AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0585240


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585240 MtrunA17_Chr4g0013291 94.975 199 10 0 1 199 1 199 8.55e-142 393
Msa0585240 MtrunA17_Chr7g0244371 61.579 190 68 2 12 197 19 207 9.95e-84 247
Msa0585240 MtrunA17_Chr7g0244321 61.257 191 68 3 13 198 21 210 6.74e-83 244
Msa0585240 MtrunA17_Chr7g0244331 61.458 192 68 3 11 197 19 209 1.15e-82 244
Msa0585240 MtrunA17_Chr7g0244341 59.788 189 70 3 15 198 23 210 1.06e-79 237
Msa0585240 MtrunA17_Chr7g0244361 54.271 199 79 3 12 200 44 240 3.82e-73 221
Msa0585240 MtrunA17_Chr7g0244111 65.254 118 41 0 80 197 4 121 2.33e-57 177
Msa0585240 MtrunA17_Chr1g0150081 43.386 189 92 6 13 192 3 185 2.88e-41 138
Msa0585240 MtrunA17_Chr2g0333101 32.749 171 98 7 39 199 43 206 5.88e-23 92.0
Msa0585240 MtrunA17_Chr2g0333111 30.769 169 104 6 39 199 44 207 3.90e-19 82.0
Msa0585240 MtrunA17_Chr4g0003271 26.396 197 131 7 10 197 2 193 1.14e-18 80.5
Msa0585240 MtrunA17_Chr1g0150091 38.095 126 57 5 83 192 11 131 3.94e-14 66.6
Msa0585240 MtrunA17_Chr1g0150101 43.038 79 41 2 114 192 5 79 2.66e-12 60.1
Msa0585240 MtrunA17_Chr5g0432221 31.159 138 86 4 57 191 80 211 5.38e-12 62.4
Msa0585240 MtrunA17_Chr8g0387561 27.011 174 106 7 41 194 59 231 3.49e-11 60.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0585240 AT5G01750.2 54.271 199 83 4 6 197 16 213 2.14e-74 224
Msa0585240 AT3G11740.1 49.741 193 90 4 14 200 2 193 7.94e-64 196
Msa0585240 AT1G33840.1 49.730 185 87 3 15 194 27 210 5.90e-58 182
Msa0585240 AT2G14560.1 49.733 187 88 3 15 196 7 192 7.28e-58 181
Msa0585240 AT2G14560.3 49.733 187 88 3 15 196 67 252 1.26e-56 180
Msa0585240 AT5G01750.1 52.532 158 67 4 6 156 16 172 1.09e-52 167
Msa0585240 AT2G14560.2 51.351 148 66 3 15 157 7 153 5.50e-45 147
Msa0585240 AT2G14560.4 51.351 148 66 3 15 157 67 213 1.06e-43 146
Msa0585240 AT1G33840.2 47.973 148 71 3 15 157 27 173 1.04e-40 137
Msa0585240 AT3G16900.1 33.500 200 108 6 1 195 1 180 1.33e-34 121
Msa0585240 AT3G56180.2 26.633 199 137 4 2 193 5 201 6.41e-22 89.4
Msa0585240 AT3G15810.1 30.909 165 103 4 39 197 45 204 9.34e-22 89.0
Msa0585240 AT3G56180.1 26.131 199 136 5 2 193 5 199 1.25e-19 83.2
Msa0585240 AT1G80120.1 30.357 168 103 5 39 197 31 193 4.38e-16 73.9
Msa0585240 AT3G10986.1 24.737 190 131 6 15 193 4 192 2.58e-12 63.5
Msa0585240 AT2G38640.1 28.221 163 105 6 38 194 36 192 1.03e-11 61.6

Find 26 sgRNAs with CRISPR-Local

Find 88 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGAAAGATAATCTCACGGTT+AGG 0.384584 4_2:-5763596 Msa0585240:CDS
GTGTTCAAAGTGTTGCGTTT+GGG 0.407302 4_2:-5763617 Msa0585240:CDS
CTTCTTTAGTATTACTAGCT+AGG 0.413877 4_2:+5763877 None:intergenic
CTGTTGACCTATCAATTGTA+AGG 0.415763 4_2:-5764291 Msa0585240:CDS
AGTGTTCAAAGTGTTGCGTT+TGG 0.433678 4_2:-5763618 Msa0585240:CDS
TGACATTCCTTACAATTGAT+AGG 0.450507 4_2:+5764284 None:intergenic
GTAAGAGACTGTGATCATAA+AGG 0.456930 4_2:+5764197 None:intergenic
TGTGATCATAAAGGAATTTG+AGG 0.464343 4_2:+5764206 None:intergenic
CGATCTTGTGTTGTTTATGC+TGG 0.470752 4_2:-5763816 Msa0585240:CDS
GAAAGATAATCTCACGGTTA+GGG 0.472008 4_2:-5763595 Msa0585240:CDS
CAATGACGGGACATGATAGA+TGG 0.479331 4_2:-5763995 Msa0585240:CDS
TTGATTGTAGATGCATAAGA+AGG 0.480843 4_2:-5763643 Msa0585240:intron
ATGAATGCATAGTCAATGTT+GGG 0.488228 4_2:+5763567 None:intergenic
ATCTCATCACATTGTTGCCC+AGG 0.500173 4_2:-5763790 Msa0585240:intron
GATGAATGCATAGTCAATGT+TGG 0.514312 4_2:+5763566 None:intergenic
AATTATGAGAGTGGTATCAT+TGG 0.521876 4_2:-5764337 Msa0585240:CDS
TTTCTTATACAGGCAATGAC+GGG 0.543853 4_2:-5764008 Msa0585240:intron
AGTCTCTTACTTGATGCAGC+TGG 0.550594 4_2:-5764184 Msa0585240:CDS
TGTCATGACGCTGCGACGAA+AGG 0.555705 4_2:-5764152 Msa0585240:intron
ATTGATAGGTCAACAGAATG+AGG 0.558385 4_2:+5764298 None:intergenic
ACTCTCATAATTTGCTGCAG+AGG 0.575251 4_2:+5764348 None:intergenic
GAATGAGGAACACGATATTG+AGG 0.585084 4_2:+5764313 None:intergenic
TCTGCAGCAAATTATGAGAG+TGG 0.622628 4_2:-5764346 Msa0585240:CDS
TTTGATCTTTGTTTGAAACA+TGG 0.637933 4_2:+5763911 None:intergenic
GTTTGGGAAAGATAATCTCA+CGG 0.663482 4_2:-5763601 Msa0585240:CDS
CATTGACTATGCATTCATCG+TGG 0.756924 4_2:-5763562 Msa0585240:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATAAAAAATTGCATTATTAA+TGG + chr4_2:5764160-5764179 None:intergenic 10.0%
!! ATAAAAAATTGCATTATTAA+TGG + chr4_2:5764160-5764179 None:intergenic 10.0%
!! TAAAAAATGATAAAATACGC+AGG + chr4_2:5763769-5763788 None:intergenic 20.0%
!! TAAAAAATGATAAAATACGC+AGG + chr4_2:5763769-5763788 None:intergenic 20.0%
!! ACGGTAAAATTTTCTTATAC+AGG - chr4_2:5763852-5763871 Msa0585240:CDS 25.0%
!! TTTGATCTTTGTTTGAAACA+TGG + chr4_2:5763962-5763981 None:intergenic 25.0%
!! AGAAGATACTAGTGATTTTA+AGG - chr4_2:5764011-5764030 Msa0585240:intron 25.0%
!! TAAACTTGCTTCTATAGAAA+GGG + chr4_2:5764112-5764131 None:intergenic 25.0%
!! ATAAACTTGCTTCTATAGAA+AGG + chr4_2:5764113-5764132 None:intergenic 25.0%
!! ACGGTAAAATTTTCTTATAC+AGG - chr4_2:5763852-5763871 Msa0585240:CDS 25.0%
!! TTTGATCTTTGTTTGAAACA+TGG + chr4_2:5763962-5763981 None:intergenic 25.0%
!! AGAAGATACTAGTGATTTTA+AGG - chr4_2:5764011-5764030 Msa0585240:intron 25.0%
!! TAAACTTGCTTCTATAGAAA+GGG + chr4_2:5764112-5764131 None:intergenic 25.0%
!! ATAAACTTGCTTCTATAGAA+AGG + chr4_2:5764113-5764132 None:intergenic 25.0%
AATTATGAGAGTGGTATCAT+TGG - chr4_2:5763533-5763552 Msa0585240:CDS 30.0%
TGACATTCCTTACAATTGAT+AGG + chr4_2:5763589-5763608 None:intergenic 30.0%
! TTCACAGTCACAGATTTTAA+TGG - chr4_2:5763626-5763645 Msa0585240:CDS 30.0%
TGTGATCATAAAGGAATTTG+AGG + chr4_2:5763667-5763686 None:intergenic 30.0%
! TTTTCTTATACAGGCAATGA+CGG - chr4_2:5763861-5763880 Msa0585240:CDS 30.0%
CTTCTTTAGTATTACTAGCT+AGG + chr4_2:5763996-5764015 None:intergenic 30.0%
!!! ACTAGTGATTTTAAGGTCAA+AGG - chr4_2:5764018-5764037 Msa0585240:intron 30.0%
!!! ATTTTAAGGTCAAAGGAAGT+TGG - chr4_2:5764025-5764044 Msa0585240:intron 30.0%
TTGATTGTAGATGCATAAGA+AGG - chr4_2:5764227-5764246 Msa0585240:CDS 30.0%
ATGAATGCATAGTCAATGTT+GGG + chr4_2:5764306-5764325 None:intergenic 30.0%
AATTATGAGAGTGGTATCAT+TGG - chr4_2:5763533-5763552 Msa0585240:CDS 30.0%
TGACATTCCTTACAATTGAT+AGG + chr4_2:5763589-5763608 None:intergenic 30.0%
! TTCACAGTCACAGATTTTAA+TGG - chr4_2:5763626-5763645 Msa0585240:CDS 30.0%
TGTGATCATAAAGGAATTTG+AGG + chr4_2:5763667-5763686 None:intergenic 30.0%
! TTTTCTTATACAGGCAATGA+CGG - chr4_2:5763861-5763880 Msa0585240:CDS 30.0%
CTTCTTTAGTATTACTAGCT+AGG + chr4_2:5763996-5764015 None:intergenic 30.0%
!!! ACTAGTGATTTTAAGGTCAA+AGG - chr4_2:5764018-5764037 Msa0585240:intron 30.0%
!!! ATTTTAAGGTCAAAGGAAGT+TGG - chr4_2:5764025-5764044 Msa0585240:intron 30.0%
TTGATTGTAGATGCATAAGA+AGG - chr4_2:5764227-5764246 Msa0585240:CDS 30.0%
ATGAATGCATAGTCAATGTT+GGG + chr4_2:5764306-5764325 None:intergenic 30.0%
ATTGATAGGTCAACAGAATG+AGG + chr4_2:5763575-5763594 None:intergenic 35.0%
CTGTTGACCTATCAATTGTA+AGG - chr4_2:5763579-5763598 Msa0585240:CDS 35.0%
GTAAGAGACTGTGATCATAA+AGG + chr4_2:5763676-5763695 None:intergenic 35.0%
TTTCTTATACAGGCAATGAC+GGG - chr4_2:5763862-5763881 Msa0585240:CDS 35.0%
GTTTGGGAAAGATAATCTCA+CGG - chr4_2:5764269-5764288 Msa0585240:CDS 35.0%
GAAAGATAATCTCACGGTTA+GGG - chr4_2:5764275-5764294 Msa0585240:CDS 35.0%
GATGAATGCATAGTCAATGT+TGG + chr4_2:5764307-5764326 None:intergenic 35.0%
ATTGATAGGTCAACAGAATG+AGG + chr4_2:5763575-5763594 None:intergenic 35.0%
CTGTTGACCTATCAATTGTA+AGG - chr4_2:5763579-5763598 Msa0585240:CDS 35.0%
GTAAGAGACTGTGATCATAA+AGG + chr4_2:5763676-5763695 None:intergenic 35.0%
TTTCTTATACAGGCAATGAC+GGG - chr4_2:5763862-5763881 Msa0585240:CDS 35.0%
GTTTGGGAAAGATAATCTCA+CGG - chr4_2:5764269-5764288 Msa0585240:CDS 35.0%
GAAAGATAATCTCACGGTTA+GGG - chr4_2:5764275-5764294 Msa0585240:CDS 35.0%
GATGAATGCATAGTCAATGT+TGG + chr4_2:5764307-5764326 None:intergenic 35.0%
!! ACTCTCATAATTTGCTGCAG+AGG + chr4_2:5763525-5763544 None:intergenic 40.0%
TCTGCAGCAAATTATGAGAG+TGG - chr4_2:5763524-5763543 Msa0585240:CDS 40.0%
GAATGAGGAACACGATATTG+AGG + chr4_2:5763560-5763579 None:intergenic 40.0%
!! AGCTTTTCGAGGTGAAAGTA+CGG - chr4_2:5763900-5763919 Msa0585240:CDS 40.0%
!! CGATCTTGTGTTGTTTATGC+TGG - chr4_2:5764054-5764073 Msa0585240:intron 40.0%
TATAGAAAGGGTCCTTACCT+GGG + chr4_2:5764100-5764119 None:intergenic 40.0%
!! AGTGTTCAAAGTGTTGCGTT+TGG - chr4_2:5764252-5764271 Msa0585240:CDS 40.0%
!! GTGTTCAAAGTGTTGCGTTT+GGG - chr4_2:5764253-5764272 Msa0585240:CDS 40.0%
GGAAAGATAATCTCACGGTT+AGG - chr4_2:5764274-5764293 Msa0585240:CDS 40.0%
! CATTGACTATGCATTCATCG+TGG - chr4_2:5764308-5764327 Msa0585240:CDS 40.0%
! GTTGTTGTCGTGTTTTGTCT+TGG + chr4_2:5764362-5764381 None:intergenic 40.0%
!! ACTCTCATAATTTGCTGCAG+AGG + chr4_2:5763525-5763544 None:intergenic 40.0%
TCTGCAGCAAATTATGAGAG+TGG - chr4_2:5763524-5763543 Msa0585240:CDS 40.0%
GAATGAGGAACACGATATTG+AGG + chr4_2:5763560-5763579 None:intergenic 40.0%
!! AGCTTTTCGAGGTGAAAGTA+CGG - chr4_2:5763900-5763919 Msa0585240:CDS 40.0%
!! CGATCTTGTGTTGTTTATGC+TGG - chr4_2:5764054-5764073 Msa0585240:intron 40.0%
TATAGAAAGGGTCCTTACCT+GGG + chr4_2:5764100-5764119 None:intergenic 40.0%
!! AGTGTTCAAAGTGTTGCGTT+TGG - chr4_2:5764252-5764271 Msa0585240:CDS 40.0%
!! GTGTTCAAAGTGTTGCGTTT+GGG - chr4_2:5764253-5764272 Msa0585240:CDS 40.0%
GGAAAGATAATCTCACGGTT+AGG - chr4_2:5764274-5764293 Msa0585240:CDS 40.0%
! CATTGACTATGCATTCATCG+TGG - chr4_2:5764308-5764327 Msa0585240:CDS 40.0%
! GTTGTTGTCGTGTTTTGTCT+TGG + chr4_2:5764362-5764381 None:intergenic 40.0%
AGTCTCTTACTTGATGCAGC+TGG - chr4_2:5763686-5763705 Msa0585240:intron 45.0%
! CAATGACGGGACATGATAGA+TGG - chr4_2:5763875-5763894 Msa0585240:CDS 45.0%
! GATAGATGGCAAGCTTTTCG+AGG - chr4_2:5763889-5763908 Msa0585240:CDS 45.0%
!! TTTTCGAGGTGAAAGTACGG+AGG - chr4_2:5763903-5763922 Msa0585240:CDS 45.0%
ATCTCATCACATTGTTGCCC+AGG - chr4_2:5764080-5764099 Msa0585240:intron 45.0%
ATCACATTGTTGCCCAGGTA+AGG - chr4_2:5764085-5764104 Msa0585240:intron 45.0%
CTATAGAAAGGGTCCTTACC+TGG + chr4_2:5764101-5764120 None:intergenic 45.0%
AGTCTCTTACTTGATGCAGC+TGG - chr4_2:5763686-5763705 Msa0585240:intron 45.0%
! CAATGACGGGACATGATAGA+TGG - chr4_2:5763875-5763894 Msa0585240:CDS 45.0%
! GATAGATGGCAAGCTTTTCG+AGG - chr4_2:5763889-5763908 Msa0585240:CDS 45.0%
!! TTTTCGAGGTGAAAGTACGG+AGG - chr4_2:5763903-5763922 Msa0585240:CDS 45.0%
ATCTCATCACATTGTTGCCC+AGG - chr4_2:5764080-5764099 Msa0585240:intron 45.0%
ATCACATTGTTGCCCAGGTA+AGG - chr4_2:5764085-5764104 Msa0585240:intron 45.0%
CTATAGAAAGGGTCCTTACC+TGG + chr4_2:5764101-5764120 None:intergenic 45.0%
!!! AGATTAATATTTTTTTATAA+CGG - chr4_2:5763833-5763852 Msa0585240:CDS 5.0%
!!! AGATTAATATTTTTTTATAA+CGG - chr4_2:5763833-5763852 Msa0585240:CDS 5.0%
TGTCATGACGCTGCGACGAA+AGG - chr4_2:5763718-5763737 Msa0585240:intron 55.0%
TGTCATGACGCTGCGACGAA+AGG - chr4_2:5763718-5763737 Msa0585240:intron 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 5763506 5764386 5763506 ID=Msa0585240;Name=Msa0585240
chr4_2 mRNA 5763506 5764386 5763506 ID=Msa0585240-mRNA-1;Parent=Msa0585240;Name=Msa0585240-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|1|3|0|203
chr4_2 exon 5764153 5764386 5764153 ID=Msa0585240-mRNA-1:exon:1409;Parent=Msa0585240-mRNA-1
chr4_2 exon 5763791 5764018 5763791 ID=Msa0585240-mRNA-1:exon:1408;Parent=Msa0585240-mRNA-1
chr4_2 exon 5763506 5763655 5763506 ID=Msa0585240-mRNA-1:exon:1407;Parent=Msa0585240-mRNA-1
chr4_2 CDS 5764153 5764386 5764153 ID=Msa0585240-mRNA-1:cds;Parent=Msa0585240-mRNA-1
chr4_2 CDS 5763791 5764018 5763791 ID=Msa0585240-mRNA-1:cds;Parent=Msa0585240-mRNA-1
chr4_2 CDS 5763506 5763655 5763506 ID=Msa0585240-mRNA-1:cds;Parent=Msa0585240-mRNA-1
Gene Sequence

>Msa0585240

ATGAAAAGAGTACAATCCTCTGCAGCAAATTATGAGAGTGGTATCATTGGTCCTCAATATCGTGTTCCTCATTCTGTTGACCTATCAATTGTAAGGAATGTCACAACATTAACTGATAATTTCACAGTCACAGATTTTAATGGCAAAATCTTTTTCAACCTCAAATTCCTTTATGATCACAGTCTCTTACTTGATGCAGCTGGAAAATCTGTTGTCATGACGCTGCGACGAAAGGCAATGACGGGACATGATAGATGGCAAGCTTTTCGAGGTGAAAGTACGGAGGTGAAAGATTTGATATTTAGCGTAAAGCGATCAACCATGTTTCAAACAAAGATCAAATTAGATGTGTTCCTAGCTAGTAATACTAAAGAAGATACTAGTGATTTTAAGGTCAAAGGAAGTTGGTTAGAGCGATCTTGTGTTGTTTATGCTGGTGAATCTCATCACATTGTTGCCCAGATGCATAAGAAGGAGAGTGTTCAAAGTGTTGCGTTTGGGAAAGATAATCTCACGGTTAGGGTGTATCCCAACATTGACTATGCATTCATCGTGGCAGTGATGTTGATTCTTGACGAAATTAACCAAGACAAAACACGACAACAACAGTAG

Protein sequence

>Msa0585240

MKRVQSSAANYESGIIGPQYRVPHSVDLSIVRNVTTLTDNFTVTDFNGKIFFNLKFLYDHSLLLDAAGKSVVMTLRRKAMTGHDRWQAFRGESTEVKDLIFSVKRSTMFQTKIKLDVFLASNTKEDTSDFKVKGSWLERSCVVYAGESHHIVAQMHKKESVQSVAFGKDNLTVRVYPNIDYAFIVAVMLILDEINQDKTRQQQ*