AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG040064


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040064 MtrunA17_Chr7g0265761 78.261 299 28 6 1 272 1 289 4.98e-133 377
MsaG040064 MtrunA17_Chr2g0320884 40.864 301 143 8 1 272 35 329 2.36e-42 147
MsaG040064 MtrunA17_Chr4g0027181 38.075 239 134 7 1 230 5 238 6.69e-28 108
MsaG040064 MtrunA17_Chr4g0027191 50.000 96 42 2 2 93 6 99 1.03e-22 95.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG040064 AT5G03740.1 40.273 293 152 7 1 271 1 292 9.33e-48 160
MsaG040064 AT3G44750.2 36.996 273 137 6 1 271 1 240 7.49e-39 136
MsaG040064 AT3G44750.1 35.531 273 144 6 1 271 1 243 1.28e-36 130
MsaG040064 AT5G22650.2 34.722 288 132 9 1 247 1 273 4.36e-26 104
MsaG040064 AT5G22650.1 34.602 289 132 9 1 247 1 274 5.73e-26 104
MsaG040064 AT2G27840.4 47.368 95 46 3 1 93 1 93 8.79e-21 86.7
MsaG040064 AT2G27840.3 47.368 95 46 3 1 93 1 93 2.12e-20 87.0
MsaG040064 AT2G27840.1 47.368 95 46 3 1 93 1 93 3.39e-20 84.7
MsaG040064 AT2G27840.2 46.575 73 35 3 23 93 1 71 5.43e-11 60.8

Find 65 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCTGCAGTCATGGAGTTT+TGG 0.184723 7:+96252636 None:intergenic
CGCTCCCATATTTCCAGTTA+TGG 0.260338 7:-96254364 None:intergenic
CTATCCCATAACTGGAAATA+TGG 0.264248 7:+96254359 MsaT040064.1:CDS
CTTTATATGACAGGCATGTT+TGG 0.291541 7:+96254196 MsaT040064.1:intron
GGTGATCACAAGCTTCAAAT+TGG 0.296127 7:+96254272 MsaT040064.1:CDS
AACACCTGTACTTGTGAAAA+AGG 0.297237 7:+96255921 MsaT040064.1:CDS
TTTGGAGTCTCCTGCTTCTC+TGG 0.303491 7:-96256564 None:intergenic
TTTATATGACAGGCATGTTT+GGG 0.313274 7:+96254197 MsaT040064.1:intron
TGCCTTAGGTTCTCATAATA+AGG 0.315168 7:+96256732 MsaT040064.1:CDS
TATGGGAGCGTCTTCCTTGC+TGG 0.325658 7:+96254377 MsaT040064.1:CDS
CAACTCCAATCACCTGTTAC+AGG 0.338113 7:-96256613 None:intergenic
CCTTCACTTGGCACTGTGCT+TGG 0.346567 7:-96256755 None:intergenic
GGGGAGGTCAGCAAGGATAA+AGG 0.362925 7:+96254218 MsaT040064.1:CDS
AATTTGAGCTATCCCATAAC+TGG 0.378730 7:+96254351 MsaT040064.1:CDS
TGATGCATTTACACCGGGTT+TGG 0.381330 7:-96254801 None:intergenic
GCAGATTTACCAGCCTGCTT+AGG 0.386812 7:-96256525 None:intergenic
TAGTCTCCAGTTACCTTCTT+CGG 0.386819 7:-96255801 None:intergenic
GCTCCCATATTTCCAGTTAT+GGG 0.386902 7:-96254363 None:intergenic
ACAGCTGCAATCCCTGTAAC+AGG 0.418416 7:+96256601 MsaT040064.1:CDS
AAGAACTAACCAGTCTTCTC+TGG 0.427252 7:-96255958 None:intergenic
TTTAAGACTGAAGATGCCTT+AGG 0.434410 7:+96256718 MsaT040064.1:CDS
TAACAAGCAGCCAGAGAAGC+AGG 0.434559 7:+96256554 MsaT040064.1:CDS
CAGATTTACCAGCCTGCTTA+GGG 0.438934 7:-96256524 None:intergenic
GCATTTACACCGGGTTTGGC+AGG 0.449487 7:-96254797 None:intergenic
CACAAGTACAGGTGTTTCCT+TGG 0.449840 7:-96255914 None:intergenic
AACTTCACATACAGGGATAC+CGG 0.456270 7:-96254248 None:intergenic
TTACCAGCCTGCTTAGGGTA+AGG 0.466162 7:-96256519 None:intergenic
GAAGATATTATACTTGCTAA+TGG 0.476177 7:+96254683 MsaT040064.1:CDS
GGGAGGTCAGCAAGGATAAA+GGG 0.482905 7:+96254219 MsaT040064.1:CDS
TATCCCATAACTGGAAATAT+GGG 0.497848 7:+96254360 MsaT040064.1:CDS
GATCACCAAACTTCACATAC+AGG 0.505258 7:-96254256 None:intergenic
CTGTAATCTCCACTAGACTT+TGG 0.505848 7:-96256582 None:intergenic
CCGATGAAATGTGGATAAGC+TGG 0.506704 7:-96254089 None:intergenic
GTATCCCTGTATGTGAAGTT+TGG 0.511130 7:+96254251 MsaT040064.1:CDS
TAGTGTCCCTTACCCTAAGC+AGG 0.513510 7:+96256512 MsaT040064.1:CDS
GGCCTTATTATGAGAACCTA+AGG 0.516695 7:-96256734 None:intergenic
GATTCATCTGATGCTAGTAC+TGG 0.522501 7:+96254869 MsaT040064.1:CDS
TTTGTTACTCCAGAGAAGAC+TGG 0.525269 7:+96255949 MsaT040064.1:CDS
GTCCCTTACCCTAAGCAGGC+TGG 0.535334 7:+96256516 MsaT040064.1:CDS
AATCAGAAGGATGCTAGTAC+TGG 0.537632 7:+96254836 MsaT040064.1:CDS
TACCAGCCTGCTTAGGGTAA+GGG 0.548023 7:-96256518 None:intergenic
AGCTAACAAAACCCTTCACT+TGG 0.555690 7:-96256767 None:intergenic
CCAAGCACAGTGCCAAGTGA+AGG 0.555760 7:+96256755 MsaT040064.1:CDS
GTCGTTTAGCCCATGGCGAA+TGG 0.558159 7:+96255723 MsaT040064.1:intron
TTTAGATACTGATTCTGAAG+AGG 0.569513 7:+96254661 MsaT040064.1:intron
CTGAAGGGAGCAACAAGAGG+AGG 0.570018 7:+96255878 MsaT040064.1:CDS
CCAGCTTATCCACATTTCAT+CGG 0.582062 7:+96254089 MsaT040064.1:CDS
ATCTGATGCTAGTGAAGATG+AGG 0.588334 7:+96254907 MsaT040064.1:CDS
GTAGGGAAACCTGCCAAACC+CGG 0.592566 7:+96254788 MsaT040064.1:intron
TGACAAGGAGACTCCGAAGA+AGG 0.592738 7:+96255788 MsaT040064.1:CDS
CAGGAGACTCCAAAGTCTAG+TGG 0.603055 7:+96256573 MsaT040064.1:CDS
AACTCCAATCACCTGTTACA+GGG 0.611246 7:-96256612 None:intergenic
GAGGGATGCTGAATCTTCCA+AGG 0.612820 7:+96255897 MsaT040064.1:CDS
TGAAGGGAGCAACAAGAGGA+GGG 0.614862 7:+96255879 MsaT040064.1:CDS
AGACTGAAGGGAGCAACAAG+AGG 0.615166 7:+96255875 MsaT040064.1:intron
AAGCATATACCGATGAAATG+TGG 0.617686 7:-96254098 None:intergenic
ACTTCACATACAGGGATACC+GGG 0.620641 7:-96254247 None:intergenic
TTAGGTGTCGAGGTAAAACA+TGG 0.629801 7:+96254036 MsaT040064.1:intron
AAAACATGGTGAACCACACA+AGG 0.630125 7:+96254050 MsaT040064.1:CDS
TATATGACAGGCATGTTTGG+GGG 0.631765 7:+96254199 MsaT040064.1:intron
TTATATGACAGGCATGTTTG+GGG 0.632570 7:+96254198 MsaT040064.1:intron
ATCACCAAACTTCACATACA+GGG 0.632725 7:-96254255 None:intergenic
CAAGGATAAAGGGAGTGACC+CGG 0.634157 7:+96254229 MsaT040064.1:CDS
AAGCGATGAAGATTCTGACA+AGG 0.637276 7:+96255773 MsaT040064.1:CDS
ACCAAATCAAAAGATGTCTG+AGG 0.650289 7:-96254317 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr7 gene 96252647 96256774 96252647 ID=MsaG040064
Chr7 mRNA 96252647 96256774 96252647 ID=MsaT040064.1;Parent=MsaG040064
Chr7 exon 96252647 96252659 96252647 ID=MsaT040064.1.exon1;Parent=MsaT040064.1
Chr7 CDS 96252647 96252659 96252647 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96254040 96254110 96254040 ID=MsaT040064.1.exon2;Parent=MsaT040064.1
Chr7 CDS 96254040 96254110 96254040 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96254209 96254413 96254209 ID=MsaT040064.1.exon3;Parent=MsaT040064.1
Chr7 CDS 96254209 96254413 96254209 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96254666 96254704 96254666 ID=MsaT040064.1.exon4;Parent=MsaT040064.1
Chr7 CDS 96254666 96254704 96254666 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96254792 96254928 96254792 ID=MsaT040064.1.exon5;Parent=MsaT040064.1
Chr7 CDS 96254792 96254928 96254792 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96255732 96255809 96255732 ID=MsaT040064.1.exon6;Parent=MsaT040064.1
Chr7 CDS 96255732 96255809 96255732 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96255877 96255970 96255877 ID=MsaT040064.1.exon7;Parent=MsaT040064.1
Chr7 CDS 96255877 96255970 96255877 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96256502 96256622 96256502 ID=MsaT040064.1.exon8;Parent=MsaT040064.1
Chr7 CDS 96256502 96256622 96256502 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Chr7 exon 96256714 96256774 96256714 ID=MsaT040064.1.exon9;Parent=MsaT040064.1
Chr7 CDS 96256714 96256774 96256714 ID=cds.MsaT040064.1;Parent=MsaT040064.1
Gene Sequence

>MsaT040064.1

ATGGAGTTTTGGGGTGTCGAGGTAAAACATGGTGAACCACACAAGGTTGTTCCAGAAAATAACCAGCTTATCCACATTTCATCGGCATGTTTGGGGGAGGTCAGCAAGGATAAAGGGAGTGACCCGGTATCCCTGTATGTGAAGTTTGGTGATCACAAGCTTCAAATTGGAACACTTTCTTCAGAAAAATTTCCTCAGACATCTTTTGATTTGGTTTTTGGGAAGGAATTTGAGCTATCCCATAACTGGAAATATGGGAGCGTCTTCCTTGCTGGATTTTTAATCGAATATACTGATTCTGAAGAGGAAGATATTATACTTGCTAATGGGAAACCTGCCAAACCCGGTGTAAATGCATCAAAACAGAAAAAGAATCAGAAGGATGCTAGTACTGGCGATAGTTCAGATTCATCTGATGCTAGTACTGGCGATAGTTCAGATTCATCTGATGCTAGTGAAGATGAGCCCATGGCGAATGGTCAAAATAAAAGTAGTAGTGAAGATGAAAGCGATGAAGATTCTGACAAGGAGACTCCGAAGAAGACTGAAGGGAGCAACAAGAGGAGGGATGCTGAATCTTCCAAGGAAACACCTGTACTTGTGAAAAAGGCAAAATTTGTTACTCCAGAGAAGACTGGTGGCAGGAGTAGTGTCCCTTACCCTAAGCAGGCTGGTAAATCTGCTGCAAATAACAAGCAGCCAGAGAAGCAGGAGACTCCAAAGTCTAGTGGAGATTACAGCTGCAATCCCTGTAACAGGTCTTTTAAGACTGAAGATGCCTTAGGTTCTCATAATAAGGCCAAGCACAGTGCCAAGTGA

Protein sequence

>MsaT040064.1

MEFWGVEVKHGEPHKVVPENNQLIHISSACLGEVSKDKGSDPVSLYVKFGDHKLQIGTLSSEKFPQTSFDLVFGKEFELSHNWKYGSVFLAGFLIEYTDSEEEDIILANGKPAKPGVNASKQKKNQKDASTGDSSDSSDASTGDSSDSSDASEDEPMANGQNKSSSEDESDEDSDKETPKKTEGSNKRRDAESSKETPVLVKKAKFVTPEKTGGRSSVPYPKQAGKSAANNKQPEKQETPKSSGDYSCNPCNRSFKTEDALGSHNKAKHSAK*