AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0589490

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0589490 MtrunA17_Chr5g0393501 33.945 109 67 2 2 105 133 241 2.29e-12 60.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 45 sgRNAs with CRISPR-Local

Find 98 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGTTCCTATTGTTGGATA+TGG 0.236386 4_2:-12515048 Msa0589490:CDS
ACCTTTGAAGTTCCTATTGT+TGG 0.324436 4_2:-12515054 Msa0589490:CDS
CACAGTGCATGTACAAAATC+AGG 0.330296 4_2:-12515473 None:intergenic
AATCGTGATGTTTCACTCTA+AGG 0.341127 4_2:+12514894 None:intergenic
AGGAATTTGCCAAAAGTATC+AGG 0.344083 4_2:+12514914 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 4_2:-12514923 Msa0589490:CDS
AAGTTTACGGAATAAGTTTA+CGG 0.358796 4_2:+12515397 None:intergenic
CGATTATTCTACGAGTTTAG+TGG 0.386306 4_2:-12515203 Msa0589490:five_prime_UTR
TCCGAACATCACATTTGGTA+TGG 0.417548 4_2:+12514808 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.447586 4_2:+12515162 None:intergenic
CCGAACATCACATTTGGTAT+GGG 0.451435 4_2:+12514809 None:intergenic
TTGTGCTGCCAATGGTATTG+AGG 0.463000 4_2:-12514768 Msa0589490:CDS
TGTTCAACAAATCAGTTTGT+CGG 0.463202 4_2:-12515256 Msa0589490:five_prime_UTR
CCCATACCAAATGTGATGTT+CGG 0.471184 4_2:-12514809 Msa0589490:CDS
GAGCAATGTCACTTGCTAGA+TGG 0.472188 4_2:-12515302 Msa0589490:five_prime_UTR
CCAAATGTGATGTTCGGAAA+AGG 0.475440 4_2:-12514803 Msa0589490:CDS
TGCCGCACTCATGGAATGAT+AGG 0.476633 4_2:+12515092 None:intergenic
GTCGATCCATATCCAACAAT+AGG 0.477497 4_2:+12515042 None:intergenic
ACATGATGTTGCCGCACTCA+TGG 0.495582 4_2:+12515083 None:intergenic
GTCATGTGTTTATGAACGCT+TGG 0.496616 4_2:+12514685 None:intergenic
TTCTATTTAAATAAGATGAA+CGG 0.497916 4_2:-12515423 Msa0589490:five_prime_UTR
TGTGCTGCCAATGGTATTGA+GGG 0.501205 4_2:-12514767 Msa0589490:CDS
ACATGAATTATATTGTCATA+AGG 0.502236 4_2:+12514854 None:intergenic
ATTATTGCTTTCCAGTACCT+TGG 0.503165 4_2:-12515173 Msa0589490:five_prime_UTR
AAATATTCAGCAACGAAGAA+TGG 0.503166 4_2:+12515338 None:intergenic
CTGCCTAACTTCTAGGATGT+CGG 0.510869 4_2:-12515371 Msa0589490:five_prime_UTR
TCTCCGACATCCTAGAAGTT+AGG 0.525775 4_2:+12515368 None:intergenic
GGTCGTTGTTGACAGATGGT+TGG 0.536898 4_2:-12515235 Msa0589490:five_prime_UTR
TCTAGCAAGTGACATTGCTC+TGG 0.545941 4_2:+12515305 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 4_2:-12515170 Msa0589490:five_prime_UTR
CGAACATCACATTTGGTATG+GGG 0.554039 4_2:+12514810 None:intergenic
TGTCGGTCGTTGTTGACAGA+TGG 0.563208 4_2:-12515239 Msa0589490:five_prime_UTR
TTTCAAGTGCAAGTGCGTCA+TGG 0.567746 4_2:-12514729 Msa0589490:CDS
GTCTCCGCCCTCAATACCAT+TGG 0.581950 4_2:+12514760 None:intergenic
TCCAACAATAGGAACTTCAA+AGG 0.588797 4_2:+12515053 None:intergenic
CACGATTACGTCATGTTGTG+CGG 0.590860 4_2:-12514878 Msa0589490:CDS
TGTCACTTGCTAGATGGTGA+TGG 0.600059 4_2:-12515296 Msa0589490:five_prime_UTR
ATGTGATGTTCGGAAAAGGT+TGG 0.606400 4_2:-12514799 Msa0589490:CDS
GTCACTTGCTAGATGGTGAT+GGG 0.623508 4_2:-12515295 Msa0589490:five_prime_UTR
ACCCTATCATTCCATGAGTG+CGG 0.636716 4_2:-12515094 Msa0589490:exon
GCCGCACTCATGGAATGATA+GGG 0.643165 4_2:+12515093 None:intergenic
GCACTCATGGAATGATAGGG+TGG 0.649652 4_2:+12515096 None:intergenic
ATTTGAATCTACTTCCACCA+AGG 0.681040 4_2:+12515156 None:intergenic
TGGATCGACGAAATCACCAA+AGG 0.681312 4_2:-12515028 Msa0589490:intron
GCTGCCAATGGTATTGAGGG+CGG 0.739556 4_2:-12514764 Msa0589490:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTCTATTTAAATAAGATGAA+CGG - chr4_2:12514740-12514759 Msa0589490:CDS 15.0%
!!! TCATTAACAGTTTTTTTTTT+AGG - chr4_2:12515221-12515240 Msa0589490:five_prime_UTR 15.0%
!! TTCTATTTAAATAAGATGAA+CGG - chr4_2:12514740-12514759 Msa0589490:CDS 15.0%
!!! TCATTAACAGTTTTTTTTTT+AGG - chr4_2:12515221-12515240 Msa0589490:five_prime_UTR 15.0%
!! AAAAAACAATAAACAACCTT+TGG + chr4_2:12515154-12515173 None:intergenic 20.0%
!! ACATGAATTATATTGTCATA+AGG + chr4_2:12515312-12515331 None:intergenic 20.0%
!! AAAAAACAATAAACAACCTT+TGG + chr4_2:12515154-12515173 None:intergenic 20.0%
!! ACATGAATTATATTGTCATA+AGG + chr4_2:12515312-12515331 None:intergenic 20.0%
! AAGTTTACGGAATAAGTTTA+CGG + chr4_2:12514769-12514788 None:intergenic 25.0%
! AAGTTTACGGAATAAGTTTA+CGG + chr4_2:12514769-12514788 None:intergenic 25.0%
AGTTAGGCAGAAAAAGTTTA+CGG + chr4_2:12514782-12514801 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG + chr4_2:12514828-12514847 None:intergenic 30.0%
TGTTCAACAAATCAGTTTGT+CGG - chr4_2:12514907-12514926 Msa0589490:CDS 30.0%
AGTTAGGCAGAAAAAGTTTA+CGG + chr4_2:12514782-12514801 None:intergenic 30.0%
AAATATTCAGCAACGAAGAA+TGG + chr4_2:12514828-12514847 None:intergenic 30.0%
TGTTCAACAAATCAGTTTGT+CGG - chr4_2:12514907-12514926 Msa0589490:CDS 30.0%
!! ACTTTTTCTGCCTAACTTCT+AGG - chr4_2:12514785-12514804 Msa0589490:CDS 35.0%
CGATTATTCTACGAGTTTAG+TGG - chr4_2:12514960-12514979 Msa0589490:intron 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr4_2:12514990-12515009 Msa0589490:intron 35.0%
ATTTGAATCTACTTCCACCA+AGG + chr4_2:12515010-12515029 None:intergenic 35.0%
!! ACCTTTGAAGTTCCTATTGT+TGG - chr4_2:12515109-12515128 Msa0589490:five_prime_UTR 35.0%
TCCAACAATAGGAACTTCAA+AGG + chr4_2:12515113-12515132 None:intergenic 35.0%
GAAGTTCCTATTGTTGGATA+TGG - chr4_2:12515115-12515134 Msa0589490:five_prime_UTR 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr4_2:12515240-12515259 Msa0589490:five_prime_UTR 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr4_2:12515252-12515271 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr4_2:12515272-12515291 None:intergenic 35.0%
!! ACTTTTTCTGCCTAACTTCT+AGG - chr4_2:12514785-12514804 Msa0589490:CDS 35.0%
CGATTATTCTACGAGTTTAG+TGG - chr4_2:12514960-12514979 Msa0589490:intron 35.0%
ATTATTGCTTTCCAGTACCT+TGG - chr4_2:12514990-12515009 Msa0589490:intron 35.0%
ATTTGAATCTACTTCCACCA+AGG + chr4_2:12515010-12515029 None:intergenic 35.0%
!! ACCTTTGAAGTTCCTATTGT+TGG - chr4_2:12515109-12515128 Msa0589490:five_prime_UTR 35.0%
TCCAACAATAGGAACTTCAA+AGG + chr4_2:12515113-12515132 None:intergenic 35.0%
GAAGTTCCTATTGTTGGATA+TGG - chr4_2:12515115-12515134 Msa0589490:five_prime_UTR 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr4_2:12515240-12515259 Msa0589490:five_prime_UTR 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr4_2:12515252-12515271 None:intergenic 35.0%
AATCGTGATGTTTCACTCTA+AGG + chr4_2:12515272-12515291 None:intergenic 35.0%
GTCGATCCATATCCAACAAT+AGG + chr4_2:12515124-12515143 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr4_2:12515356-12515375 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + chr4_2:12515357-12515376 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - chr4_2:12515354-12515373 Msa0589490:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + chr4_2:12515358-12515377 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr4_2:12515363-12515382 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr4_2:12515360-12515379 Msa0589490:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr4_2:12515364-12515383 Msa0589490:five_prime_UTR 40.0%
GTCGATCCATATCCAACAAT+AGG + chr4_2:12515124-12515143 None:intergenic 40.0%
CGAACATCACATTTGGTATG+GGG + chr4_2:12515356-12515375 None:intergenic 40.0%
CCGAACATCACATTTGGTAT+GGG + chr4_2:12515357-12515376 None:intergenic 40.0%
CCCATACCAAATGTGATGTT+CGG - chr4_2:12515354-12515373 Msa0589490:five_prime_UTR 40.0%
TCCGAACATCACATTTGGTA+TGG + chr4_2:12515358-12515377 None:intergenic 40.0%
! CCTTTTCCGAACATCACATT+TGG + chr4_2:12515363-12515382 None:intergenic 40.0%
CCAAATGTGATGTTCGGAAA+AGG - chr4_2:12515360-12515379 Msa0589490:five_prime_UTR 40.0%
ATGTGATGTTCGGAAAAGGT+TGG - chr4_2:12515364-12515383 Msa0589490:five_prime_UTR 40.0%
!! CTGCCTAACTTCTAGGATGT+CGG - chr4_2:12514792-12514811 Msa0589490:CDS 45.0%
TCTCCGACATCCTAGAAGTT+AGG + chr4_2:12514798-12514817 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+TGG + chr4_2:12514861-12514880 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG - chr4_2:12514861-12514880 Msa0589490:CDS 45.0%
! TGTCACTTGCTAGATGGTGA+TGG - chr4_2:12514867-12514886 Msa0589490:CDS 45.0%
! GTCACTTGCTAGATGGTGAT+GGG - chr4_2:12514868-12514887 Msa0589490:CDS 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr4_2:12514993-12515012 Msa0589490:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr4_2:12515004-12515023 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - chr4_2:12515069-12515088 Msa0589490:CDS 45.0%
TGGATCGACGAAATCACCAA+AGG - chr4_2:12515135-12515154 Msa0589490:five_prime_UTR 45.0%
CACGATTACGTCATGTTGTG+CGG - chr4_2:12515285-12515304 Msa0589490:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr4_2:12515387-12515406 Msa0589490:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr4_2:12515395-12515414 Msa0589490:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr4_2:12515396-12515415 Msa0589490:five_prime_UTR 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - chr4_2:12515434-12515453 Msa0589490:five_prime_UTR 45.0%
!! CTGCCTAACTTCTAGGATGT+CGG - chr4_2:12514792-12514811 Msa0589490:CDS 45.0%
TCTCCGACATCCTAGAAGTT+AGG + chr4_2:12514798-12514817 None:intergenic 45.0%
TCTAGCAAGTGACATTGCTC+TGG + chr4_2:12514861-12514880 None:intergenic 45.0%
! GAGCAATGTCACTTGCTAGA+TGG - chr4_2:12514861-12514880 Msa0589490:CDS 45.0%
! TGTCACTTGCTAGATGGTGA+TGG - chr4_2:12514867-12514886 Msa0589490:CDS 45.0%
! GTCACTTGCTAGATGGTGAT+GGG - chr4_2:12514868-12514887 Msa0589490:CDS 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr4_2:12514993-12515012 Msa0589490:intron 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr4_2:12515004-12515023 None:intergenic 45.0%
ACCCTATCATTCCATGAGTG+CGG - chr4_2:12515069-12515088 Msa0589490:CDS 45.0%
TGGATCGACGAAATCACCAA+AGG - chr4_2:12515135-12515154 Msa0589490:five_prime_UTR 45.0%
CACGATTACGTCATGTTGTG+CGG - chr4_2:12515285-12515304 Msa0589490:five_prime_UTR 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr4_2:12515387-12515406 Msa0589490:five_prime_UTR 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr4_2:12515395-12515414 Msa0589490:five_prime_UTR 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr4_2:12515396-12515415 Msa0589490:five_prime_UTR 45.0%
! TTTCAAGTGCAAGTGCGTCA+TGG - chr4_2:12515434-12515453 Msa0589490:five_prime_UTR 45.0%
TGTCGGTCGTTGTTGACAGA+TGG - chr4_2:12514924-12514943 Msa0589490:intron 50.0%
GGTCGTTGTTGACAGATGGT+TGG - chr4_2:12514928-12514947 Msa0589490:intron 50.0%
GCACTCATGGAATGATAGGG+TGG + chr4_2:12515070-12515089 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + chr4_2:12515073-12515092 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + chr4_2:12515074-12515093 None:intergenic 50.0%
ACATGATGTTGCCGCACTCA+TGG + chr4_2:12515083-12515102 None:intergenic 50.0%
TGTCGGTCGTTGTTGACAGA+TGG - chr4_2:12514924-12514943 Msa0589490:intron 50.0%
GGTCGTTGTTGACAGATGGT+TGG - chr4_2:12514928-12514947 Msa0589490:intron 50.0%
GCACTCATGGAATGATAGGG+TGG + chr4_2:12515070-12515089 None:intergenic 50.0%
GCCGCACTCATGGAATGATA+GGG + chr4_2:12515073-12515092 None:intergenic 50.0%
TGCCGCACTCATGGAATGAT+AGG + chr4_2:12515074-12515093 None:intergenic 50.0%
ACATGATGTTGCCGCACTCA+TGG + chr4_2:12515083-12515102 None:intergenic 50.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr4_2:12515399-12515418 Msa0589490:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr4_2:12515406-12515425 None:intergenic 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr4_2:12515399-12515418 Msa0589490:five_prime_UTR 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr4_2:12515406-12515425 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 12514694 12515491 12514694 ID=Msa0589490;Name=Msa0589490
chr4_2 mRNA 12514694 12515491 12514694 ID=Msa0589490-mRNA-1;Parent=Msa0589490;Name=Msa0589490-mRNA-1;_AED=0.05;_eAED=0.05;_QI=388|1|0.5|1|1|1|2|0|107
chr4_2 exon 12514694 12514942 12514694 ID=Msa0589490-mRNA-1:exon:3648;Parent=Msa0589490-mRNA-1
chr4_2 exon 12515029 12515491 12515029 ID=Msa0589490-mRNA-1:exon:3647;Parent=Msa0589490-mRNA-1
chr4_2 five_prime_UTR 12515104 12515491 12515104 ID=Msa0589490-mRNA-1:five_prime_utr;Parent=Msa0589490-mRNA-1
chr4_2 CDS 12515029 12515103 12515029 ID=Msa0589490-mRNA-1:cds;Parent=Msa0589490-mRNA-1
chr4_2 CDS 12514694 12514942 12514694 ID=Msa0589490-mRNA-1:cds;Parent=Msa0589490-mRNA-1
Gene Sequence

>Msa0589490

ATGAGTGCGGCAACATCATGTTATTGTACCTTTGAAGTTCCTATTGTTGGATATGGATCGACGAAATCACCAAAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCACGATTACGTCATGTTGTGCGGACCTTATGACAATATAATTCATGTGAGACTCAAATATACAGATGACCCCATACCAAATGTGATGTTCGGAAAAGGTTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTGATTTTCAAGTGCAAGTGCGTCATGGACAAAAAATATGTTATCGTATCCAAGCGTTCATAA
Protein sequence

>Msa0589490

MSAATSCYCTFEVPIVGYGSTKSPKELPDTFGKFLRVKHHDYVMLCGPYDNIIHVRLKYTDDPIPNVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSKRS*