AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG001241


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001241 MtrunA17_Chr1g0161031 96.358 302 11 0 1 302 60 361 0.0 592
MsaG001241 MtrunA17_Chr6g0478581 32.381 315 138 9 16 277 102 394 7.81e-30 117
MsaG001241 MtrunA17_Chr2g0301131 30.061 163 82 3 113 275 110 240 3.02e-14 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG001241 AT3G17860.3 38.153 249 126 8 41 274 64 299 2.30e-31 119
MsaG001241 AT3G17860.4 38.153 249 126 8 41 274 64 299 2.30e-31 119
MsaG001241 AT3G17860.2 38.153 249 126 8 41 274 84 319 3.87e-31 119
MsaG001241 AT3G17860.1 38.153 249 126 8 41 274 97 332 4.92e-31 119
MsaG001241 AT1G70700.1 35.938 256 117 10 39 293 58 267 3.65e-27 107
MsaG001241 AT1G70700.2 34.375 256 97 8 39 293 58 243 3.22e-26 104
MsaG001241 AT1G70700.3 35.714 224 99 9 39 261 58 237 1.31e-22 95.1
MsaG001241 AT1G48500.1 37.755 196 96 5 81 274 118 289 7.96e-22 93.6
MsaG001241 AT1G48500.3 37.705 183 88 5 81 261 88 246 1.92e-18 83.2
MsaG001241 AT1G48500.2 32.203 236 125 7 29 261 73 276 3.95e-18 82.8

Find 73 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGTAGCAGTGATGAGTTTA+TGG 0.220743 1:-17302075 MsaT001241.1:CDS
GATTTCTTGTTGAGGTTATA+TGG 0.291399 1:+17301000 None:intergenic
ATGTCTACAGGTGGACTTAT+AGG 0.310065 1:+17302170 None:intergenic
GAGCTAGATGCCTGAACTTC+AGG 0.316257 1:+17302221 None:intergenic
CCGATCGTTGGTACTGTTGC+TGG 0.321376 1:-17302853 MsaT001241.1:CDS
AGAAAGTGAATTTGCTTGAT+TGG 0.344513 1:+17302993 None:intergenic
CGTTGGTACTGTTGCTGGTT+TGG 0.366943 1:-17302848 MsaT001241.1:CDS
TTATCTGTTTCTTCACATAC+TGG 0.372825 1:-17302119 MsaT001241.1:CDS
TCGAGCCAATGATGCTTTGC+GGG 0.375285 1:+17301794 None:intergenic
GCTTATCTGCAGCTTCAAAC+AGG 0.376253 1:-17302250 MsaT001241.1:CDS
GAATTTGCTTGATTGGAAAC+TGG 0.385359 1:+17303000 None:intergenic
AAGGCTAAAATGATATCTTC+TGG 0.412380 1:-17303516 None:intergenic
CAGGGCTCAACCTGAAGTTC+AGG 0.416821 1:-17302231 MsaT001241.1:CDS
ATGTTAGCACCTATTGAATT+CGG 0.423665 1:+17300961 None:intergenic
GTGGTTGCATTGACTACTTT+GGG 0.425771 1:+17301996 None:intergenic
GATATCTTCTGGTTTCATAC+AGG 0.429332 1:-17303505 MsaT001241.1:intron
GCAGGCCCGCAAAGCATCAT+TGG 0.432249 1:-17301799 MsaT001241.1:CDS
GCACAAATGCCGAATTCAAT+AGG 0.448545 1:-17300970 MsaT001241.1:CDS
GGTGGTTGCATTGACTACTT+TGG 0.451731 1:+17301995 None:intergenic
AAATTCACATTGTGTTGTAC+AGG 0.451805 1:+17303054 None:intergenic
CAAGCAGATGTTGTAGGAGT+AGG 0.457532 1:+17302032 None:intergenic
GGCACAAGCCATCATGTTGT+TGG 0.459085 1:-17302282 MsaT001241.1:CDS
AGGACTTGAAATACCAGAGC+AGG 0.472355 1:+17302142 None:intergenic
CTGCTACTTGAGCCACTCCC+TGG 0.474711 1:+17302089 None:intergenic
TGTTATCCTTGGTTTGCTAC+CGG 0.482361 1:+17300910 None:intergenic
ACTTTGCAAGCAGATGTTGT+AGG 0.484196 1:+17302026 None:intergenic
TCACATACTGGTCCACAGCC+AGG 0.488582 1:-17302107 MsaT001241.1:CDS
CTTGAGCCACTCCCTGGCTG+TGG 0.494035 1:+17302095 None:intergenic
GTATGTGAAGAAACAGATAA+AGG 0.494684 1:+17302122 None:intergenic
ATCATGTTGTTGGCTGGAAG+TGG 0.494803 1:-17302272 MsaT001241.1:CDS
ATCGAGCCAATGATGCTTTG+CGG 0.499003 1:+17301793 None:intergenic
CAAGCCATCATGTTGTTGGC+TGG 0.503763 1:-17302278 MsaT001241.1:CDS
AATGCGAAGCAATCACTACT+TGG 0.504587 1:-17302910 MsaT001241.1:CDS
GAGTTACTCACTGTTATCCT+TGG 0.504866 1:+17300899 None:intergenic
GCAACCACCATGGTTCCATC+AGG 0.516533 1:-17301981 MsaT001241.1:intron
CATCCTCAGATTTCTTGTTG+AGG 0.517588 1:+17300992 None:intergenic
AACATGGTAAGTTGAGGAGC+AGG 0.523147 1:+17302708 None:intergenic
AAATTCGCATCAGGTGATGA+TGG 0.528192 1:-17302197 MsaT001241.1:CDS
GAGCAGGGTGGTATGTCTAC+AGG 0.528533 1:+17302158 None:intergenic
CATTCAGTTCTTCCGATCGT+TGG 0.534965 1:-17302865 MsaT001241.1:CDS
TCTAGCTCGAAATTCGCATC+AGG 0.536374 1:-17302206 MsaT001241.1:CDS
CACTAGTACTGCTAATATGC+CGG 0.542872 1:-17300929 MsaT001241.1:CDS
AGTTGAGGAGCAGGTGCAGA+TGG 0.548573 1:+17302717 None:intergenic
GTAGACATACCACCCTGCTC+TGG 0.550254 1:-17302155 MsaT001241.1:CDS
AAGCAGATGTTGTAGGAGTA+GGG 0.553445 1:+17302033 None:intergenic
CACAGTACCGCCATAAAACA+TGG 0.558159 1:+17302692 None:intergenic
GCGAAGCAATCACTACTTGG+TGG 0.562781 1:-17302907 MsaT001241.1:CDS
AATGATGCTTTGCGGGCCTG+CGG 0.566874 1:+17301801 None:intergenic
CAATGATATCACTCCTGAGA+AGG 0.574823 1:-17302661 MsaT001241.1:intron
ACTGGTCCACAGCCAGGGAG+TGG 0.579269 1:-17302101 MsaT001241.1:CDS
ATTAGCAGTACTAGTGGTCG+CGG 0.581937 1:+17300936 None:intergenic
CACATACTGGTCCACAGCCA+GGG 0.588678 1:-17302106 MsaT001241.1:CDS
CTTATCTGCAGCTTCAAACA+GGG 0.597255 1:-17302249 MsaT001241.1:CDS
TCAAGCAAATTCACTTTCTG+CGG 0.601727 1:-17302989 MsaT001241.1:CDS
ACTTCCAGCCAACAACATGA+TGG 0.615633 1:+17302274 None:intergenic
CGGCATATTAGCAGTACTAG+TGG 0.617445 1:+17300930 None:intergenic
TCTTTCAAACACGATGGACA+AGG 0.634289 1:-17303105 MsaT001241.1:CDS
TAGAACTCTTTCAAACACGA+TGG 0.634861 1:-17303111 MsaT001241.1:CDS
GGACTTGAAATACCAGAGCA+GGG 0.635730 1:+17302143 None:intergenic
CCAGCAACAGTACCAACGAT+CGG 0.636094 1:+17302853 None:intergenic
CCATAAAACATGGTAAGTTG+AGG 0.638856 1:+17302702 None:intergenic
ATGGCTGCTAAAACATCTAG+AGG 0.639805 1:-17302056 MsaT001241.1:CDS
ACGATCGGAAGAACTGAATG+AGG 0.643920 1:+17302868 None:intergenic
CAGGGTGGTATGTCTACAGG+TGG 0.644694 1:+17302161 None:intergenic
TTGCTGGTTTGGTTGAACCA+TGG 0.654058 1:-17302837 MsaT001241.1:intron
TAACCTCAACAAGAAATCTG+AGG 0.657118 1:-17300995 MsaT001241.1:CDS
TTACATACCTGATGGAACCA+TGG 0.681302 1:+17301974 None:intergenic
AATATGCCGGTAGCAAACCA+AGG 0.684244 1:-17300916 MsaT001241.1:CDS
AGTAGTCAATGCAACCACCA+TGG 0.687562 1:-17301991 MsaT001241.1:CDS
TTCAAACACGATGGACAAGG+TGG 0.707235 1:-17303102 MsaT001241.1:CDS
ACTGAATGAGGTGCTGTAAG+CGG 0.719108 1:+17302880 None:intergenic
CTTGAAATACCAGAGCAGGG+TGG 0.775660 1:+17302146 None:intergenic
CATACCTGATGGAACCATGG+TGG 0.816498 1:+17301977 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr1 gene 17300912 17303529 17300912 ID=MsaG001241
Chr1 mRNA 17300912 17303529 17300912 ID=MsaT001241.1;Parent=MsaG001241
Chr1 exon 17300912 17301038 17300912 ID=MsaT001241.1.exon6;Parent=MsaT001241.1
Chr1 CDS 17300912 17301038 17300912 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Chr1 exon 17301771 17301828 17301771 ID=MsaT001241.1.exon5;Parent=MsaT001241.1
Chr1 CDS 17301771 17301828 17301771 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Chr1 exon 17301982 17302303 17301982 ID=MsaT001241.1.exon4;Parent=MsaT001241.1
Chr1 CDS 17301982 17302303 17301982 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Chr1 exon 17302662 17302746 17302662 ID=MsaT001241.1.exon3;Parent=MsaT001241.1
Chr1 CDS 17302662 17302746 17302662 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Chr1 exon 17302838 17303130 17302838 ID=MsaT001241.1.exon2;Parent=MsaT001241.1
Chr1 CDS 17302838 17303130 17302838 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Chr1 exon 17303506 17303529 17303506 ID=MsaT001241.1.exon1;Parent=MsaT001241.1
Chr1 CDS 17303506 17303529 17303506 ID=cds.MsaT001241.1;Parent=MsaT001241.1
Gene Sequence

>MsaT001241.1

ATGATATCTTCTGGTTTCATACAGAACTCTTTCAAACACGATGGACAAGGTGGTATTCATTTTTCTGTGAATCAGTATCCTGTACAACACAATGTGAATTTTATGAATCGTCATCATGATGTGAAGATGTTTCCAGTTTCCAATCAAGCAAATTCACTTTCTGCGGTACATCCGCTCCTAAAAAATCATCTTGTAACTTTTGGTCAGAATATGAACGGTGCTAATGCGAAGCAATCACTACTTGGTGGATCACCGCTTACAGCACCTCATTCAGTTCTTCCGATCGTTGGTACTGTTGCTGGTTTGGTTGAACCATGTGAGAAACCATCTGCACCTGCTCCTCAACTTACCATGTTTTATGGCGGTACTGTGAACATCTTCAATGATATCACTCCTGAGAAGGCACAAGCCATCATGTTGTTGGCTGGAAGTGGCTTATCTGCAGCTTCAAACAGGGCTCAACCTGAAGTTCAGGCATCTAGCTCGAAATTCGCATCAGGTGATGATGGTTTGCCTATAAGTCCACCTGTAGACATACCACCCTGCTCTGGTATTTCAAGTCCTTTATCTGTTTCTTCACATACTGGTCCACAGCCAGGGAGTGGCTCAAGTAGCAGTGATGAGTTTATGGCTGCTAAAACATCTAGAGGCCCTACTCCTACAACATCTGCTTGCAAAGTTGTGACTCCCAAAGTAGTCAATGCAACCACCATGGTTCCATCAGCTATACCGCAGGCCCGCAAAGCATCATTGGCTCGATTTTTGGAGAAGCGCAAGGAAAGGGTGATGAGTACAGCACCATATAACCTCAACAAGAAATCTGAGGATGCACAAATGCCGAATTCAATAGGTGCTAACATCTCCGCGACCACTAGTACTGCTAATATGCCGGTAGCAAACCAAGGATAA

Protein sequence

>MsaT001241.1

MISSGFIQNSFKHDGQGGIHFSVNQYPVQHNVNFMNRHHDVKMFPVSNQANSLSAVHPLLKNHLVTFGQNMNGANAKQSLLGGSPLTAPHSVLPIVGTVAGLVEPCEKPSAPAPQLTMFYGGTVNIFNDITPEKAQAIMLLAGSGLSAASNRAQPEVQASSSKFASGDDGLPISPPVDIPPCSGISSPLSVSSHTGPQPGSGSSSSDEFMAAKTSRGPTPTTSACKVVTPKVVNATTMVPSAIPQARKASLARFLEKRKERVMSTAPYNLNKKSEDAQMPNSIGANISATTSTANMPVANQG*