AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0910000


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0910000 MtrunA17_Chr6g0462391 70.588 68 15 2 1 64 1 67 3.97e-22 82.0
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 10 sgRNAs with CRISPR-Local

Find 74 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCAAGCAGTTTCTGTTGT+TGG 0.278640 6_2:+13351851 None:intergenic
ATATTTGACTATTATCTCTT+TGG 0.278759 6_2:+13352055 None:intergenic
TCTTTGGTCATTAGACAAAA+AGG 0.309182 6_2:+13352071 None:intergenic
GTTGACACCACTTCTCAAAA+TGG 0.343287 6_2:-13351790 Msa0910000:CDS
CTGAGAGAGAGATGCATCTA+TGG 0.350559 6_2:-13351954 Msa0910000:exon
GAATCTCTCAGATTCTTTGT+TGG 0.383111 6_2:+13351931 None:intergenic
TAAGAGAAGGTCATGACATA+TGG 0.455280 6_2:+13351756 None:intergenic
TACTGTTGTTTCTGCTGTGG+CGG 0.585711 6_2:-13351718 Msa0910000:intron
TGTTACTGTTGTTTCTGCTG+TGG 0.590386 6_2:-13351721 Msa0910000:CDS
AGCAAGAGAGAAGTAAGAGA+AGG 0.602248 6_2:+13351743 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGTAAAAAAAAAAACAAAAA+GGG + chr6_2:13351471-13351490 None:intergenic 10.0%
!! AAGTAAAAAAAAAAACAAAA+AGG + chr6_2:13351472-13351491 None:intergenic 10.0%
!! TTGAATAAAACTATATTAAA+TGG - chr6_2:13351635-13351654 Msa0910000:intron 10.0%
!! AGTAAAAAAAAAAACAAAAA+GGG + chr6_2:13351471-13351490 None:intergenic 10.0%
!! AAGTAAAAAAAAAAACAAAA+AGG + chr6_2:13351472-13351491 None:intergenic 10.0%
!! TTGAATAAAACTATATTAAA+TGG - chr6_2:13351635-13351654 Msa0910000:intron 10.0%
!! TTAACGATATTCAATAAAAA+CGG + chr6_2:13351534-13351553 None:intergenic 15.0%
!! TTAACGATATTCAATAAAAA+CGG + chr6_2:13351534-13351553 None:intergenic 15.0%
!! ATATTTGACTATTATCTCTT+TGG + chr6_2:13351094-13351113 None:intergenic 20.0%
!! AAAACATTCAATTGAGTATA+TGG - chr6_2:13351860-13351879 Msa0910000:CDS 20.0%
!!! ATACCATGTATTGAAAATTT+TGG - chr6_2:13351893-13351912 Msa0910000:CDS 20.0%
!!! TAACCAAAATTTTCAATACA+TGG + chr6_2:13351899-13351918 None:intergenic 20.0%
!! ATATTTGACTATTATCTCTT+TGG + chr6_2:13351094-13351113 None:intergenic 20.0%
!! AAAACATTCAATTGAGTATA+TGG - chr6_2:13351860-13351879 Msa0910000:CDS 20.0%
!!! ATACCATGTATTGAAAATTT+TGG - chr6_2:13351893-13351912 Msa0910000:CDS 20.0%
!!! TAACCAAAATTTTCAATACA+TGG + chr6_2:13351899-13351918 None:intergenic 20.0%
!!! GTTAACTCAATTGATTTTGA+TGG + chr6_2:13351968-13351987 None:intergenic 25.0%
! AAAATCAATTGAGTTAACCT+CGG - chr6_2:13351970-13351989 Msa0910000:five_prime_UTR 25.0%
!!! GTTAACTCAATTGATTTTGA+TGG + chr6_2:13351968-13351987 None:intergenic 25.0%
! AAAATCAATTGAGTTAACCT+CGG - chr6_2:13351970-13351989 Msa0910000:five_prime_UTR 25.0%
TCTTTGGTCATTAGACAAAA+AGG + chr6_2:13351078-13351097 None:intergenic 30.0%
ATCATCATACCTGAAAAAAC+TGG - chr6_2:13351244-13351263 Msa0910000:intron 30.0%
!!! TATTCCATTCCAGTTTTTTC+AGG + chr6_2:13351256-13351275 None:intergenic 30.0%
CAATGTCGATATTATTAGAC+TGG - chr6_2:13351776-13351795 Msa0910000:CDS 30.0%
TCAATTCACACTCAAAATTG+TGG + chr6_2:13351940-13351959 None:intergenic 30.0%
ATTAACCAGTAAGGAAAACT+GGG - chr6_2:13352004-13352023 Msa0910000:five_prime_UTR 30.0%
TCTTTGGTCATTAGACAAAA+AGG + chr6_2:13351078-13351097 None:intergenic 30.0%
ATCATCATACCTGAAAAAAC+TGG - chr6_2:13351244-13351263 Msa0910000:intron 30.0%
!!! TATTCCATTCCAGTTTTTTC+AGG + chr6_2:13351256-13351275 None:intergenic 30.0%
CAATGTCGATATTATTAGAC+TGG - chr6_2:13351776-13351795 Msa0910000:CDS 30.0%
TCAATTCACACTCAAAATTG+TGG + chr6_2:13351940-13351959 None:intergenic 30.0%
ATTAACCAGTAAGGAAAACT+GGG - chr6_2:13352004-13352023 Msa0910000:five_prime_UTR 30.0%
GAATCTCTCAGATTCTTTGT+TGG + chr6_2:13351218-13351237 None:intergenic 35.0%
CATACCTGAAAAAACTGGAA+TGG - chr6_2:13351249-13351268 Msa0910000:intron 35.0%
!! TACAGTTCCATTTTGAGAAG+TGG + chr6_2:13351366-13351385 None:intergenic 35.0%
TAAGAGAAGGTCATGACATA+TGG + chr6_2:13351393-13351412 None:intergenic 35.0%
GTTAATCACATGCGAAATTG+TGG - chr6_2:13351716-13351735 Msa0910000:intron 35.0%
! TAGTTGTGTGTTTGAGTTTC+AGG - chr6_2:13351820-13351839 Msa0910000:CDS 35.0%
GATTAACCAGTAAGGAAAAC+TGG - chr6_2:13352003-13352022 Msa0910000:five_prime_UTR 35.0%
GAATCTCTCAGATTCTTTGT+TGG + chr6_2:13351218-13351237 None:intergenic 35.0%
CATACCTGAAAAAACTGGAA+TGG - chr6_2:13351249-13351268 Msa0910000:intron 35.0%
!! TACAGTTCCATTTTGAGAAG+TGG + chr6_2:13351366-13351385 None:intergenic 35.0%
TAAGAGAAGGTCATGACATA+TGG + chr6_2:13351393-13351412 None:intergenic 35.0%
GTTAATCACATGCGAAATTG+TGG - chr6_2:13351716-13351735 Msa0910000:intron 35.0%
! TAGTTGTGTGTTTGAGTTTC+AGG - chr6_2:13351820-13351839 Msa0910000:CDS 35.0%
GATTAACCAGTAAGGAAAAC+TGG - chr6_2:13352003-13352022 Msa0910000:five_prime_UTR 35.0%
CATCAAGCAGTTTCTGTTGT+TGG + chr6_2:13351298-13351317 None:intergenic 40.0%
GTTGACACCACTTCTCAAAA+TGG - chr6_2:13351356-13351375 Msa0910000:intron 40.0%
AGCAAGAGAGAAGTAAGAGA+AGG + chr6_2:13351406-13351425 None:intergenic 40.0%
!! TGTTACTGTTGTTTCTGCTG+TGG - chr6_2:13351425-13351444 Msa0910000:intron 40.0%
AACGCAGATGTAGGAAGAAT+TGG + chr6_2:13351699-13351718 None:intergenic 40.0%
CATGTGATTAACGCAGATGT+AGG + chr6_2:13351708-13351727 None:intergenic 40.0%
TTAGACTGGACACTTTCAGT+AGG - chr6_2:13351790-13351809 Msa0910000:CDS 40.0%
TAGACTGGACACTTTCAGTA+GGG - chr6_2:13351791-13351810 Msa0910000:CDS 40.0%
TTGAGCGTGATTAACCAGTA+AGG - chr6_2:13351995-13352014 Msa0910000:five_prime_UTR 40.0%
CATCAAGCAGTTTCTGTTGT+TGG + chr6_2:13351298-13351317 None:intergenic 40.0%
GTTGACACCACTTCTCAAAA+TGG - chr6_2:13351356-13351375 Msa0910000:intron 40.0%
AGCAAGAGAGAAGTAAGAGA+AGG + chr6_2:13351406-13351425 None:intergenic 40.0%
!! TGTTACTGTTGTTTCTGCTG+TGG - chr6_2:13351425-13351444 Msa0910000:intron 40.0%
AACGCAGATGTAGGAAGAAT+TGG + chr6_2:13351699-13351718 None:intergenic 40.0%
CATGTGATTAACGCAGATGT+AGG + chr6_2:13351708-13351727 None:intergenic 40.0%
TTAGACTGGACACTTTCAGT+AGG - chr6_2:13351790-13351809 Msa0910000:CDS 40.0%
TAGACTGGACACTTTCAGTA+GGG - chr6_2:13351791-13351810 Msa0910000:CDS 40.0%
TTGAGCGTGATTAACCAGTA+AGG - chr6_2:13351995-13352014 Msa0910000:five_prime_UTR 40.0%
CTGAGAGAGAGATGCATCTA+TGG - chr6_2:13351192-13351211 Msa0910000:intron 45.0%
!! TACTGTTGTTTCTGCTGTGG+CGG - chr6_2:13351428-13351447 Msa0910000:intron 45.0%
GTTAATCACGCTCAAAACCG+AGG + chr6_2:13351990-13352009 None:intergenic 45.0%
! AGACACCCAGTTTTCCTTAC+TGG + chr6_2:13352012-13352031 None:intergenic 45.0%
CTGAGAGAGAGATGCATCTA+TGG - chr6_2:13351192-13351211 Msa0910000:intron 45.0%
!! TACTGTTGTTTCTGCTGTGG+CGG - chr6_2:13351428-13351447 Msa0910000:intron 45.0%
GTTAATCACGCTCAAAACCG+AGG + chr6_2:13351990-13352009 None:intergenic 45.0%
! AGACACCCAGTTTTCCTTAC+TGG + chr6_2:13352012-13352031 None:intergenic 45.0%
!!! TATTTTTTTAAATTATTTCT+AGG - chr6_2:13352048-13352067 Msa0910000:five_prime_UTR 5.0%
!!! TATTTTTTTAAATTATTTCT+AGG - chr6_2:13352048-13352067 Msa0910000:five_prime_UTR 5.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 13351044 13352124 13351044 ID=Msa0910000;Name=Msa0910000
chr6_2 mRNA 13351044 13352124 13351044 ID=Msa0910000-mRNA-1;Parent=Msa0910000;Name=Msa0910000-mRNA-1;_AED=0.25;_eAED=0.25;_QI=159|0|0.5|0.5|0|0|2|0|84
chr6_2 exon 13351044 13351051 13351044 ID=Msa0910000-mRNA-1:exon:3044;Parent=Msa0910000-mRNA-1
chr6_2 exon 13351719 13352124 13351719 ID=Msa0910000-mRNA-1:exon:3043;Parent=Msa0910000-mRNA-1
chr6_2 five_prime_UTR 13351966 13352124 13351966 ID=Msa0910000-mRNA-1:five_prime_utr;Parent=Msa0910000-mRNA-1
chr6_2 CDS 13351719 13351965 13351719 ID=Msa0910000-mRNA-1:cds;Parent=Msa0910000-mRNA-1
chr6_2 CDS 13351044 13351051 13351044 ID=Msa0910000-mRNA-1:cds;Parent=Msa0910000-mRNA-1
Gene Sequence

>Msa0910000

ATGCATCTATGGCCAACAAAGAATCTGAGAGATTCATTCAAATCATCATACCTGAAAAAACTGGAATGGAATACTCAAAGAATGAAAAACAACCAACAACAGAAACTGCTTGATGATGAAGAAGACAACAACAACAATAACAACGTTGTTGTCGTTGACACCACTTCTCAAAATGGAACTGTAACTTCCATATGTCATGACCTTCTCTTACTTCTCTCTTGCTGTTACTGTTGTTTCTGCTGTGGCGTGTTCTAG

Protein sequence

>Msa0910000

MHLWPTKNLRDSFKSSYLKKLEWNTQRMKNNQQQKLLDDEEDNNNNNNVVVVDTTSQNGTVTSICHDLLLLLSCCYCCFCCGVF*