AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG012023


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012023 MtrunA17_Chr3g0082161 96.364 275 10 0 89 363 10 284 0.0 551
MsaG012023 MtrunA17_Chr1g0164511 95.636 275 12 0 89 363 10 284 0.0 548
MsaG012023 MtrunA17_Chr1g0164501 95.434 219 10 0 145 363 1 219 1.42e-155 436
MsaG012023 MtrunA17_Chr8g0353321 65.909 264 89 1 88 351 36 298 1.62e-131 378
MsaG012023 MtrunA17_Chr3g0082151 78.333 60 9 2 46 104 1 57 2.13e-22 89.4
MsaG012023 MtrunA17_Chr1g0164521 78.333 60 9 2 46 104 1 57 2.13e-22 89.4
MsaG012023 MtrunA17_Chr2g0277381 26.471 272 172 10 92 356 77 327 1.31e-12 68.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG012023 AT1G72050.2 54.499 389 124 3 14 350 15 402 5.36e-146 419
MsaG012023 AT1G72050.3 54.499 389 124 3 14 350 30 417 6.14e-146 420
MsaG012023 AT1G72050.1 54.140 314 92 2 88 350 2 314 4.88e-117 342
MsaG012023 AT1G72050.4 51.812 276 82 1 88 312 2 277 1.55e-97 293

Find 67 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGTCTAATATCTCTGAATTT+TGG 0.068375 3:+17333315 None:intergenic
AATTGATGTGGGATGTAATT+AGG 0.159176 3:+17333250 None:intergenic
AAGATTTAACATGAGCTTTA+AGG 0.205162 3:+17331344 None:intergenic
ACCTTTCCACAGCCAATTTC+AGG 0.226103 3:+17331610 None:intergenic
TTCAAACCACCCTCTGATTC+AGG 0.233682 3:+17332783 None:intergenic
ATTGATGTGGGATGTAATTA+GGG 0.319248 3:+17333251 None:intergenic
AAGAAGCTGATGAAGAATTC+AGG 0.351513 3:-17330840 MsaT012023.1:CDS
GCAAACCTCATTCCACAATT+AGG 0.364679 3:+17331012 None:intergenic
CCACAGTAGAAATGTTAGTT+AGG 0.390467 3:-17330780 MsaT012023.1:CDS
CAGTTTGTATGTCCTGAAAT+TGG 0.397925 3:-17331622 MsaT012023.1:CDS
ATCTACAGATACCGCAGAAT+TGG 0.415201 3:+17333283 None:intergenic
TTTCTCTTCACCCCTCCCCT+TGG 0.432023 3:+17330811 None:intergenic
AGCATTTAATTGTGAATTTG+AGG 0.433303 3:-17331224 MsaT012023.1:CDS
AAATTCACAATTAAATGCTT+CGG 0.436689 3:+17331228 None:intergenic
AGAGAACTTGTTATTCGTGC+AGG 0.446937 3:-17330731 MsaT012023.1:CDS
ATGTAGCCTTGAAGATTGTA+AGG 0.454317 3:-17331824 MsaT012023.1:CDS
AAATGCTTCGGAGGAACTGC+TGG 0.458312 3:+17331240 None:intergenic
GTGTGTGGGTTTCCTAATTG+TGG 0.466837 3:-17331024 MsaT012023.1:CDS
AGCTTGCCTTACAATCTTCA+AGG 0.479189 3:+17331818 None:intergenic
ATGTGAACTGTGACACTTGT+GGG 0.479574 3:-17331312 MsaT012023.1:CDS
CAAGTAAAGCCGTTTGTGTG+TGG 0.487892 3:-17331039 MsaT012023.1:CDS
CAGGTCAAGGCCAAGGGGAG+GGG 0.490449 3:-17330821 MsaT012023.1:CDS
GCATTTAATTGTGAATTTGA+GGG 0.504026 3:-17331223 MsaT012023.1:CDS
TGTCACAGTTCACATATTGA+TGG 0.505697 3:+17331320 None:intergenic
TCAGGTCAAGGCCAAGGGGA+GGG 0.518065 3:-17330822 MsaT012023.1:CDS
TCTTCAAGGCTACATACAAA+TGG 0.524961 3:+17331832 None:intergenic
TGAAACTGAACCTGAATCAG+AGG 0.525785 3:-17332793 MsaT012023.1:CDS
AACATGAGCTTTAAGGCACT+CGG 0.529952 3:+17331351 None:intergenic
AAGTAAAGCCGTTTGTGTGT+GGG 0.534040 3:-17331038 MsaT012023.1:CDS
CCTGTTGAGAATTGCAAAAG+TGG 0.541424 3:-17331733 MsaT012023.1:CDS
AAGAATTCAGGTCAAGGCCA+AGG 0.544513 3:-17330828 MsaT012023.1:CDS
GTATGTCCTGAAATTGGCTG+TGG 0.551180 3:-17331616 MsaT012023.1:CDS
TAAGGCAAGCTACAGAAGAA+AGG 0.551380 3:-17331806 MsaT012023.1:CDS
GGTTTCCTAATTGTGGAATG+AGG 0.556382 3:-17331017 MsaT012023.1:CDS
TTAGGAAACCCACACACAAA+CGG 0.558755 3:+17331030 None:intergenic
CTAACTAACATTTCTACTGT+GGG 0.561562 3:+17330781 None:intergenic
CGTCACCTTCTACAACATCA+AGG 0.564236 3:-17331772 MsaT012023.1:CDS
AGTTCTCTAATTGACTAGGT+GGG 0.566365 3:+17330746 None:intergenic
CCTAACTAACATTTCTACTG+TGG 0.575540 3:+17330780 None:intergenic
CCACATCAATTCTGAACACA+AGG 0.577487 3:-17333238 MsaT012023.1:intron
CGCTATTACTGCCAATTCTG+CGG 0.581521 3:-17333294 MsaT012023.1:CDS
TTCACAATTAAATGCTTCGG+AGG 0.582461 3:+17331231 None:intergenic
TTCAGGTCAAGGCCAAGGGG+AGG 0.583372 3:-17330823 MsaT012023.1:CDS
AAGTTCTCTAATTGACTAGG+TGG 0.584481 3:+17330745 None:intergenic
AGAATTCAGGTCAAGGCCAA+GGG 0.585579 3:-17330827 MsaT012023.1:CDS
GAAGTGGTGTGCTTAGAGCC+TGG 0.587135 3:-17331397 MsaT012023.1:CDS
AACTGCTGGCTTCATGTGTG+CGG 0.588715 3:+17331254 None:intergenic
CAGAAGCATGAAGATTCTCA+TGG 0.597767 3:-17331565 MsaT012023.1:intron
CCTTGTGTTCAGAATTGATG+TGG 0.601822 3:+17333238 None:intergenic
AACTGAAGAAGAATATGAAG+AGG 0.602793 3:-17331282 MsaT012023.1:CDS
TCCTGAAATTGGCTGTGGAA+AGG 0.608455 3:-17331611 MsaT012023.1:CDS
TAATTGAACAAATACCTCGA+GGG 0.608678 3:+17332686 None:intergenic
GTTCTCTAATTGACTAGGTG+GGG 0.608887 3:+17330747 None:intergenic
GTCACCTTCTACAACATCAA+GGG 0.613362 3:-17331771 MsaT012023.1:CDS
TAGGCTCGAAACAATTGAAG+TGG 0.632928 3:-17331413 MsaT012023.1:CDS
CTGATGAAGAATTCAGGTCA+AGG 0.636136 3:-17330834 MsaT012023.1:CDS
ACTAACATTTCTACTGTGGG+AGG 0.639382 3:+17330784 None:intergenic
AGTTCTACCCCTCCTCGTAG+TGG 0.640750 3:-17331658 MsaT012023.1:CDS
TTTGAAAGCTAATGCTTGTG+AGG 0.642767 3:-17332766 MsaT012023.1:CDS
CTTGTGTTCAGAATTGATGT+GGG 0.647147 3:+17333239 None:intergenic
AACAAGTTCTCTAATTGACT+AGG 0.656480 3:+17330742 None:intergenic
GAAACTGAACCTGAATCAGA+GGG 0.660004 3:-17332792 MsaT012023.1:CDS
GCTAATGCTTGTGAGGAATG+TGG 0.681495 3:-17332759 MsaT012023.1:CDS
GAATTCAGGTCAAGGCCAAG+GGG 0.693128 3:-17330826 MsaT012023.1:CDS
ACTGAACCTGAATCAGAGGG+TGG 0.697062 3:-17332789 MsaT012023.1:CDS
TATGTGAACTGTGACACTTG+TGG 0.719735 3:-17331313 MsaT012023.1:CDS
TATGCAAAGTCATTCCCTCG+AGG 0.752078 3:-17332700 MsaT012023.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 17330720 17333367 17330720 ID=MsaG012023
Chr3 mRNA 17330720 17333367 17330720 ID=MsaT012023.1;Parent=MsaG012023
Chr3 exon 17330720 17330872 17330720 ID=MsaT012023.1.exon6;Parent=MsaT012023.1
Chr3 CDS 17330720 17330872 17330720 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Chr3 exon 17330957 17331100 17330957 ID=MsaT012023.1.exon5;Parent=MsaT012023.1
Chr3 CDS 17330957 17331100 17330957 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Chr3 exon 17331201 17331436 17331201 ID=MsaT012023.1.exon4;Parent=MsaT012023.1
Chr3 CDS 17331201 17331436 17331201 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Chr3 exon 17331566 17331857 17331566 ID=MsaT012023.1.exon3;Parent=MsaT012023.1
Chr3 CDS 17331566 17331857 17331566 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Chr3 exon 17332701 17332838 17332701 ID=MsaT012023.1.exon2;Parent=MsaT012023.1
Chr3 CDS 17332701 17332838 17332701 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Chr3 exon 17333239 17333367 17333239 ID=MsaT012023.1.exon1;Parent=MsaT012023.1
Chr3 CDS 17333239 17333367 17333239 ID=cds.MsaT012023.1;Parent=MsaT012023.1
Gene Sequence

>MsaT012023.1

ATGGAAGAATCAATCCAAAACGATGCAATCCCAAAATTCAGAGATATTAGACGCTATTACTGCCAATTCTGCGGTATCTGTAGATCCAAAAAAACCCTAATTACATCCCACATCAATTCTGAACACAAGGAGGAGATGGAGAAAGCAAGAGTTGAAACTGAACCTGAATCAGAGGGTGGTTTGAAAGCTAATGCTTGTGAGGAATGTGGTGCTAGTTTCAAAAAACATGCTTATTTGTTGCAGCATATGCAAAGTCATTCCCTCGAGAGGCCATTTGTATGTAGCCTTGAAGATTGTAAGGCAAGCTACAGAAGAAAGGATCATCTGAATCGTCACCTTCTACAACATCAAGGGAAAACTTTTAAATGTCCTGTTGAGAATTGCAAAAGTGGCTTCTCTGTGCAAAGCAATTTGAAAAGACATGTTGAAGAGATGCATGATGAAAGTTCTACCCCTCCTCGTAGTGGTGAAAATCAGAAGCAGTTTGTATGTCCTGAAATTGGCTGTGGAAAGGTTTTCAGATATGCATCACAATTACAGAAGCATGAAGATTCTCATGTTAGGCTCGAAACAATTGAAGTGGTGTGCTTAGAGCCTGGTTGCATGAAATTTTTCACTAATTCCGAGTGCCTTAAAGCTCATGTTAAATCTTGCCATCAATATGTGAACTGTGACACTTGTGGGACTAAGCAACTGAAGAAGAATATGAAGAGGCATCTCCGCACACATGAAGCCAGCAGTTCCTCCGAAGCATTTAATTGTGAATTTGAGGGTTGTGACAGCACATTCTCAACTAAATCTAATCTTCATAAGCATGAGAAAGTCGTACACTTTCAAGTAAAGCCGTTTGTGTGTGGGTTTCCTAATTGTGGAATGAGGTTTGCTTACAAACATGTGAGAGATAATCATGAAAAGACTGCAAAACATCTTTTTGCCCTTGGTGATTTTGAAGAAGCTGATGAAGAATTCAGGTCAAGGCCAAGGGGAGGGGTGAAGAGAAAATGTCCTCCCACAGTAGAAATGTTAGTTAGGAAGAGAGTTACCCCACCTAGTCAATTAGAGAACTTGTTATTCGTGCAGGATTGTCAGTAA

Protein sequence

>MsaT012023.1

MEESIQNDAIPKFRDIRRYYCQFCGICRSKKTLITSHINSEHKEEMEKARVETEPESEGGLKANACEECGASFKKHAYLLQHMQSHSLERPFVCSLEDCKASYRRKDHLNRHLLQHQGKTFKCPVENCKSGFSVQSNLKRHVEEMHDESSTPPRSGENQKQFVCPEIGCGKVFRYASQLQKHEDSHVRLETIEVVCLEPGCMKFFTNSECLKAHVKSCHQYVNCDTCGTKQLKKNMKRHLRTHEASSSSEAFNCEFEGCDSTFSTKSNLHKHEKVVHFQVKPFVCGFPNCGMRFAYKHVRDNHEKTAKHLFALGDFEEADEEFRSRPRGGVKRKCPPTVEMLVRKRVTPPSQLENLLFVQDCQ*