AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1132630


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1132630 MtrunA17_Chr4g0056141 100.000 62 0 0 1 62 1 62 1.68e-39 124
Msa1132630 MtrunA17_Chr5g0399231 100.000 62 0 0 1 62 1 62 1.68e-39 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1132630 AT2G19750.1 95.161 62 3 0 1 62 1 62 4.30e-30 100
Msa1132630 AT5G56670.1 95.161 62 3 0 1 62 1 62 4.30e-30 100
Msa1132630 AT4G29390.1 95.161 62 3 0 1 62 1 62 4.30e-30 100

Find 29 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGTATTGTGGACTAGGGTT+AGG 0.265232 7_3:-85516631 None:intergenic
GAGCTTTAACGAAAATAGTT+TGG 0.335033 7_3:-85516664 None:intergenic
GCTTTGCTACCTTTGGTGTT+TGG 0.335294 7_3:-85516921 None:intergenic
TGCTATTTGTATTGTGGACT+AGG 0.346479 7_3:-85516637 None:intergenic
TTTCGTTAAAGCTCCGATTC+TGG 0.348037 7_3:+85516673 Msa1132630:five_prime_UTR
TTGTCTTGCTTTGCTACCTT+TGG 0.348505 7_3:-85516928 None:intergenic
TGTTTGGCCTCTAACCTTAC+CGG 0.358772 7_3:-85516905 None:intergenic
TCTTACTTCTCAGATGAGTT+TGG 0.367396 7_3:-85517142 None:intergenic
TGTATTGTGGACTAGGGTTA+GGG 0.371742 7_3:-85516630 None:intergenic
GTTATTGTAGTTGTTGGATT+CGG 0.405984 7_3:+85517106 Msa1132630:intron
GCCTCTAACCTTACCGGCAC+GGG 0.419662 7_3:-85516899 None:intergenic
ATCGTTGGCCCGTGCCGGTA+AGG 0.433030 7_3:+85516891 Msa1132630:CDS
GCCCGTGCCGGTAAGGTTAG+AGG 0.445776 7_3:+85516898 Msa1132630:CDS
ACGCTTGTGAGCACGGCCAC+GGG 0.451262 7_3:-85516962 None:intergenic
CACGGATCGTTGGCCCGTGC+CGG 0.457604 7_3:+85516886 Msa1132630:CDS
TACGCTTGTGAGCACGGCCA+CGG 0.461093 7_3:-85516963 None:intergenic
GCTATTTGTATTGTGGACTA+GGG 0.472642 7_3:-85516636 None:intergenic
CTCTCTCTCTTTAGCTTCTG+CGG 0.475217 7_3:-85516708 None:intergenic
GCTTGAGGCAAAACCAGAAT+CGG 0.497884 7_3:-85516686 None:intergenic
GGCCTCTAACCTTACCGGCA+CGG 0.499402 7_3:-85516900 None:intergenic
TCTTTAGCTTCTGCGGCTTG+AGG 0.529758 7_3:-85516701 None:intergenic
ACTGCATACGCTTGTGAGCA+CGG 0.575185 7_3:-85516969 None:intergenic
CGCTTGTGAGCACGGCCACG+GGG 0.579942 7_3:-85516961 None:intergenic
AGGAAAGGTTCACGGATCGT+TGG 0.583409 7_3:+85516876 Msa1132630:intron
TACCGGCAGTGACGAATCTG+CGG 0.585546 7_3:-85516996 None:intergenic
AACCGCAGATTCGTCACTGC+CGG 0.593013 7_3:+85516994 Msa1132630:CDS
GTTGGATTCGGTAAGAAGAG+AGG 0.609691 7_3:+85517118 Msa1132630:CDS
GGTTAGAGGCCAAACACCAA+AGG 0.645954 7_3:+85516912 Msa1132630:CDS
GACAAGAAGAAGCAGCCCCG+TGG 0.665991 7_3:+85516946 Msa1132630:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATCTTTTTTTTTTCAATCAT+GGG + chr7_3:85516759-85516778 Msa1132630:exon 15.0%
!! TGAATAAATCTAAAAAATGA+GGG - chr7_3:85517033-85517052 None:intergenic 15.0%
!! ATGAATAAATCTAAAAAATG+AGG - chr7_3:85517034-85517053 None:intergenic 15.0%
!!! CTCCTTTTTTTTTTTTTTTT+GGG + chr7_3:85517240-85517259 Msa1132630:intron 15.0%
!! ATCCCAAAAAAAAAAAAAAA+AGG - chr7_3:85517245-85517264 None:intergenic 15.0%
!!! ATCTTTTTTTTTTCAATCAT+GGG + chr7_3:85516759-85516778 Msa1132630:exon 15.0%
!! TGAATAAATCTAAAAAATGA+GGG - chr7_3:85517033-85517052 None:intergenic 15.0%
!! ATGAATAAATCTAAAAAATG+AGG - chr7_3:85517034-85517053 None:intergenic 15.0%
!!! CTCCTTTTTTTTTTTTTTTT+GGG + chr7_3:85517240-85517259 Msa1132630:intron 15.0%
!! ATCCCAAAAAAAAAAAAAAA+AGG - chr7_3:85517245-85517264 None:intergenic 15.0%
!!! CATCTTTTTTTTTTCAATCA+TGG + chr7_3:85516758-85516777 Msa1132630:exon 20.0%
!! TAACATATTTCAAAAGCTAA+GGG - chr7_3:85517194-85517213 None:intergenic 20.0%
!! TTAACATATTTCAAAAGCTA+AGG - chr7_3:85517195-85517214 None:intergenic 20.0%
!! CCAAAAAAAAAAAAAAAAGG+AGG - chr7_3:85517242-85517261 None:intergenic 20.0%
!!! CCTCCTTTTTTTTTTTTTTT+TGG + chr7_3:85517239-85517258 Msa1132630:intron 20.0%
!! ATATTTAACTAGCACAAAAA+AGG - chr7_3:85517294-85517313 None:intergenic 20.0%
!!! CATCTTTTTTTTTTCAATCA+TGG + chr7_3:85516758-85516777 Msa1132630:exon 20.0%
!! TAACATATTTCAAAAGCTAA+GGG - chr7_3:85517194-85517213 None:intergenic 20.0%
!! TTAACATATTTCAAAAGCTA+AGG - chr7_3:85517195-85517214 None:intergenic 20.0%
!! CCAAAAAAAAAAAAAAAAGG+AGG - chr7_3:85517242-85517261 None:intergenic 20.0%
!!! CCTCCTTTTTTTTTTTTTTT+TGG + chr7_3:85517239-85517258 Msa1132630:intron 20.0%
!! ATATTTAACTAGCACAAAAA+AGG - chr7_3:85517294-85517313 None:intergenic 20.0%
!!! ATTCTTGTTATTGTAGTTGT+TGG + chr7_3:85517100-85517119 Msa1132630:intron 25.0%
! AACATATTTCAAAAGCTAAG+GGG - chr7_3:85517193-85517212 None:intergenic 25.0%
! AACTAAAGCCTAATTTCTTA+GGG - chr7_3:85517349-85517368 None:intergenic 25.0%
! TAACTAAAGCCTAATTTCTT+AGG - chr7_3:85517350-85517369 None:intergenic 25.0%
! TTATATCTGCTGAATAATTG+TGG + chr7_3:85517388-85517407 Msa1132630:intron 25.0%
!!! ATTCTTGTTATTGTAGTTGT+TGG + chr7_3:85517100-85517119 Msa1132630:intron 25.0%
! AACATATTTCAAAAGCTAAG+GGG - chr7_3:85517193-85517212 None:intergenic 25.0%
! AACTAAAGCCTAATTTCTTA+GGG - chr7_3:85517349-85517368 None:intergenic 25.0%
! TAACTAAAGCCTAATTTCTT+AGG - chr7_3:85517350-85517369 None:intergenic 25.0%
! TTATATCTGCTGAATAATTG+TGG + chr7_3:85517388-85517407 Msa1132630:intron 25.0%
!!! GGTTTTTGCTATTTGTATTG+TGG - chr7_3:85516646-85516665 None:intergenic 30.0%
! GAGCTTTAACGAAAATAGTT+TGG - chr7_3:85516667-85516686 None:intergenic 30.0%
!! AACAATGAAATCGATTTTGC+AGG + chr7_3:85516856-85516875 Msa1132630:intron 30.0%
GTTATTGTAGTTGTTGGATT+CGG + chr7_3:85517106-85517125 Msa1132630:intron 30.0%
! GTCTTATTCCCTAAGAAATT+AGG + chr7_3:85517338-85517357 Msa1132630:intron 30.0%
!!! GGTTTTTGCTATTTGTATTG+TGG - chr7_3:85516646-85516665 None:intergenic 30.0%
! GAGCTTTAACGAAAATAGTT+TGG - chr7_3:85516667-85516686 None:intergenic 30.0%
!! AACAATGAAATCGATTTTGC+AGG + chr7_3:85516856-85516875 Msa1132630:intron 30.0%
GTTATTGTAGTTGTTGGATT+CGG + chr7_3:85517106-85517125 Msa1132630:intron 30.0%
! GTCTTATTCCCTAAGAAATT+AGG + chr7_3:85517338-85517357 Msa1132630:intron 30.0%
! GCTATTTGTATTGTGGACTA+GGG - chr7_3:85516639-85516658 None:intergenic 35.0%
! TGCTATTTGTATTGTGGACT+AGG - chr7_3:85516640-85516659 None:intergenic 35.0%
!! TGAAATCGATTTTGCAGGAA+AGG + chr7_3:85516861-85516880 Msa1132630:intron 35.0%
TCTAAAAAATGAGGGTTTCG+AGG - chr7_3:85517025-85517044 None:intergenic 35.0%
TCTTACTTCTCAGATGAGTT+TGG - chr7_3:85517145-85517164 None:intergenic 35.0%
! CTTTTGCTTTCATTTTGCTG+TGG - chr7_3:85517481-85517500 None:intergenic 35.0%
! GCTATTTGTATTGTGGACTA+GGG - chr7_3:85516639-85516658 None:intergenic 35.0%
! TGCTATTTGTATTGTGGACT+AGG - chr7_3:85516640-85516659 None:intergenic 35.0%
!! TGAAATCGATTTTGCAGGAA+AGG + chr7_3:85516861-85516880 Msa1132630:intron 35.0%
TCTAAAAAATGAGGGTTTCG+AGG - chr7_3:85517025-85517044 None:intergenic 35.0%
TCTTACTTCTCAGATGAGTT+TGG - chr7_3:85517145-85517164 None:intergenic 35.0%
! CTTTTGCTTTCATTTTGCTG+TGG - chr7_3:85517481-85517500 None:intergenic 35.0%
!! TGTATTGTGGACTAGGGTTA+GGG - chr7_3:85516633-85516652 None:intergenic 40.0%
!! TTGTATTGTGGACTAGGGTT+AGG - chr7_3:85516634-85516653 None:intergenic 40.0%
TTTCGTTAAAGCTCCGATTC+TGG + chr7_3:85516673-85516692 Msa1132630:five_prime_UTR 40.0%
! GATTTTGCAGGAAAGGTTCA+CGG + chr7_3:85516868-85516887 Msa1132630:intron 40.0%
TTGTCTTGCTTTGCTACCTT+TGG - chr7_3:85516931-85516950 None:intergenic 40.0%
TCATCTGAGAAGTAAGATCG+TGG + chr7_3:85517148-85517167 Msa1132630:intron 40.0%
TAATTGTGGTGCGAATTGCA+TGG + chr7_3:85517402-85517421 Msa1132630:intron 40.0%
!! TGTATTGTGGACTAGGGTTA+GGG - chr7_3:85516633-85516652 None:intergenic 40.0%
!! TTGTATTGTGGACTAGGGTT+AGG - chr7_3:85516634-85516653 None:intergenic 40.0%
TTTCGTTAAAGCTCCGATTC+TGG + chr7_3:85516673-85516692 Msa1132630:five_prime_UTR 40.0%
! GATTTTGCAGGAAAGGTTCA+CGG + chr7_3:85516868-85516887 Msa1132630:intron 40.0%
TTGTCTTGCTTTGCTACCTT+TGG - chr7_3:85516931-85516950 None:intergenic 40.0%
TCATCTGAGAAGTAAGATCG+TGG + chr7_3:85517148-85517167 Msa1132630:intron 40.0%
TAATTGTGGTGCGAATTGCA+TGG + chr7_3:85517402-85517421 Msa1132630:intron 40.0%
GCTTGAGGCAAAACCAGAAT+CGG - chr7_3:85516689-85516708 None:intergenic 45.0%
! CTCTCTCTCTTTAGCTTCTG+CGG - chr7_3:85516711-85516730 None:intergenic 45.0%
TGTTTGGCCTCTAACCTTAC+CGG - chr7_3:85516908-85516927 None:intergenic 45.0%
!! GCTTTGCTACCTTTGGTGTT+TGG - chr7_3:85516924-85516943 None:intergenic 45.0%
! TGAGGGTTTCGAGGTATTAC+CGG - chr7_3:85517016-85517035 None:intergenic 45.0%
! GTTGGATTCGGTAAGAAGAG+AGG + chr7_3:85517118-85517137 Msa1132630:CDS 45.0%
TGCGAATTGCATGGTAGAAG+TGG + chr7_3:85517411-85517430 Msa1132630:intron 45.0%
GCTTGAGGCAAAACCAGAAT+CGG - chr7_3:85516689-85516708 None:intergenic 45.0%
! CTCTCTCTCTTTAGCTTCTG+CGG - chr7_3:85516711-85516730 None:intergenic 45.0%
TGTTTGGCCTCTAACCTTAC+CGG - chr7_3:85516908-85516927 None:intergenic 45.0%
!! GCTTTGCTACCTTTGGTGTT+TGG - chr7_3:85516924-85516943 None:intergenic 45.0%
! TGAGGGTTTCGAGGTATTAC+CGG - chr7_3:85517016-85517035 None:intergenic 45.0%
! GTTGGATTCGGTAAGAAGAG+AGG + chr7_3:85517118-85517137 Msa1132630:CDS 45.0%
TGCGAATTGCATGGTAGAAG+TGG + chr7_3:85517411-85517430 Msa1132630:intron 45.0%
! TCTTTAGCTTCTGCGGCTTG+AGG - chr7_3:85516704-85516723 None:intergenic 50.0%
AGGAAAGGTTCACGGATCGT+TGG + chr7_3:85516876-85516895 Msa1132630:intron 50.0%
GGTTAGAGGCCAAACACCAA+AGG + chr7_3:85516912-85516931 Msa1132630:CDS 50.0%
ACTGCATACGCTTGTGAGCA+CGG - chr7_3:85516972-85516991 None:intergenic 50.0%
! TCTTTAGCTTCTGCGGCTTG+AGG - chr7_3:85516704-85516723 None:intergenic 50.0%
AGGAAAGGTTCACGGATCGT+TGG + chr7_3:85516876-85516895 Msa1132630:intron 50.0%
GGTTAGAGGCCAAACACCAA+AGG + chr7_3:85516912-85516931 Msa1132630:CDS 50.0%
ACTGCATACGCTTGTGAGCA+CGG - chr7_3:85516972-85516991 None:intergenic 50.0%
AACCGCAGATTCGTCACTGC+CGG + chr7_3:85516994-85517013 Msa1132630:CDS 55.0%
TACCGGCAGTGACGAATCTG+CGG - chr7_3:85516999-85517018 None:intergenic 55.0%
AACCGCAGATTCGTCACTGC+CGG + chr7_3:85516994-85517013 Msa1132630:CDS 55.0%
TACCGGCAGTGACGAATCTG+CGG - chr7_3:85516999-85517018 None:intergenic 55.0%
GCCTCTAACCTTACCGGCAC+GGG - chr7_3:85516902-85516921 None:intergenic 60.0%
GGCCTCTAACCTTACCGGCA+CGG - chr7_3:85516903-85516922 None:intergenic 60.0%
GACAAGAAGAAGCAGCCCCG+TGG + chr7_3:85516946-85516965 Msa1132630:CDS 60.0%
TACGCTTGTGAGCACGGCCA+CGG - chr7_3:85516966-85516985 None:intergenic 60.0%
GCCTCTAACCTTACCGGCAC+GGG - chr7_3:85516902-85516921 None:intergenic 60.0%
GGCCTCTAACCTTACCGGCA+CGG - chr7_3:85516903-85516922 None:intergenic 60.0%
GACAAGAAGAAGCAGCCCCG+TGG + chr7_3:85516946-85516965 Msa1132630:CDS 60.0%
TACGCTTGTGAGCACGGCCA+CGG - chr7_3:85516966-85516985 None:intergenic 60.0%
! ATCGTTGGCCCGTGCCGGTA+AGG + chr7_3:85516891-85516910 Msa1132630:CDS 65.0%
! GCCCGTGCCGGTAAGGTTAG+AGG + chr7_3:85516898-85516917 Msa1132630:CDS 65.0%
ACGCTTGTGAGCACGGCCAC+GGG - chr7_3:85516965-85516984 None:intergenic 65.0%
! ATCGTTGGCCCGTGCCGGTA+AGG + chr7_3:85516891-85516910 Msa1132630:CDS 65.0%
! GCCCGTGCCGGTAAGGTTAG+AGG + chr7_3:85516898-85516917 Msa1132630:CDS 65.0%
ACGCTTGTGAGCACGGCCAC+GGG - chr7_3:85516965-85516984 None:intergenic 65.0%
CACGGATCGTTGGCCCGTGC+CGG + chr7_3:85516886-85516905 Msa1132630:CDS 70.0%
CGCTTGTGAGCACGGCCACG+GGG - chr7_3:85516964-85516983 None:intergenic 70.0%
CACGGATCGTTGGCCCGTGC+CGG + chr7_3:85516886-85516905 Msa1132630:CDS 70.0%
CGCTTGTGAGCACGGCCACG+GGG - chr7_3:85516964-85516983 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 85516624 85517504 85516624 ID=Msa1132630;Name=Msa1132630
chr7_3 mRNA 85516624 85517504 85516624 ID=Msa1132630-mRNA-1;Parent=Msa1132630;Name=Msa1132630-mRNA-1;_AED=0.28;_eAED=0.28;_QI=153|0.66|0.5|0.75|1|1|4|0|71
chr7_3 exon 85516624 85516780 85516624 ID=Msa1132630-mRNA-1:exon:25649;Parent=Msa1132630-mRNA-1
chr7_3 exon 85516878 85517015 85516878 ID=Msa1132630-mRNA-1:exon:25650;Parent=Msa1132630-mRNA-1
chr7_3 exon 85517116 85517158 85517116 ID=Msa1132630-mRNA-1:exon:25651;Parent=Msa1132630-mRNA-1
chr7_3 exon 85517474 85517504 85517474 ID=Msa1132630-mRNA-1:exon:25652;Parent=Msa1132630-mRNA-1
chr7_3 five_prime_UTR 85516624 85516776 85516624 ID=Msa1132630-mRNA-1:five_prime_utr;Parent=Msa1132630-mRNA-1
chr7_3 CDS 85516777 85516780 85516777 ID=Msa1132630-mRNA-1:cds;Parent=Msa1132630-mRNA-1
chr7_3 CDS 85516878 85517015 85516878 ID=Msa1132630-mRNA-1:cds;Parent=Msa1132630-mRNA-1
chr7_3 CDS 85517116 85517158 85517116 ID=Msa1132630-mRNA-1:cds;Parent=Msa1132630-mRNA-1
chr7_3 CDS 85517474 85517504 85517474 ID=Msa1132630-mRNA-1:cds;Parent=Msa1132630-mRNA-1
Gene Sequence

>Msa1132630

ATGGGAAAGGTTCACGGATCGTTGGCCCGTGCCGGTAAGGTTAGAGGCCAAACACCAAAGGTAGCAAAGCAAGACAAGAAGAAGCAGCCCCGTGGCCGTGCTCACAAGCGTATGCAGTACAACCGCAGATTCGTCACTGCCGTTGTTGGATTCGGTAAGAAGAGAGGACCAAACTCATCTGAGAAAAAACCACAGCAAAATGAAAGCAAAAGCTAA

Protein sequence

>Msa1132630

MGKVHGSLARAGKVRGQTPKVAKQDKKKQPRGRAHKRMQYNRRFVTAVVGFGKKRGPNSSEKKPQQNESKS*