGAGAATC+TGG 0.434063 4_1:+62821745 None:intergenic
GACCAAGGATACTCCATGTC+TGG 0.435462 4_1:+62821980 None:intergenic
TAATCTTCAGGATCAGCAAA+AGG 0.448767 4_1:+62821911 None:intergenic
TTACAACTGAATTCCATTCA+AGG 0.466600 4_1:+62821789 None:intergenic
ATGATTTGTTGGGAGTTTGA+TGG 0.489204 4_1:+62821881 None:intergenic
TGTCTGTATCAATCTTGTTA+GGG 0.494650 4_1:+62821672 None:intergenic
ATCCAGACATGGAGTATCCT+TGG 0.501281 4_1:-62821982 Msa0562740:CDS
ATAATCCGCAAGAACTTTGG+TGG 0.502309 4_1:-62822401 Msa0562740:CDS
TTCTCACTTTCAACGTTGAA+CGG 0.503012 4_1:-62821740 Msa0562740:three_prime_UTR
AACGGTGTCAAACTGCCGAT+TGG 0.507175 4_1:-62821722 Msa0562740:three_prime_UTR
CCAGTGACTGCTAATGCTGC+TGG 0.526137 4_1:+62822432 None:intergenic
CCAGCAGCATTAGCAGTCAC+TGG 0.537269 4_1:-62822432 Msa0562740:CDS
AACTTCCTGAAGTTTAGAAA+CGG 0.540412 4_1:+62822013 None:intergenic
TACTCCATGTCTGGATCCCG+TGG 0.543899 4_1:+62821989 None:intergenic
ATAAGTTTAACGAATCCAAT+CGG 0.546420 4_1:+62821707 None:intergenic
AATCTTCAGGATCAGCAAAA+GGG 0.561326 4_1:+62821912 None:intergenic
CTAACAAGATTGATACAGAC+AGG 0.562588 4_1:-62821670 Msa0562740:three_prime_UTR
TAAACTTCAGGAAGTTCCCA+CGG 0.579936 4_1:-62822006 Msa0562740:CDS
AAACTTCAGGAAGTTCCCAC+GGG 0.581934 4_1:-62822005 Msa0562740:CDS
AAAATCCACCAAAGTTCTTG+CGG 0.588377 4_1:+62822396 None:intergenic
GTTCCCACGGGATCCAGACA+TGG 0.595079 4_1:-62821993 Msa0562740:CDS
TGACTGCTAATGCTGCTGGT+TGG 0.620328 4_1:+62822436 None:intergenic
TAAAACTTACTGGCCCAACA+AGG 0.670047 4_1:+62822340 None:intergenic
GGATCATCAGGTATAGACCA+AGG 0.670305 4_1:+62821965 None:intergenic
ACTCCATGTCTGGATCCCGT+GGG 0.684029 4_1:+62821990 None:intergenic
TAACAAGATTGATACAGACA+GGG 0.718181 4_1:-62821669 Msa0562740:three_prime_UTR
ATGGTACAGAAGAAAGCTTG+CGG 0.727997 4_1:-62822210 Msa0562740:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATTCAGTTGTAAAAATTAA+AGG - chr4_1:62822340-62822359 Msa0562740:intron 15.0%
!! AATTCAGTTGTAAAAATTAA+AGG - chr4_1:62822340-62822359 Msa0562740:intron 15.0%
!! TTGTAAATACTTATAAGAGA+AGG + chr4_1:62821987-62822006 None:intergenic 20.0%
!!! TATGCATTTCTTATTTTTGA+AGG + chr4_1:62822178-62822197 None:intergenic 20.0%
!!! AATGATACATATGATTTGTT+GGG + chr4_1:62822251-62822270 None:intergenic 20.0%
!!! AAATGATACATATGATTTGT+TGG + chr4_1:62822252-62822271 None:intergenic 20.0%
!! TTACTCCTAAACTATATTAT+TGG - chr4_1:62822271-62822290 Msa0562740:intron 20.0%
!! TTGTAAATACTTATAAGAGA+AGG + chr4_1:62821987-62822006 None:intergenic 20.0%
!!! TATGCATTTCTTATTTTTGA+AGG + chr4_1:62822178-62822197 None:intergenic 20.0%
!!! AATGATACATATGATTTGTT+GGG + chr4_1:62822251-62822270 None:intergenic 20.0%
!!! AAATGATACATATGATTTGT+TGG + chr4_1:62822252-62822271 None:intergenic 20.0%
!! TTACTCCTAAACTATATTAT+TGG - chr4_1:62822271-62822290 Msa0562740:intron 20.0%
! GATGTGATATTAAAACTTAC+TGG + chr4_1:62821792-62821811 None:intergenic 25.0%
! AAATGAAGACAAACATGAAT+TGG + chr4_1:62821945-62821964 None:intergenic 25.0%
! CATCACCAATAATATAGTTT+AGG + chr4_1:62822279-62822298 None:intergenic 25.0%
! ATAAGTTTAACGAATCCAAT+CGG + chr4_1:62822415-62822434 None:intergenic 25.0%
! GATGTGATATTAAAACTTAC+TGG + chr4_1:62821792-62821811 None:intergenic 25.0%
! AAATGAAGACAAACATGAAT+TGG + chr4_1:62821945-62821964 None:intergenic 25.0%
! CATCACCAATAATATAGTTT+AGG + chr4_1:62822279-62822298 None:intergenic 25.0%
! ATAAGTTTAACGAATCCAAT+CGG + chr4_1:62822415-62822434 None:intergenic 25.0%
ATAATAATCCGCAAGAACTT+TGG - chr4_1:62821715-62821734 Msa0562740:three_prime_UTR 30.0%
! TTCTTTTTCTACTTCCTTGT+TGG - chr4_1:62821765-62821784 Msa0562740:three_prime_UTR 30.0%
! TCTTTTTCTACTTCCTTGTT+GGG - chr4_1:62821766-62821785 Msa0562740:three_prime_UTR 30.0%
!!! GCAACTTATTTTAATGTGCA+TGG - chr4_1:62822013-62822032 Msa0562740:CDS 30.0%
!! ATTTTAATGTGCATGGTGAT+TGG - chr4_1:62822020-62822039 Msa0562740:CDS 30.0%
!! TTTCGTTTTTCTTGTGATGT+AGG - chr4_1:62822068-62822087 Msa0562740:intron 30.0%
AACTTCCTGAAGTTTAGAAA+CGG + chr4_1:62822109-62822128 None:intergenic 30.0%
!!! CTTATTTTTGAAGGATCATC+AGG + chr4_1:62822169-62822188 None:intergenic 30.0%
CAAGGATCAAAAGCAAAAAA+AGG + chr4_1:62822315-62822334 None:intergenic 30.0%
!! TTTTGCTTTTGATCCTTGAA+TGG - chr4_1:62822317-62822336 Msa0562740:intron 30.0%
TTACAACTGAATTCCATTCA+AGG + chr4_1:62822333-62822352 None:intergenic 30.0%
TGTCTGTATCAATCTTGTTA+GGG + chr4_1:62822450-62822469 None:intergenic 30.0%
TAACAAGATTGATACAGACA+GGG - chr4_1:62822450-62822469 Msa0562740:CDS 30.0%
ATAATAATCCGCAAGAACTT+TGG - chr4_1:62821715-62821734 Msa0562740:three_prime_UTR 30.0%
! TTCTTTTTCTACTTCCTTGT+TGG - chr4_1:62821765-62821784 Msa0562740:three_prime_UTR 30.0%
! TCTTTTTCTACTTCCTTGTT+GGG - chr4_1:62821766-62821785 Msa0562740:three_prime_UTR 30.0%
!!! GCAACTTATTTTAATGTGCA+TGG - chr4_1:62822013-62822032 Msa0562740:CDS 30.0%
!! ATTTTAATGTGCATGGTGAT+TGG - chr4_1:62822020-62822039 Msa0562740:CDS 30.0%
!! TTTCGTTTTTCTTGTGATGT+AGG - chr4_1:62822068-62822087 Msa0562740:intron 30.0%
AACTTCCTGAAGTTTAGAAA+CGG + chr4_1:62822109-62822128 None:intergenic 30.0%
!!! CTTATTTTTGAAGGATCATC+AGG + chr4_1:62822169-62822188 None:intergenic 30.0%
CAAGGATCAAAAGCAAAAAA+AGG + chr4_1:62822315-62822334 None:intergenic 30.0%
!! TTTTGCTTTTGATCCTTGAA+TGG - chr4_1:62822317-62822336 Msa0562740:intron 30.0%
TTACAACTGAATTCCATTCA+AGG + chr4_1:62822333-62822352 None:intergenic 30.0%
TGTCTGTATCAATCTTGTTA+GGG + chr4_1:62822450-62822469 None:intergenic 30.0%
AAAATCCACCAAAGTTCTTG+CGG + chr4_1:62821726-62821745 None:intergenic 35.0%
! TGAGAGCATAGTGTATTAAC+AGG - chr4_1:62821837-62821856 Msa0562740:three_prime_UTR 35.0%
! GAGAGCATAGTGTATTAACA+GGG - chr4_1:62821838-62821857 Msa0562740:three_prime_UTR 35.0%
CAAAGCCAGAACAAGATTAT+TGG + chr4_1:62821883-62821902 None:intergenic 35.0%
!! CAATAATCTTGTTCTGGCTT+TGG - chr4_1:62821881-62821900 Msa0562740:three_prime_UTR 35.0%
AATCTTCAGGATCAGCAAAA+GGG + chr4_1:62822210-62822229 None:intergenic 35.0%
TAATCTTCAGGATCAGCAAA+AGG + chr4_1:62822211-62822230 None:intergenic 35.0%
!! ATGATTTGTTGGGAGTTTGA+TGG + chr4_1:62822241-62822260 None:intergenic 35.0%
TTCTCACTTTCAACGTTGAA+CGG - chr4_1:62822379-62822398 Msa0562740:CDS 35.0%
CTGTCTGTATCAATCTTGTT+AGG + chr4_1:62822451-62822470 None:intergenic 35.0%
CTAACAAGATTGATACAGAC+AGG - chr4_1:62822449-62822468 Msa0562740:CDS 35.0%
AAAATCCACCAAAGTTCTTG+CGG + chr4_1:62821726-62821745 None:intergenic 35.0%
! TGAGAGCATAGTGTATTAAC+AGG - chr4_1:62821837-62821856 Msa0562740:three_prime_UTR 35.0%
! GAGAGCATAGTGTATTAACA+GGG - chr4_1:62821838-62821857 Msa0562740:three_prime_UTR 35.0%
CAAAGCCAGAACAAGATTAT+TGG + chr4_1:62821883-62821902 None:intergenic 35.0%
!! CAATAATCTTGTTCTGGCTT+TGG - chr4_1:62821881-62821900 Msa0562740:three_prime_UTR 35.0%
AATCTTCAGGATCAGCAAAA+GGG + chr4_1:62822210-62822229 None:intergenic 35.0%
TAATCTTCAGGATCAGCAAA+AGG + chr4_1:62822211-62822230 None:intergenic 35.0%
!! ATGATTTGTTGGGAGTTTGA+TGG + chr4_1:62822241-62822260 None:intergenic 35.0%
TTCTCACTTTCAACGTTGAA+CGG - chr4_1:62822379-62822398 Msa0562740:CDS 35.0%
CTGTCTGTATCAATCTTGTT+AGG + chr4_1:62822451-62822470 None:intergenic 35.0%
CTAACAAGATTGATACAGAC+AGG - chr4_1:62822449-62822468 Msa0562740:CDS 35.0%
ATAATCCGCAAGAACTTTGG+TGG - chr4_1:62821718-62821737 Msa0562740:three_prime_UTR 40.0%
!!! GCAAGAACTTTGGTGGATTT+TGG - chr4_1:62821725-62821744 Msa0562740:three_prime_UTR 40.0%
!!! TTGGTGGATTTTGGCACAAT+TGG - chr4_1:62821734-62821753 Msa0562740:three_prime_UTR 40.0%
!!! TGGTGGATTTTGGCACAATT+GGG - chr4_1:62821735-62821754 Msa0562740:three_prime_UTR 40.0%
TAAAACTTACTGGCCCAACA+AGG + chr4_1:62821782-62821801 None:intergenic 40.0%
TGCAGCCAATAATCTTGTTC+TGG - chr4_1:62821875-62821894 Msa0562740:three_prime_UTR 40.0%
!! TGTTCTGGCTTTGGAAAAGA+TGG - chr4_1:62821890-62821909 Msa0562740:exon 40.0%
ATGGTACAGAAGAAAGCTTG+CGG - chr4_1:62821909-62821928 Msa0562740:CDS 40.0%
TGTGATGTAGGCTCATTGTT+TGG - chr4_1:62822080-62822099 Msa0562740:intron 40.0%
GTGATGTAGGCTCATTGTTT+GGG - chr4_1:62822081-62822100 Msa0562740:intron 40.0%
TAAACTTCAGGAAGTTCCCA+CGG - chr4_1:62822113-62822132 Msa0562740:intron 40.0%
! GATGGCTAGTCATAATCTTC+AGG + chr4_1:62822223-62822242 None:intergenic 40.0%
CAACGTTGAAAGTGAGAATC+TGG + chr4_1:62822377-62822396 None:intergenic 40.0%
ATAATCCGCAAGAACTTTGG+TGG - chr4_1:62821718-62821737 Msa0562740:three_prime_UTR 40.0%
!!! GCAAGAACTTTGGTGGATTT+TGG - chr4_1:62821725-62821744 Msa0562740:three_prime_UTR 40.0%
!!! TTGGTGGATTTTGGCACAAT+TGG - chr4_1:62821734-62821753 Msa0562740:three_prime_UTR 40.0%
!!! TGGTGGATTTTGGCACAATT+GGG - chr4_1:62821735-62821754 Msa0562740:three_prime_UTR 40.0%
TAAAACTTACTGGCCCAACA+AGG + chr4_1:62821782-62821801 None:intergenic 40.0%
TGCAGCCAATAATCTTGTTC+TGG - chr4_1:62821875-62821894 Msa0562740:three_prime_UTR 40.0%
!! TGTTCTGGCTTTGGAAAAGA+TGG - chr4_1:62821890-62821909 Msa0562740:exon 40.0%
ATGGTACAGAAGAAAGCTTG+CGG - chr4_1:62821909-62821928 Msa0562740:CDS 40.0%
TGTGATGTAGGCTCATTGTT+TGG - chr4_1:62822080-62822099 Msa0562740:intron 40.0%
GTGATGTAGGCTCATTGTTT+GGG - chr4_1:62822081-62822100 Msa0562740:intron 40.0%
TAAACTTCAGGAAGTTCCCA+CGG - chr4_1:62822113-62822132 Msa0562740:intron 40.0%
! GATGGCTAGTCATAATCTTC+AGG + chr4_1:62822223-62822242 None:intergenic 40.0%
CAACGTTGAAAGTGAGAATC+TGG + chr4_1:62822377-62822396 None:intergenic 40.0%
!! GGTGGATTTTGGCACAATTG+GGG - chr4_1:62821736-62821755 Msa0562740:three_prime_UTR 45.0%
!! GTGGATTTTGGCACAATTGG+GGG - chr4_1:62821737-62821756 Msa0562740:three_prime_UTR 45.0%
! GGGTACCGTTTCTAAACTTC+AGG - chr4_1:62822101-62822120 Msa0562740:intron 45.0%
AAACTTCAGGAAGTTCCCAC+GGG - chr4_1:62822114-62822133 Msa0562740:intron 45.0%
! ATCCAGACATGGAGTATCCT+TGG - chr4_1:62822137-62822156 Msa0562740:intron 45.0%
GGATCATCAGGTATAGACCA+AGG + chr4_1:62822157-62822176 None:intergenic 45.0%
!! GGTGGATTTTGGCACAATTG+GGG - chr4_1:62821736-62821755 Msa0562740:three_prime_UTR 45.0%
!! GTGGATTTTGGCACAATTGG+GGG - chr4_1:62821737-62821756 Msa0562740:three_prime_UTR 45.0%
! GGGTACCGTTTCTAAACTTC+AGG - chr4_1:62822101-62822120 Msa0562740:intron 45.0%
AAACTTCAGGAAGTTCCCAC+GGG - chr4_1:62822114-62822133 Msa0562740:intron 45.0%
! ATCCAGACATGGAGTATCCT+TGG - chr4_1:62822137-62822156 Msa0562740:intron 45.0%
GGATCATCAGGTATAGACCA+AGG + chr4_1:62822157-62822176 None:intergenic 45.0%
TGACTGCTAATGCTGCTGGT+TGG + chr4_1:62821686-62821705 None:intergenic 50.0%
GACCAAGGATACTCCATGTC+TGG + chr4_1:62822142-62822161 None:intergenic 50.0%
! AACGGTGTCAAACTGCCGAT+TGG - chr4_1:62822397-62822416 Msa0562740:CDS 50.0%
TGACTGCTAATGCTGCTGGT+TGG + chr4_1:62821686-62821705 None:intergenic 50.0%
GACCAAGGATACTCCATGTC+TGG + chr4_1:62822142-62822161 None:intergenic 50.0%
! AACGGTGTCAAACTGCCGAT+TGG - chr4_1:62822397-62822416 Msa0562740:CDS 50.0%
CCAGTGACTGCTAATGCTGC+TGG + chr4_1:62821690-62821709 None:intergenic 55.0%
CCAGCAGCATTAGCAGTCAC+TGG - chr4_1:62821687-62821706 Msa0562740:three_prime_UTR 55.0%
! AGAGAAGGTGCACTCACGCT+GGG + chr4_1:62821972-62821991 None:intergenic 55.0%
! AAGAGAAGGTGCACTCACGC+TGG + chr4_1:62821973-62821992 None:intergenic 55.0%
ACTCCATGTCTGGATCCCGT+GGG + chr4_1:62822132-62822151 None:intergenic 55.0%
TACTCCATGTCTGGATCCCG+TGG + chr4_1:62822133-62822152 None:intergenic 55.0%
CCAGTGACTGCTAATGCTGC+TGG + chr4_1:62821690-62821709 None:intergenic 55.0%
CCAGCAGCATTAGCAGTCAC+TGG - chr4_1:62821687-62821706 Msa0562740:three_prime_UTR 55.0%
! AGAGAAGGTGCACTCACGCT+GGG + chr4_1:62821972-62821991 None:intergenic 55.0%
! AAGAGAAGGTGCACTCACGC+TGG + chr4_1:62821973-62821992 None:intergenic 55.0%
ACTCCATGTCTGGATCCCGT+GGG + chr4_1:62822132-62822151 None:intergenic 55.0%
TACTCCATGTCTGGATCCCG+TGG + chr4_1:62822133-62822152 None:intergenic 55.0%
GTTCCCACGGGATCCAGACA+TGG - chr4_1:62822126-62822145 Msa0562740:intron 60.0%
GTTCCCACGGGATCCAGACA+TGG - chr4_1:62822126-62822145 Msa0562740:intron 60.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 62821669 62822472 62821669 ID=Msa0562740;Name=Msa0562740
chr4_1 mRNA 62821669 62822472 62821669 ID=Msa0562740-mRNA-1;Parent=Msa0562740;Name=Msa0562740-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|1|1|1|1|1|3|235|121
chr4_1 exon 62821669 62822051 62821669 ID=Msa0562740-mRNA-1:exon:19860;Parent=Msa0562740-mRNA-1
chr4_1 exon 62822167 62822261 62822167 ID=Msa0562740-mRNA-1:exon:19859;Parent=Msa0562740-mRNA-1
chr4_1 exon 62822350 62822472 62822350 ID=Msa0562740-mRNA-1:exon:19858;Parent=Msa0562740-mRNA-1
chr4_1 CDS 62822350 62822472 62822350 ID=Msa0562740-mRNA-1:cds;Parent=Msa0562740-mRNA-1
chr4_1 CDS 62822167 62822261 62822167 ID=Msa0562740-mRNA-1:cds;Parent=Msa0562740-mRNA-1
chr4_1 CDS 62821904 62822051 62821904 ID=Msa0562740-mRNA-1:cds;Parent=Msa0562740-mRNA-1
chr4_1 three_prime_UTR 62821669 62821903 62821669 ID=Msa0562740-mRNA-1:three_prime_utr;Parent=Msa0562740-mRNA-1
Gene Sequence

>Msa0562740

TTTGAACAGGCTGACCAACCAGCAGCATTAGCAGTCACTGGATTAAATAATAATCCGCAAGAACTTTGGTGGATTTTGGCACAATTGGGGGTTGTATTCTTTTTCTACTTCCTTGTTGGGCCACCAATAATCTTGTTCTGGCTTTGGAAAAGATGGTACAGAAGAAAGCTTGCGGAGATGTATTTCCAATTCATGTTTGTCTTCATTTTCTTCCCAGCGCTCATTGTTTGGGTACCGTTTCTAAACTTCAGGAAGTTCCCACGGGATCCAGACATGGAGTATCCTTGGTCTATACCTGATGATCCTTCAAAAATAAGAAATGCATACTATAAGTACCCTTTTGCTGATCCTGAAGATTATGACTAG

Protein sequence

>Msa0562740

FEQADQPAALAVTGLNNNPQELWWILAQLGVVFFFYFLVGPPIILFWLWKRWYRRKLAEMYFQFMFVFIFFPALIVWVPFLNFRKFPRDPDMEYPWSIPDDPSKIRNAYYKYPFADPEDYD*