AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1379990


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGTTGTCGTTGTCGGCTATT+TGG 0.216325 tig0020315:+132402 None:intergenic
GGCGGGGAACCCATGAAATT+TGG 0.274459 tig0020315:-132361 Msa1379990:CDS
CGCTCTCCACACCGTCCATT+GGG 0.361017 tig0020315:+132147 None:intergenic
ACCGAGCACGCCAAATTTCA+TGG 0.361507 tig0020315:+132351 None:intergenic
GTTGTCGTTGTCGGCTATTT+GGG 0.377596 tig0020315:+132403 None:intergenic
GTTGTCGGCTATTTGGGTTT+TGG 0.377940 tig0020315:+132409 None:intergenic
ATGGGTTCCCCGCCAGTGTA+TGG 0.378975 tig0020315:+132370 None:intergenic
ACGGTGTGGAGAGCGATTTA+TGG 0.387961 tig0020315:-132139 Msa1379990:CDS
TTGCTCAGACCACTGAAGTT+GGG 0.412418 tig0020315:+132239 None:intergenic
TGTCTCCGGCGTTGTGAAGA+AGG 0.439983 tig0020315:+132273 None:intergenic
CCCATGAAATTTGGCGTGCT+CGG 0.450530 tig0020315:-132352 Msa1379990:intron
GGTCATTGTTGACAAGATCT+AGG 0.455636 tig0020315:-132190 Msa1379990:CDS
ACGCCGGAGACACGAGATCT+AGG 0.456123 tig0020315:-132262 Msa1379990:CDS
TCGCTCTCCACACCGTCCAT+TGG 0.457821 tig0020315:+132146 None:intergenic
CGGTGTGGAGAGCGATTTAT+GGG 0.459062 tig0020315:-132138 Msa1379990:CDS
GGGCTAATACCACTTGAGTT+GGG 0.464825 tig0020315:+132167 None:intergenic
TGGGTCGTCAGTGACGAGAT+TGG 0.479654 tig0020315:-132119 Msa1379990:CDS
GGGTCGTCAGTGACGAGATT+GGG 0.488139 tig0020315:-132118 Msa1379990:CDS
TGGGCTAATACCACTTGAGT+TGG 0.493264 tig0020315:+132166 None:intergenic
ATTATACACCATACACTGGC+GGG 0.503855 tig0020315:-132378 Msa1379990:CDS
GTTGCTCAGACCACTGAAGT+TGG 0.509679 tig0020315:+132238 None:intergenic
CCTAACGGAATAGTCGTGTC+TGG 0.519833 tig0020315:-132445 Msa1379990:intron
AAAACGCTCTCTTCATCAGT+TGG 0.519969 tig0020315:+132216 None:intergenic
GTCAGTGACGAGATTGGGTA+AGG 0.523532 tig0020315:-132113 None:intergenic
CCGAGCACGCCAAATTTCAT+GGG 0.529791 tig0020315:+132352 None:intergenic
GGGCCTAGATCTCGTGTCTC+CGG 0.553368 tig0020315:+132259 None:intergenic
GTCTCCGGCGTTGTGAAGAA+GGG 0.555639 tig0020315:+132274 None:intergenic
GTATAATGAGTTGTCGTTGT+CGG 0.567321 tig0020315:+132394 None:intergenic
TCCTCCCTTCTTCACAACGC+CGG 0.583529 tig0020315:-132278 Msa1379990:CDS
CTCAAGTGGTATTAGCCCAA+TGG 0.604300 tig0020315:-132162 Msa1379990:CDS
AGATCTAGGCCCAACTTCAG+TGG 0.618428 tig0020315:-132248 Msa1379990:CDS
AGATCTAGGCCCAACTCAAG+TGG 0.625323 tig0020315:-132176 Msa1379990:CDS
TTATACACCATACACTGGCG+GGG 0.628230 tig0020315:-132377 Msa1379990:CDS
CATTATACACCATACACTGG+CGG 0.637045 tig0020315:-132379 Msa1379990:CDS
ACTCATTATACACCATACAC+TGG 0.644543 tig0020315:-132382 Msa1379990:CDS
TCCGGCGTTGTGAAGAAGGG+AGG 0.654657 tig0020315:+132277 None:intergenic
AGTGGTATTAGCCCAATGGA+CGG 0.656425 tig0020315:-132158 Msa1379990:CDS
TATTAGCCCAATGGACGGTG+TGG 0.670800 tig0020315:-132153 Msa1379990:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATTTTTAGGTTTTGGTTT+GGG - tig0020315:132225-132244 Msa1379990:CDS 25.0%
GTATATTCATGATCTACTCT+CGG - tig0020315:132123-132142 Msa1379990:CDS 30.0%
TATATTCATGATCTACTCTC+GGG - tig0020315:132124-132143 Msa1379990:CDS 30.0%
!! CGTTTTATTCCATACATTGA+TGG + tig0020315:132198-132217 None:intergenic 30.0%
!!! GTTGTCGAATTTTTAGGTTT+TGG - tig0020315:132219-132238 Msa1379990:CDS 30.0%
!!! CGAATTTTTAGGTTTTGGTT+TGG - tig0020315:132224-132243 Msa1379990:CDS 30.0%
ATTGGATTGCCATCAATGTA+TGG - tig0020315:132186-132205 Msa1379990:CDS 35.0%
! AAACGCGTTGTCGAATTTTT+AGG - tig0020315:132213-132232 Msa1379990:CDS 35.0%
GTATAATGAGTTGTCGTTGT+CGG + tig0020315:132339-132358 None:intergenic 35.0%
ACTCATTATACACCATACAC+TGG - tig0020315:132348-132367 Msa1379990:intron 35.0%
!! GAGTAGGGTAGTGGAATATT+TGG + tig0020315:132156-132175 None:intergenic 40.0%
CCAATGAAATCTGGAGAGTA+GGG + tig0020315:132171-132190 None:intergenic 40.0%
TCCAATGAAATCTGGAGAGT+AGG + tig0020315:132172-132191 None:intergenic 40.0%
GATGGCAATCCAATGAAATC+TGG + tig0020315:132180-132199 None:intergenic 40.0%
!!! GGCTATTTGGGTTTTGGTTT+GGG + tig0020315:132318-132337 None:intergenic 40.0%
CATTATACACCATACACTGG+CGG - tig0020315:132351-132370 Msa1379990:intron 40.0%
ATTATACACCATACACTGGC+GGG - tig0020315:132352-132371 Msa1379990:intron 40.0%
AAAACGCTCTCTTCATCAGT+TGG + tig0020315:132517-132536 None:intergenic 40.0%
GGTCATTGTTGACAAGATCT+AGG - tig0020315:132540-132559 Msa1379990:intron 40.0%
AAATCTGGAGAGTAGGGTAG+TGG + tig0020315:132165-132184 None:intergenic 45.0%
CCCTACTCTCCAGATTTCAT+TGG - tig0020315:132168-132187 Msa1379990:CDS 45.0%
!!! TTAGGTTTTGGTTTGGGTCG+AGG - tig0020315:132231-132250 Msa1379990:CDS 45.0%
CGTAACAGAATAGTCGTGTC+TGG + tig0020315:132258-132277 None:intergenic 45.0%
!!! CGGCTATTTGGGTTTTGGTT+TGG + tig0020315:132319-132338 None:intergenic 45.0%
!! GTTGTCGGCTATTTGGGTTT+TGG + tig0020315:132324-132343 None:intergenic 45.0%
! GTTGTCGTTGTCGGCTATTT+GGG + tig0020315:132330-132349 None:intergenic 45.0%
! AGTTGTCGTTGTCGGCTATT+TGG + tig0020315:132331-132350 None:intergenic 45.0%
TTATACACCATACACTGGCG+GGG - tig0020315:132353-132372 Msa1379990:CDS 45.0%
TTGCTCAGACCACTGAAGTT+GGG + tig0020315:132494-132513 None:intergenic 45.0%
!!! CTGATGAAGAGAGCGTTTTG+CGG - tig0020315:132518-132537 Msa1379990:intron 45.0%
!!! TGATGAAGAGAGCGTTTTGC+GGG - tig0020315:132519-132538 Msa1379990:intron 45.0%
GGGCTAATACCACTTGAGTT+GGG + tig0020315:132566-132585 None:intergenic 45.0%
TGGGCTAATACCACTTGAGT+TGG + tig0020315:132567-132586 None:intergenic 45.0%
CTCAAGTGGTATTAGCCCAA+TGG - tig0020315:132568-132587 Msa1379990:intron 45.0%
AGTGGTATTAGCCCAATGGA+CGG - tig0020315:132572-132591 Msa1379990:intron 45.0%
CTGTTACGTACTCCGCCTAA+CGG - tig0020315:132270-132289 Msa1379990:CDS 50.0%
GACACGACTATTCCGTTAGG+CGG + tig0020315:132285-132304 None:intergenic 50.0%
CCAGACACGACTATTCCGTT+AGG + tig0020315:132288-132307 None:intergenic 50.0%
CCTAACGGAATAGTCGTGTC+TGG - tig0020315:132285-132304 Msa1379990:CDS 50.0%
!!! TTGGGTTTTGGTTTGGGTCG+AGG + tig0020315:132312-132331 None:intergenic 50.0%
CCGAGCACGCCAAATTTCAT+GGG + tig0020315:132381-132400 None:intergenic 50.0%
CCCATGAAATTTGGCGTGCT+CGG - tig0020315:132378-132397 Msa1379990:CDS 50.0%
ACCGAGCACGCCAAATTTCA+TGG + tig0020315:132382-132401 None:intergenic 50.0%
AGATCTAGGCCCAACTTCAG+TGG - tig0020315:132482-132501 Msa1379990:intron 50.0%
GTTGCTCAGACCACTGAAGT+TGG + tig0020315:132495-132514 None:intergenic 50.0%
AGATCTAGGCCCAACTCAAG+TGG - tig0020315:132554-132573 Msa1379990:intron 50.0%
TATTAGCCCAATGGACGGTG+TGG - tig0020315:132577-132596 Msa1379990:intron 50.0%
ACGGTGTGGAGAGCGATTTA+TGG - tig0020315:132591-132610 Msa1379990:intron 50.0%
CGGTGTGGAGAGCGATTTAT+GGG - tig0020315:132592-132611 Msa1379990:intron 50.0%
GGCGGGGAACCCATGAAATT+TGG - tig0020315:132369-132388 Msa1379990:CDS 55.0%
TCCTCCCTTCTTCACAACGC+CGG - tig0020315:132452-132471 Msa1379990:intron 55.0%
GTCTCCGGCGTTGTGAAGAA+GGG + tig0020315:132459-132478 None:intergenic 55.0%
TGTCTCCGGCGTTGTGAAGA+AGG + tig0020315:132460-132479 None:intergenic 55.0%
TGGGTCGTCAGTGACGAGAT+TGG - tig0020315:132611-132630 Msa1379990:intron 55.0%
GGGTCGTCAGTGACGAGATT+GGG - tig0020315:132612-132631 Msa1379990:intron 55.0%
ATGGGTTCCCCGCCAGTGTA+TGG + tig0020315:132363-132382 None:intergenic 60.0%
TCCGGCGTTGTGAAGAAGGG+AGG + tig0020315:132456-132475 None:intergenic 60.0%
ACGCCGGAGACACGAGATCT+AGG - tig0020315:132468-132487 Msa1379990:intron 60.0%
GGGCCTAGATCTCGTGTCTC+CGG + tig0020315:132474-132493 None:intergenic 60.0%
CGCTCTCCACACCGTCCATT+GGG + tig0020315:132586-132605 None:intergenic 60.0%
TCGCTCTCCACACCGTCCAT+TGG + tig0020315:132587-132606 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
tig0020315 gene 132115 132637 132115 ID=Msa1379990;Name=Msa1379990
tig0020315 mRNA 132115 132637 132115 ID=Msa1379990-mRNA-1;Parent=Msa1379990;Name=Msa1379990-mRNA-1;_AED=0.37;_eAED=0.57;_QI=0|0|0|0.66|0|0|3|0|107
tig0020315 exon 132630 132637 132630 ID=Msa1379990-mRNA-1:exon:6888;Parent=Msa1379990-mRNA-1
tig0020315 exon 132353 132454 132353 ID=Msa1379990-mRNA-1:exon:6887;Parent=Msa1379990-mRNA-1
tig0020315 exon 132115 132328 132115 ID=Msa1379990-mRNA-1:exon:6886;Parent=Msa1379990-mRNA-1
tig0020315 CDS 132630 132637 132630 ID=Msa1379990-mRNA-1:cds;Parent=Msa1379990-mRNA-1
tig0020315 CDS 132353 132454 132353 ID=Msa1379990-mRNA-1:cds;Parent=Msa1379990-mRNA-1
tig0020315 CDS 132115 132328 132115 ID=Msa1379990-mRNA-1:cds;Parent=Msa1379990-mRNA-1
Gene Sequence

>Msa1379990

ATGGACGCTCGTGTCTGGTCCTCGACCCAAACCAAAACCCAAATAGCCGACAACGACAACTCATTATACACCATACACTGGCGGGGAACCCATGAAATTTGGCGTGCTCGAGTATATCATATATCTACATATTCATCATCCTCCCTTCTTCACAACGCCGGAGACACGAGATCTAGGCCCAACTTCAGTGGTCTGAGCAACCAACTGATGAAGAGAGCGTTTTGCGGGTCATTGTTGACAAGATCTAGGCCCAACTCAAGTGGTATTAGCCCAATGGACGGTGTGGAGAGCGATTTATGGGTCGTCAGTGACGAGATTGGGTAA

Protein sequence

>Msa1379990

MDARVWSSTQTKTQIADNDNSLYTIHWRGTHEIWRARVYHISTYSSSSLLHNAGDTRSRPNFSGLSNQLMKRAFCGSLLTRSRPNSSGISPMDGVESDLWVVSDEIG*