AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1165650

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1165650 MtrunA17_Chr7g0269781 50.265 189 26 3 1 122 50 237 2.96e-52 167
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1165650 AT1G01350.1 50.968 155 26 1 20 124 95 249 5.74e-46 152
Msa1165650 AT5G06420.1 51.634 153 24 1 22 124 132 284 1.37e-45 152
Msa1165650 AT5G06420.2 51.634 153 24 1 22 124 132 284 1.37e-45 152

Find 52 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTAACGATGCGATTGAAAT+TGG 0.135492 7_4:-57593624 None:intergenic
TGCGATTGAAATTGGGAAAT+TGG 0.161287 7_4:-57593616 None:intergenic
AAAATGAAAGATGTGCTTCT+TGG 0.227049 7_4:-57594040 None:intergenic
GCGATTGAAATTGGGAAATT+GGG 0.304505 7_4:-57593615 None:intergenic
GTTGTGAAGGAAATCGAAAT+TGG 0.338386 7_4:-57593679 None:intergenic
TTGAAGTCTTTGCATATGTC+AGG 0.387439 7_4:-57594219 None:intergenic
GTAACGATGCGATTGAAATT+GGG 0.393252 7_4:-57593623 None:intergenic
TCAGCGCACCCTCCTCTTCT+CGG 0.409916 7_4:-57594340 None:intergenic
TGACATATGCAAAGACTTCA+AGG 0.411330 7_4:+57594221 Msa1165650:CDS
CTGCTGGCTGGGTACTGTTA+AGG 0.417348 7_4:-57593715 None:intergenic
TTGTGAAGGAAATCGAAATT+GGG 0.425591 7_4:-57593678 None:intergenic
TAGCAAAGCAACAGCAACTT+TGG 0.436558 7_4:+57594095 Msa1165650:CDS
TGTGGGTTGTTTAGAAAAGT+TGG 0.448560 7_4:+57593898 Msa1165650:five_prime_UTR
ACACACTGAAGAAGCAGGTT+TGG 0.459341 7_4:-57593878 None:intergenic
GACCGAGGCGATTACAAGTC+CGG 0.470020 7_4:+57594288 Msa1165650:CDS
TGATGAAACTCTAATATAAG+TGG 0.474441 7_4:-57594181 None:intergenic
TGCAAAGACTTCAAGGAGAC+CGG 0.477457 7_4:+57594228 Msa1165650:CDS
CGATTGAAATTGGGAAATTG+GGG 0.479601 7_4:-57593614 None:intergenic
GGAAATCGAAATTGGGGAAT+CGG 0.479921 7_4:-57593671 None:intergenic
AACCTGCTTCTTCAGTGTGT+GGG 0.483768 7_4:+57593881 Msa1165650:five_prime_UTR
AAGAAACCTAACCTGCTGGC+TGG 0.483916 7_4:-57593727 None:intergenic
AAACCTGCTTCTTCAGTGTG+TGG 0.491141 7_4:+57593880 Msa1165650:five_prime_UTR
TGAGAATGAAGAAGATAATG+AGG 0.496162 7_4:+57593951 Msa1165650:five_prime_UTR
GGTGGCAGTTGGACAAAGAA+TGG 0.496757 7_4:+57594310 Msa1165650:CDS
GTTACAACGCATAAGCTTGA+GGG 0.510648 7_4:+57593641 Msa1165650:five_prime_UTR
CGTTACAACGCATAAGCTTG+AGG 0.517668 7_4:+57593640 Msa1165650:five_prime_UTR
AGAAACCTAACCTGCTGGCT+GGG 0.540786 7_4:-57593726 None:intergenic
TTCAAGGAGACCGGGTATTG+TGG 0.545327 7_4:+57594237 Msa1165650:CDS
AGAAGAGGAGGGTGCGCTGA+TGG 0.548558 7_4:+57594343 Msa1165650:CDS
TTCTTTGTCCAACTGCCACC+CGG 0.548782 7_4:-57594307 None:intergenic
ACCGAGGCGATTACAAGTCC+GGG 0.556767 7_4:+57594289 Msa1165650:CDS
GGAATGAAGCCGAGAAGAGG+AGG 0.558808 7_4:+57594331 Msa1165650:CDS
ACCCGGACTTGTAATCGCCT+CGG 0.560050 7_4:-57594290 None:intergenic
TTACAAGTCCGGGTGGCAGT+TGG 0.560817 7_4:+57594299 Msa1165650:CDS
TGCAAGTTTCTTCACGACCG+AGG 0.564969 7_4:+57594273 Msa1165650:CDS
CTTAACAGTACCCAGCCAGC+AGG 0.565300 7_4:+57593716 Msa1165650:five_prime_UTR
GAGACCGGGTATTGTGGCTA+CGG 0.578795 7_4:+57594243 Msa1165650:CDS
TTGGTGCTAAGAAGAATTTG+AGG 0.580649 7_4:+57593917 Msa1165650:five_prime_UTR
ATCGCCGTAGCCACAATACC+CGG 0.586901 7_4:-57594247 None:intergenic
AACCCACACACTGAAGAAGC+AGG 0.595301 7_4:-57593883 None:intergenic
AATGGAATGAAGCCGAGAAG+AGG 0.595307 7_4:+57594328 Msa1165650:CDS
GAAACTCTAATATAAGTGGA+AGG 0.596767 7_4:-57594177 None:intergenic
ATCCGTGGGTCACACTCACA+CGG 0.602004 7_4:+57594144 Msa1165650:CDS
ATAACAGCGATGCGTTGTGA+AGG 0.608312 7_4:-57593692 None:intergenic
TAGTATGGAAGATTCTTCTG+AGG 0.619198 7_4:+57593855 Msa1165650:intron
GCAAAGACTTCAAGGAGACC+GGG 0.633254 7_4:+57594229 Msa1165650:CDS
GTGTGAGTGTGACCCACGGA+TGG 0.640412 7_4:-57594142 None:intergenic
GAATGAAGCCGAGAAGAGGA+GGG 0.646762 7_4:+57594332 Msa1165650:CDS
TGTGAAGGAAATCGAAATTG+GGG 0.647632 7_4:-57593677 None:intergenic
ATATAAGTGGAAGGTCTGAG+AGG 0.681694 7_4:-57594168 None:intergenic
GACCGTGTGAGTGTGACCCA+CGG 0.684896 7_4:-57594146 None:intergenic
GAGGCGATTACAAGTCCGGG+TGG 0.724834 7_4:+57594292 Msa1165650:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AATACAACATAGTTAGTTTT+AGG + chr7_4:57593581-57593600 Msa1165650:five_prime_UTR 20.0%
!!! AATACAACATAGTTAGTTTT+AGG + chr7_4:57593581-57593600 Msa1165650:five_prime_UTR 20.0%
! TTAGTCATCTCAATTTGATT+TGG + chr7_4:57593794-57593813 Msa1165650:intron 25.0%
!! TAGTCATCTCAATTTGATTT+GGG + chr7_4:57593795-57593814 Msa1165650:intron 25.0%
! TGATGAAACTCTAATATAAG+TGG - chr7_4:57594184-57594203 None:intergenic 25.0%
! TTAGTCATCTCAATTTGATT+TGG + chr7_4:57593794-57593813 Msa1165650:intron 25.0%
!! TAGTCATCTCAATTTGATTT+GGG + chr7_4:57593795-57593814 Msa1165650:intron 25.0%
! TGATGAAACTCTAATATAAG+TGG - chr7_4:57594184-57594203 None:intergenic 25.0%
TTGTGAAGGAAATCGAAATT+GGG - chr7_4:57593681-57593700 None:intergenic 30.0%
AATTGAGATGACTAAAAGTG+TGG - chr7_4:57593789-57593808 None:intergenic 30.0%
CTTAGCTTAGCTTATTAGTA+TGG + chr7_4:57593840-57593859 Msa1165650:intron 30.0%
TGAGAATGAAGAAGATAATG+AGG + chr7_4:57593951-57593970 Msa1165650:five_prime_UTR 30.0%
TGAGAAAAAGAACATGAAGA+AGG + chr7_4:57593999-57594018 Msa1165650:CDS 30.0%
AAAATGAAAGATGTGCTTCT+TGG - chr7_4:57594043-57594062 None:intergenic 30.0%
GAAACTCTAATATAAGTGGA+AGG - chr7_4:57594180-57594199 None:intergenic 30.0%
TTGTGAAGGAAATCGAAATT+GGG - chr7_4:57593681-57593700 None:intergenic 30.0%
AATTGAGATGACTAAAAGTG+TGG - chr7_4:57593789-57593808 None:intergenic 30.0%
CTTAGCTTAGCTTATTAGTA+TGG + chr7_4:57593840-57593859 Msa1165650:intron 30.0%
TGAGAATGAAGAAGATAATG+AGG + chr7_4:57593951-57593970 Msa1165650:five_prime_UTR 30.0%
TGAGAAAAAGAACATGAAGA+AGG + chr7_4:57593999-57594018 Msa1165650:CDS 30.0%
AAAATGAAAGATGTGCTTCT+TGG - chr7_4:57594043-57594062 None:intergenic 30.0%
GAAACTCTAATATAAGTGGA+AGG - chr7_4:57594180-57594199 None:intergenic 30.0%
CGATTGAAATTGGGAAATTG+GGG - chr7_4:57593617-57593636 None:intergenic 35.0%
GCGATTGAAATTGGGAAATT+GGG - chr7_4:57593618-57593637 None:intergenic 35.0%
TGCGATTGAAATTGGGAAAT+TGG - chr7_4:57593619-57593638 None:intergenic 35.0%
GTAACGATGCGATTGAAATT+GGG - chr7_4:57593626-57593645 None:intergenic 35.0%
TGTAACGATGCGATTGAAAT+TGG - chr7_4:57593627-57593646 None:intergenic 35.0%
TGTGAAGGAAATCGAAATTG+GGG - chr7_4:57593680-57593699 None:intergenic 35.0%
GTTGTGAAGGAAATCGAAAT+TGG - chr7_4:57593682-57593701 None:intergenic 35.0%
TAGTATGGAAGATTCTTCTG+AGG + chr7_4:57593855-57593874 Msa1165650:intron 35.0%
! TGTGGGTTGTTTAGAAAAGT+TGG + chr7_4:57593898-57593917 Msa1165650:five_prime_UTR 35.0%
!! TTGGTGCTAAGAAGAATTTG+AGG + chr7_4:57593917-57593936 Msa1165650:five_prime_UTR 35.0%
!!! ATTTTTCAAGTTCCATCCGT+GGG + chr7_4:57594130-57594149 Msa1165650:CDS 35.0%
TTGAAGTCTTTGCATATGTC+AGG - chr7_4:57594222-57594241 None:intergenic 35.0%
TGACATATGCAAAGACTTCA+AGG + chr7_4:57594221-57594240 Msa1165650:CDS 35.0%
CGATTGAAATTGGGAAATTG+GGG - chr7_4:57593617-57593636 None:intergenic 35.0%
GCGATTGAAATTGGGAAATT+GGG - chr7_4:57593618-57593637 None:intergenic 35.0%
TGCGATTGAAATTGGGAAAT+TGG - chr7_4:57593619-57593638 None:intergenic 35.0%
GTAACGATGCGATTGAAATT+GGG - chr7_4:57593626-57593645 None:intergenic 35.0%
TGTAACGATGCGATTGAAAT+TGG - chr7_4:57593627-57593646 None:intergenic 35.0%
TGTGAAGGAAATCGAAATTG+GGG - chr7_4:57593680-57593699 None:intergenic 35.0%
GTTGTGAAGGAAATCGAAAT+TGG - chr7_4:57593682-57593701 None:intergenic 35.0%
TAGTATGGAAGATTCTTCTG+AGG + chr7_4:57593855-57593874 Msa1165650:intron 35.0%
! TGTGGGTTGTTTAGAAAAGT+TGG + chr7_4:57593898-57593917 Msa1165650:five_prime_UTR 35.0%
!! TTGGTGCTAAGAAGAATTTG+AGG + chr7_4:57593917-57593936 Msa1165650:five_prime_UTR 35.0%
!!! ATTTTTCAAGTTCCATCCGT+GGG + chr7_4:57594130-57594149 Msa1165650:CDS 35.0%
TTGAAGTCTTTGCATATGTC+AGG - chr7_4:57594222-57594241 None:intergenic 35.0%
TGACATATGCAAAGACTTCA+AGG + chr7_4:57594221-57594240 Msa1165650:CDS 35.0%
GTTACAACGCATAAGCTTGA+GGG + chr7_4:57593641-57593660 Msa1165650:five_prime_UTR 40.0%
GGAAATCGAAATTGGGGAAT+CGG - chr7_4:57593674-57593693 None:intergenic 40.0%
TCAAAAGAAACCTAACCTGC+TGG - chr7_4:57593734-57593753 None:intergenic 40.0%
TAGCAAAGCAACAGCAACTT+TGG + chr7_4:57594095-57594114 Msa1165650:CDS 40.0%
!!! CATTTTTCAAGTTCCATCCG+TGG + chr7_4:57594129-57594148 Msa1165650:CDS 40.0%
ATATAAGTGGAAGGTCTGAG+AGG - chr7_4:57594171-57594190 None:intergenic 40.0%
GTTACAACGCATAAGCTTGA+GGG + chr7_4:57593641-57593660 Msa1165650:five_prime_UTR 40.0%
GGAAATCGAAATTGGGGAAT+CGG - chr7_4:57593674-57593693 None:intergenic 40.0%
TCAAAAGAAACCTAACCTGC+TGG - chr7_4:57593734-57593753 None:intergenic 40.0%
TAGCAAAGCAACAGCAACTT+TGG + chr7_4:57594095-57594114 Msa1165650:CDS 40.0%
!!! CATTTTTCAAGTTCCATCCG+TGG + chr7_4:57594129-57594148 Msa1165650:CDS 40.0%
ATATAAGTGGAAGGTCTGAG+AGG - chr7_4:57594171-57594190 None:intergenic 40.0%
CGTTACAACGCATAAGCTTG+AGG + chr7_4:57593640-57593659 Msa1165650:five_prime_UTR 45.0%
ATAACAGCGATGCGTTGTGA+AGG - chr7_4:57593695-57593714 None:intergenic 45.0%
ACACACTGAAGAAGCAGGTT+TGG - chr7_4:57593881-57593900 None:intergenic 45.0%
AAACCTGCTTCTTCAGTGTG+TGG + chr7_4:57593880-57593899 Msa1165650:five_prime_UTR 45.0%
AACCTGCTTCTTCAGTGTGT+GGG + chr7_4:57593881-57593900 Msa1165650:five_prime_UTR 45.0%
TGCAAAGACTTCAAGGAGAC+CGG + chr7_4:57594228-57594247 Msa1165650:CDS 45.0%
AATGGAATGAAGCCGAGAAG+AGG + chr7_4:57594328-57594347 Msa1165650:CDS 45.0%
CGTTACAACGCATAAGCTTG+AGG + chr7_4:57593640-57593659 Msa1165650:five_prime_UTR 45.0%
ATAACAGCGATGCGTTGTGA+AGG - chr7_4:57593695-57593714 None:intergenic 45.0%
ACACACTGAAGAAGCAGGTT+TGG - chr7_4:57593881-57593900 None:intergenic 45.0%
AAACCTGCTTCTTCAGTGTG+TGG + chr7_4:57593880-57593899 Msa1165650:five_prime_UTR 45.0%
AACCTGCTTCTTCAGTGTGT+GGG + chr7_4:57593881-57593900 Msa1165650:five_prime_UTR 45.0%
TGCAAAGACTTCAAGGAGAC+CGG + chr7_4:57594228-57594247 Msa1165650:CDS 45.0%
AATGGAATGAAGCCGAGAAG+AGG + chr7_4:57594328-57594347 Msa1165650:CDS 45.0%
! AGAAACCTAACCTGCTGGCT+GGG - chr7_4:57593729-57593748 None:intergenic 50.0%
AAGAAACCTAACCTGCTGGC+TGG - chr7_4:57593730-57593749 None:intergenic 50.0%
AACCCACACACTGAAGAAGC+AGG - chr7_4:57593886-57593905 None:intergenic 50.0%
GCAAAGACTTCAAGGAGACC+GGG + chr7_4:57594229-57594248 Msa1165650:CDS 50.0%
! TTCAAGGAGACCGGGTATTG+TGG + chr7_4:57594237-57594256 Msa1165650:CDS 50.0%
TGCAAGTTTCTTCACGACCG+AGG + chr7_4:57594273-57594292 Msa1165650:CDS 50.0%
TTCTTTGTCCAACTGCCACC+CGG - chr7_4:57594310-57594329 None:intergenic 50.0%
GGTGGCAGTTGGACAAAGAA+TGG + chr7_4:57594310-57594329 Msa1165650:CDS 50.0%
GAATGAAGCCGAGAAGAGGA+GGG + chr7_4:57594332-57594351 Msa1165650:CDS 50.0%
! AGAAACCTAACCTGCTGGCT+GGG - chr7_4:57593729-57593748 None:intergenic 50.0%
AAGAAACCTAACCTGCTGGC+TGG - chr7_4:57593730-57593749 None:intergenic 50.0%
AACCCACACACTGAAGAAGC+AGG - chr7_4:57593886-57593905 None:intergenic 50.0%
GCAAAGACTTCAAGGAGACC+GGG + chr7_4:57594229-57594248 Msa1165650:CDS 50.0%
! TTCAAGGAGACCGGGTATTG+TGG + chr7_4:57594237-57594256 Msa1165650:CDS 50.0%
TGCAAGTTTCTTCACGACCG+AGG + chr7_4:57594273-57594292 Msa1165650:CDS 50.0%
TTCTTTGTCCAACTGCCACC+CGG - chr7_4:57594310-57594329 None:intergenic 50.0%
GGTGGCAGTTGGACAAAGAA+TGG + chr7_4:57594310-57594329 Msa1165650:CDS 50.0%
GAATGAAGCCGAGAAGAGGA+GGG + chr7_4:57594332-57594351 Msa1165650:CDS 50.0%
! CTGCTGGCTGGGTACTGTTA+AGG - chr7_4:57593718-57593737 None:intergenic 55.0%
CTTAACAGTACCCAGCCAGC+AGG + chr7_4:57593716-57593735 Msa1165650:five_prime_UTR 55.0%
ATCCGTGGGTCACACTCACA+CGG + chr7_4:57594144-57594163 Msa1165650:CDS 55.0%
! GAGACCGGGTATTGTGGCTA+CGG + chr7_4:57594243-57594262 Msa1165650:CDS 55.0%
ATCGCCGTAGCCACAATACC+CGG - chr7_4:57594250-57594269 None:intergenic 55.0%
GACCGAGGCGATTACAAGTC+CGG + chr7_4:57594288-57594307 Msa1165650:CDS 55.0%
ACCGAGGCGATTACAAGTCC+GGG + chr7_4:57594289-57594308 Msa1165650:CDS 55.0%
ACCCGGACTTGTAATCGCCT+CGG - chr7_4:57594293-57594312 None:intergenic 55.0%
TTACAAGTCCGGGTGGCAGT+TGG + chr7_4:57594299-57594318 Msa1165650:CDS 55.0%
GGAATGAAGCCGAGAAGAGG+AGG + chr7_4:57594331-57594350 Msa1165650:CDS 55.0%
! CTGCTGGCTGGGTACTGTTA+AGG - chr7_4:57593718-57593737 None:intergenic 55.0%
CTTAACAGTACCCAGCCAGC+AGG + chr7_4:57593716-57593735 Msa1165650:five_prime_UTR 55.0%
ATCCGTGGGTCACACTCACA+CGG + chr7_4:57594144-57594163 Msa1165650:CDS 55.0%
! GAGACCGGGTATTGTGGCTA+CGG + chr7_4:57594243-57594262 Msa1165650:CDS 55.0%
ATCGCCGTAGCCACAATACC+CGG - chr7_4:57594250-57594269 None:intergenic 55.0%
GACCGAGGCGATTACAAGTC+CGG + chr7_4:57594288-57594307 Msa1165650:CDS 55.0%
ACCGAGGCGATTACAAGTCC+GGG + chr7_4:57594289-57594308 Msa1165650:CDS 55.0%
ACCCGGACTTGTAATCGCCT+CGG - chr7_4:57594293-57594312 None:intergenic 55.0%
TTACAAGTCCGGGTGGCAGT+TGG + chr7_4:57594299-57594318 Msa1165650:CDS 55.0%
GGAATGAAGCCGAGAAGAGG+AGG + chr7_4:57594331-57594350 Msa1165650:CDS 55.0%
CAGTACCCAGCCAGCAGGTT+AGG + chr7_4:57593721-57593740 Msa1165650:intron 60.0%
GTGTGAGTGTGACCCACGGA+TGG - chr7_4:57594145-57594164 None:intergenic 60.0%
GACCGTGTGAGTGTGACCCA+CGG - chr7_4:57594149-57594168 None:intergenic 60.0%
GAGGCGATTACAAGTCCGGG+TGG + chr7_4:57594292-57594311 Msa1165650:CDS 60.0%
TCAGCGCACCCTCCTCTTCT+CGG - chr7_4:57594343-57594362 None:intergenic 60.0%
CAGTACCCAGCCAGCAGGTT+AGG + chr7_4:57593721-57593740 Msa1165650:intron 60.0%
GTGTGAGTGTGACCCACGGA+TGG - chr7_4:57594145-57594164 None:intergenic 60.0%
GACCGTGTGAGTGTGACCCA+CGG - chr7_4:57594149-57594168 None:intergenic 60.0%
GAGGCGATTACAAGTCCGGG+TGG + chr7_4:57594292-57594311 Msa1165650:CDS 60.0%
TCAGCGCACCCTCCTCTTCT+CGG - chr7_4:57594343-57594362 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 57593571 57594362 57593571 ID=Msa1165650;Name=Msa1165650
chr7_4 mRNA 57593571 57594362 57593571 ID=Msa1165650-mRNA-1;Parent=Msa1165650;Name=Msa1165650-mRNA-1;_AED=0.24;_eAED=0.39;_QI=289|0|0.5|1|0|0|2|0|124
chr7_4 exon 57593571 57593737 57593571 ID=Msa1165650-mRNA-1:exon:17475;Parent=Msa1165650-mRNA-1
chr7_4 exon 57593866 57594362 57593866 ID=Msa1165650-mRNA-1:exon:17476;Parent=Msa1165650-mRNA-1
chr7_4 five_prime_UTR 57593571 57593737 57593571 ID=Msa1165650-mRNA-1:five_prime_utr;Parent=Msa1165650-mRNA-1
chr7_4 five_prime_UTR 57593866 57593987 57593866 ID=Msa1165650-mRNA-1:five_prime_utr;Parent=Msa1165650-mRNA-1
chr7_4 CDS 57593988 57594362 57593988 ID=Msa1165650-mRNA-1:cds;Parent=Msa1165650-mRNA-1
Gene Sequence

>Msa1165650

ATGATGAATGTTGAGAAAAAGAACATGAAGAAGGCTGACAGTAATGAAGAATCCAAGAAGCACATCTTTCATTTTGAGTCTTCAAAAGAGATTCAAGTTCAACATGATAGCAAAGCAACAGCAACTTTGGAGACTGAGACTCATTTTTCAAGTTCCATCCGTGGGTCACACTCACACGGTCCTCTCAGACCTTCCACTTATATTAGAGTTTCATCAAGAATCGATTATCAACCTGACATATGCAAAGACTTCAAGGAGACCGGGTATTGTGGCTACGGCGATTCATGCAAGTTTCTTCACGACCGAGGCGATTACAAGTCCGGGTGGCAGTTGGACAAAGAATGGAATGAAGCCGAGAAGAGGAGGGTGCGCTGA
Protein sequence

>Msa1165650

MMNVEKKNMKKADSNEESKKHIFHFESSKEIQVQHDSKATATLETETHFSSSIRGSHSHGPLRPSTYIRVSSRIDYQPDICKDFKETGYCGYGDSCKFLHDRGDYKSGWQLDKEWNEAEKRRVR*