AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0242360


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0242360 MtrunA17_Chr2g0294531 36.364 121 32 1 1 121 1 76 1.30e-16 69.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 58 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGGAGGGGAGGGGAGGGTTT+TGG 0.212662 2_2:+18490214 Msa0242360:CDS
TAAGGCTTTGTTTGGGAGTT+TGG 0.212875 2_2:-18490552 None:intergenic
TTAGGCTTTGTTTGGGAGTT+TGG 0.225567 2_2:+18490189 Msa0242360:CDS
ATTTGCACGGGCGTTGATTT+TGG 0.227744 2_2:-18490611 None:intergenic
TTTGGAGGGGAGGGGAGGGG+AGG 0.254388 2_2:+18490207 Msa0242360:CDS
AGTACCATGGTTGGTGGATT+TGG 0.268216 2_2:-18490156 None:intergenic
ATGGTTGTTAAGGCTTTGTT+TGG 0.269647 2_2:-18490560 None:intergenic
GGGAGTTTGGAGGGGAGGGG+AGG 0.289218 2_2:+18490202 Msa0242360:CDS
GAGTTTGGAGGGGAGGGGAG+GGG 0.299317 2_2:+18490204 Msa0242360:CDS
AAATTCATTTAGGCTTTGTT+TGG 0.328746 2_2:+18490181 Msa0242360:CDS
TTTGGGAGTTTGGAGGGGAG+GGG 0.336426 2_2:+18490199 Msa0242360:CDS
TTGGGAGGAGAGGGCTTTGC+AGG 0.338479 2_2:+18490273 Msa0242360:CDS
GTTTGGGAGTTTGGAGGGGA+GGG 0.354818 2_2:+18490198 Msa0242360:CDS
TGTTTGGGAGTTTGGAGGGG+AGG 0.355934 2_2:+18490197 Msa0242360:CDS
GGAGTTTGGAGGGGAGGGGA+GGG 0.360686 2_2:+18490203 Msa0242360:CDS
GCCTTAACAACCATGGTAAC+GGG 0.361815 2_2:+18490569 Msa0242360:CDS
GCTTTGTTTGGGAGTTTGGA+GGG 0.374549 2_2:-18490548 None:intergenic
CCCCGTTACCATGGTTGTTA+AGG 0.378195 2_2:-18490570 None:intergenic
GCTTTGTTTGGGAGTTTGGA+GGG 0.388556 2_2:+18490193 Msa0242360:CDS
ATGGTACTGGAAATTCATTT+AGG 0.401075 2_2:+18490171 Msa0242360:CDS
GGCTTTGTTTGGGAGTTTGG+AGG 0.401752 2_2:+18490192 Msa0242360:CDS
GGCTTTGTTTGGGAGTTTGG+AGG 0.401752 2_2:-18490549 None:intergenic
TTGGAGGGGAGGGGAGGGGA+GGG 0.405392 2_2:+18490208 Msa0242360:CDS
ATCAACGCCCGTGCAAATGC+CGG 0.417551 2_2:+18490616 Msa0242360:CDS
AATTCATTTAGGCTTTGTTT+GGG 0.432275 2_2:+18490182 Msa0242360:CDS
CTTTGTTTGGGAGTTTGGAG+GGG 0.437713 2_2:+18490194 Msa0242360:CDS
TACGGTCCCCGGCATTTGCA+CGG 0.446381 2_2:-18490624 None:intergenic
TCAACGCCCGTGCAAATGCC+GGG 0.453778 2_2:+18490617 Msa0242360:CDS
AAATCCACCAACCATGGTAC+TGG 0.464639 2_2:+18490158 Msa0242360:CDS
CTTTGTTTGGGAGTTTGGAG+GGG 0.468174 2_2:-18490547 None:intergenic
GCGGTGTTTGTTACGGTCCC+CGG 0.472456 2_2:-18490635 None:intergenic
CACCGCACCACCAATAGTTA+TGG 0.478897 2_2:+18490652 Msa0242360:CDS
TGGTGGTGCGGTGTTTGTTA+CGG 0.482221 2_2:-18490642 None:intergenic
AGTGCGGCCACCATAACTAT+TGG 0.482716 2_2:-18490662 None:intergenic
TGGTTGTTAAGGCTTTGTTT+GGG 0.484424 2_2:-18490559 None:intergenic
ACGGTCCCCGGCATTTGCAC+GGG 0.492122 2_2:-18490623 None:intergenic
TGGAAGAAATAGAAGACATT+GGG 0.497892 2_2:+18490255 Msa0242360:CDS
TAGAAGACATTGGGAGGAGA+GGG 0.505993 2_2:+18490264 Msa0242360:CDS
ATTTCCAGTACCATGGTTGG+TGG 0.513143 2_2:-18490162 None:intergenic
AGCCTTAACAACCATGGTAA+CGG 0.529548 2_2:+18490568 Msa0242360:CDS
GTGGAAGAAATAGAAGACAT+TGG 0.540645 2_2:+18490254 Msa0242360:CDS
AACGGGGACCAAAATTTCTC+CGG 0.541630 2_2:+18490586 Msa0242360:CDS
AAACCTCATCGCAATGCTTG+AGG 0.561734 2_2:+18490112 Msa0242360:CDS
TGAATTTCCAGTACCATGGT+TGG 0.563510 2_2:-18490165 None:intergenic
ATAGAAGACATTGGGAGGAG+AGG 0.564987 2_2:+18490263 Msa0242360:CDS
CACCATAACTATTGGTGGTG+CGG 0.572312 2_2:-18490654 None:intergenic
AAGAAATAGAAGACATTGGG+AGG 0.586992 2_2:+18490258 Msa0242360:CDS
TGGCCGCACTATTAATAACA+AGG 0.609381 2_2:+18490675 Msa0242360:CDS
TAAATGAATTTCCAGTACCA+TGG 0.609714 2_2:-18490169 None:intergenic
TACCCTTGTTATTAATAGTG+CGG 0.610643 2_2:-18490678 None:intergenic
CGCACCACCAATAGTTATGG+TGG 0.610700 2_2:+18490655 Msa0242360:CDS
CAGCCTCAAGCATTGCGATG+AGG 0.612561 2_2:-18490115 None:intergenic
GCGGCCACCATAACTATTGG+TGG 0.630307 2_2:-18490659 None:intergenic
CAACGCCCGTGCAAATGCCG+GGG 0.636406 2_2:+18490618 Msa0242360:CDS
GCTTCCAAATCCACCAACCA+TGG 0.636574 2_2:+18490152 Msa0242360:CDS
CCTTAACAACCATGGTAACG+GGG 0.661779 2_2:+18490570 Msa0242360:CDS
GGCCGCACTATTAATAACAA+GGG 0.679607 2_2:+18490676 Msa0242360:CDS
AAACAAAGCCTTAACAACCA+TGG 0.691518 2_2:+18490562 Msa0242360:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAATTCATTTAGGCTTTGTT+TGG + chr2_2:18490181-18490200 Msa0242360:CDS 25.0%
!!! AATTCATTTAGGCTTTGTTT+GGG + chr2_2:18490182-18490201 Msa0242360:CDS 25.0%
TAAATGAATTTCCAGTACCA+TGG - chr2_2:18490172-18490191 None:intergenic 30.0%
! ATGGTACTGGAAATTCATTT+AGG + chr2_2:18490171-18490190 Msa0242360:CDS 30.0%
TGGAAGAAATAGAAGACATT+GGG + chr2_2:18490255-18490274 Msa0242360:CDS 30.0%
AATAAAAAATCCCCCTCATT+TGG + chr2_2:18490312-18490331 Msa0242360:intron 30.0%
ATAAAAAATCCCCCTCATTT+GGG + chr2_2:18490313-18490332 Msa0242360:intron 30.0%
!! TACCCTTGTTATTAATAGTG+CGG - chr2_2:18490681-18490700 None:intergenic 30.0%
GTGGAAGAAATAGAAGACAT+TGG + chr2_2:18490254-18490273 Msa0242360:CDS 35.0%
AAGAAATAGAAGACATTGGG+AGG + chr2_2:18490258-18490277 Msa0242360:CDS 35.0%
TAAAAAATCCCCCTCATTTG+GGG + chr2_2:18490314-18490333 Msa0242360:intron 35.0%
GGGAACTCAAAAATTGCATT+GGG + chr2_2:18490335-18490354 Msa0242360:intron 35.0%
GGAACTCAAAAATTGCATTG+GGG + chr2_2:18490336-18490355 Msa0242360:intron 35.0%
GAACTCAAAAATTGCATTGG+GGG + chr2_2:18490337-18490356 Msa0242360:intron 35.0%
!! TGGTTGTTAAGGCTTTGTTT+GGG - chr2_2:18490562-18490581 None:intergenic 35.0%
!! ATGGTTGTTAAGGCTTTGTT+TGG - chr2_2:18490563-18490582 None:intergenic 35.0%
AAACAAAGCCTTAACAACCA+TGG + chr2_2:18490562-18490581 Msa0242360:CDS 35.0%
! GATGAGGTTTTTGATCACAC+GGG - chr2_2:18490102-18490121 None:intergenic 40.0%
! CGATGAGGTTTTTGATCACA+CGG - chr2_2:18490103-18490122 None:intergenic 40.0%
TGAATTTCCAGTACCATGGT+TGG - chr2_2:18490168-18490187 None:intergenic 40.0%
!! TTAGGCTTTGTTTGGGAGTT+TGG + chr2_2:18490189-18490208 Msa0242360:CDS 40.0%
!!! GAGGGTTTTGGAAAAAAGGA+AGG + chr2_2:18490226-18490245 Msa0242360:CDS 40.0%
AAAAAATCCCCCTCATTTGG+GGG + chr2_2:18490315-18490334 Msa0242360:intron 40.0%
!!! TTTTGAGTTCCCCCAAATGA+GGG - chr2_2:18490327-18490346 None:intergenic 40.0%
!!! TTTTTGAGTTCCCCCAAATG+AGG - chr2_2:18490328-18490347 None:intergenic 40.0%
GGGGAACTCAAAAATTGCAT+TGG + chr2_2:18490334-18490353 Msa0242360:intron 40.0%
TCAAAAATTGCATTGGGGGA+GGG + chr2_2:18490341-18490360 Msa0242360:intron 40.0%
!! TAAGGCTTTGTTTGGGAGTT+TGG - chr2_2:18490555-18490574 None:intergenic 40.0%
AGCCTTAACAACCATGGTAA+CGG + chr2_2:18490568-18490587 Msa0242360:CDS 40.0%
!! TTTTGGCACCGGAGAAATTT+TGG - chr2_2:18490597-18490616 None:intergenic 40.0%
TGGCCGCACTATTAATAACA+AGG + chr2_2:18490675-18490694 Msa0242360:CDS 40.0%
GGCCGCACTATTAATAACAA+GGG + chr2_2:18490676-18490695 Msa0242360:CDS 40.0%
AAACCTCATCGCAATGCTTG+AGG + chr2_2:18490112-18490131 Msa0242360:CDS 45.0%
!! AGTACCATGGTTGGTGGATT+TGG - chr2_2:18490159-18490178 None:intergenic 45.0%
AAATCCACCAACCATGGTAC+TGG + chr2_2:18490158-18490177 Msa0242360:CDS 45.0%
ATTTCCAGTACCATGGTTGG+TGG - chr2_2:18490165-18490184 None:intergenic 45.0%
!! GCTTTGTTTGGGAGTTTGGA+GGG + chr2_2:18490193-18490212 Msa0242360:CDS 45.0%
! CTTTGTTTGGGAGTTTGGAG+GGG + chr2_2:18490194-18490213 Msa0242360:CDS 45.0%
!!! AGGGGAGGGTTTTGGAAAAA+AGG + chr2_2:18490222-18490241 Msa0242360:CDS 45.0%
GGAAAAAAGGAAGGAGCAAG+TGG + chr2_2:18490235-18490254 Msa0242360:CDS 45.0%
ATAGAAGACATTGGGAGGAG+AGG + chr2_2:18490263-18490282 Msa0242360:CDS 45.0%
TAGAAGACATTGGGAGGAGA+GGG + chr2_2:18490264-18490283 Msa0242360:CDS 45.0%
! TTTGAGTTCCCCCAAATGAG+GGG - chr2_2:18490326-18490345 None:intergenic 45.0%
CTCAAAAATTGCATTGGGGG+AGG + chr2_2:18490340-18490359 Msa0242360:intron 45.0%
! CTTTGTTTGGGAGTTTGGAG+GGG - chr2_2:18490194-18490213 None:intergenic 45.0%
!! GCTTTGTTTGGGAGTTTGGA+GGG - chr2_2:18490193-18490212 None:intergenic 45.0%
GCCTTAACAACCATGGTAAC+GGG + chr2_2:18490569-18490588 Msa0242360:CDS 45.0%
! CCTTAACAACCATGGTAACG+GGG + chr2_2:18490570-18490589 Msa0242360:CDS 45.0%
!! AATTTTGGTCCCCGTTACCA+TGG - chr2_2:18490582-18490601 None:intergenic 45.0%
AACGGGGACCAAAATTTCTC+CGG + chr2_2:18490586-18490605 Msa0242360:CDS 45.0%
!!! ATTTGCACGGGCGTTGATTT+TGG - chr2_2:18490614-18490633 None:intergenic 45.0%
!! CACCATAACTATTGGTGGTG+CGG - chr2_2:18490657-18490676 None:intergenic 45.0%
GCTTCCAAATCCACCAACCA+TGG + chr2_2:18490152-18490171 Msa0242360:CDS 50.0%
!! GGCTTTGTTTGGGAGTTTGG+AGG + chr2_2:18490192-18490211 Msa0242360:CDS 50.0%
TTGAGTTCCCCCAAATGAGG+GGG - chr2_2:18490325-18490344 None:intergenic 50.0%
! ATTGCATTGGGGGAGGGTTT+TGG + chr2_2:18490347-18490366 Msa0242360:intron 50.0%
! TTGCATTGGGGGAGGGTTTT+GGG + chr2_2:18490348-18490367 Msa0242360:intron 50.0%
!!! AGGGTTTTGGGGGGTTATAG+AGG + chr2_2:18490360-18490379 Msa0242360:intron 50.0%
!!! GGGTTTTGGGGGGTTATAGA+GGG + chr2_2:18490361-18490380 Msa0242360:intron 50.0%
AGTTTGGAGGGGAGAGCTTT+GGG - chr2_2:18490539-18490558 None:intergenic 50.0%
!! GGCTTTGTTTGGGAGTTTGG+AGG - chr2_2:18490192-18490211 None:intergenic 50.0%
CCCCGTTACCATGGTTGTTA+AGG - chr2_2:18490573-18490592 None:intergenic 50.0%
! TGGTGGTGCGGTGTTTGTTA+CGG - chr2_2:18490645-18490664 None:intergenic 50.0%
CACCGCACCACCAATAGTTA+TGG + chr2_2:18490652-18490671 Msa0242360:CDS 50.0%
CGCACCACCAATAGTTATGG+TGG + chr2_2:18490655-18490674 Msa0242360:CDS 50.0%
AGTGCGGCCACCATAACTAT+TGG - chr2_2:18490665-18490684 None:intergenic 50.0%
! CAGCCTCAAGCATTGCGATG+AGG - chr2_2:18490118-18490137 None:intergenic 55.0%
TGTTTGGGAGTTTGGAGGGG+AGG + chr2_2:18490197-18490216 Msa0242360:CDS 55.0%
GTTTGGGAGTTTGGAGGGGA+GGG + chr2_2:18490198-18490217 Msa0242360:CDS 55.0%
TTTGGGAGTTTGGAGGGGAG+GGG + chr2_2:18490199-18490218 Msa0242360:CDS 55.0%
! TGCATTGGGGGAGGGTTTTG+GGG + chr2_2:18490349-18490368 Msa0242360:intron 55.0%
! TTTGGAGGGGAGAGCTTTGG+GGG - chr2_2:18490537-18490556 None:intergenic 55.0%
GTTTGGAGGGGAGAGCTTTG+GGG - chr2_2:18490538-18490557 None:intergenic 55.0%
GAGTTTGGAGGGGAGAGCTT+TGG - chr2_2:18490540-18490559 None:intergenic 55.0%
!!! ACGGGCGTTGATTTTGGCAC+CGG - chr2_2:18490608-18490627 None:intergenic 55.0%
ATCAACGCCCGTGCAAATGC+CGG + chr2_2:18490616-18490635 Msa0242360:CDS 55.0%
GCGGCCACCATAACTATTGG+TGG - chr2_2:18490662-18490681 None:intergenic 55.0%
TTGGGAGGAGAGGGCTTTGC+AGG + chr2_2:18490273-18490292 Msa0242360:CDS 60.0%
!! GCATTGGGGGAGGGTTTTGG+GGG + chr2_2:18490350-18490369 Msa0242360:intron 60.0%
!!! CATTGGGGGAGGGTTTTGGG+GGG + chr2_2:18490351-18490370 Msa0242360:intron 60.0%
!! TTGGAGGGGAGAGCTTTGGG+GGG - chr2_2:18490536-18490555 None:intergenic 60.0%
TCAACGCCCGTGCAAATGCC+GGG + chr2_2:18490617-18490636 Msa0242360:CDS 60.0%
TACGGTCCCCGGCATTTGCA+CGG - chr2_2:18490627-18490646 None:intergenic 60.0%
! GCGGTGTTTGTTACGGTCCC+CGG - chr2_2:18490638-18490657 None:intergenic 60.0%
GGAGTTTGGAGGGGAGGGGA+GGG + chr2_2:18490203-18490222 Msa0242360:CDS 65.0%
GAGTTTGGAGGGGAGGGGAG+GGG + chr2_2:18490204-18490223 Msa0242360:CDS 65.0%
CAACGCCCGTGCAAATGCCG+GGG + chr2_2:18490618-18490637 Msa0242360:CDS 65.0%
ACGGTCCCCGGCATTTGCAC+GGG - chr2_2:18490626-18490645 None:intergenic 65.0%
GGGAGTTTGGAGGGGAGGGG+AGG + chr2_2:18490202-18490221 Msa0242360:CDS 70.0%
TTTGGAGGGGAGGGGAGGGG+AGG + chr2_2:18490207-18490226 Msa0242360:CDS 70.0%
TTGGAGGGGAGGGGAGGGGA+GGG + chr2_2:18490208-18490227 Msa0242360:CDS 70.0%
! GGGAGGGGAGGGGAGGGTTT+TGG + chr2_2:18490214-18490233 Msa0242360:CDS 70.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 18490092 18490705 18490092 ID=Msa0242360;Name=Msa0242360
chr2_2 mRNA 18490092 18490705 18490092 ID=Msa0242360-mRNA-1;Parent=Msa0242360;Name=Msa0242360-mRNA-1;_AED=0.61;_eAED=1.00;_QI=0|0|0|0.5|1|1|2|0|121
chr2_2 exon 18490092 18490294 18490092 ID=Msa0242360-mRNA-1:exon:7579;Parent=Msa0242360-mRNA-1
chr2_2 exon 18490543 18490705 18490543 ID=Msa0242360-mRNA-1:exon:7580;Parent=Msa0242360-mRNA-1
chr2_2 CDS 18490092 18490294 18490092 ID=Msa0242360-mRNA-1:cds;Parent=Msa0242360-mRNA-1
chr2_2 CDS 18490543 18490705 18490543 ID=Msa0242360-mRNA-1:cds;Parent=Msa0242360-mRNA-1
Gene Sequence

>Msa0242360

ATGTCATCCCGTGTGATCAAAAACCTCATCGCAATGCTTGAGGCTGAGAAAGCAGCTGAAGCTTCCAAATCCACCAACCATGGTACTGGAAATTCATTTAGGCTTTGTTTGGGAGTTTGGAGGGGAGGGGAGGGGAGGGTTTTGGAAAAAAGGAAGGAGCAAGTGGAAGAAATAGAAGACATTGGGAGGAGAGGGCTTTGCAGCTCTCCCCTCCAAACTCCCAAACAAAGCCTTAACAACCATGGTAACGGGGACCAAAATTTCTCCGGTGCCAAAATCAACGCCCGTGCAAATGCCGGGGACCGTAACAAACACCGCACCACCAATAGTTATGGTGGCCGCACTATTAATAACAAGGGTACGTAG

Protein sequence

>Msa0242360

MSSRVIKNLIAMLEAEKAAEASKSTNHGTGNSFRLCLGVWRGGEGRVLEKRKEQVEEIEDIGRRGLCSSPLQTPKQSLNNHGNGDQNFSGAKINARANAGDRNKHRTTNSYGGRTINNKGT*