AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0672680


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0672680 MtrunA17_Chr4g0013291 94.975 199 10 0 1 199 1 199 8.55e-142 393
Msa0672680 MtrunA17_Chr7g0244371 61.579 190 68 2 12 197 19 207 9.95e-84 247
Msa0672680 MtrunA17_Chr7g0244321 61.257 191 68 3 13 198 21 210 6.74e-83 244
Msa0672680 MtrunA17_Chr7g0244331 61.458 192 68 3 11 197 19 209 1.15e-82 244
Msa0672680 MtrunA17_Chr7g0244341 59.788 189 70 3 15 198 23 210 1.06e-79 237
Msa0672680 MtrunA17_Chr7g0244361 54.271 199 79 3 12 200 44 240 3.82e-73 221
Msa0672680 MtrunA17_Chr7g0244111 65.254 118 41 0 80 197 4 121 2.33e-57 177
Msa0672680 MtrunA17_Chr1g0150081 43.386 189 92 6 13 192 3 185 2.88e-41 138
Msa0672680 MtrunA17_Chr2g0333101 32.749 171 98 7 39 199 43 206 5.88e-23 92.0
Msa0672680 MtrunA17_Chr2g0333111 30.769 169 104 6 39 199 44 207 3.90e-19 82.0
Msa0672680 MtrunA17_Chr4g0003271 26.396 197 131 7 10 197 2 193 1.14e-18 80.5
Msa0672680 MtrunA17_Chr1g0150091 38.095 126 57 5 83 192 11 131 3.94e-14 66.6
Msa0672680 MtrunA17_Chr1g0150101 43.038 79 41 2 114 192 5 79 2.66e-12 60.1
Msa0672680 MtrunA17_Chr5g0432221 31.159 138 86 4 57 191 80 211 5.38e-12 62.4
Msa0672680 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
Msa0672680 AT5G01750.2 54.271 199 83 4 6 197 16 213 2.14e-74 224
Msa0672680 AT3G11740.1 49.741 193 90 4 14 200 2 193 7.94e-64 196
Msa0672680 AT1G33840.1 49.730 185 87 3 15 194 27 210 5.90e-58 182
Msa0672680 AT2G14560.1 49.733 187 88 3 15 196 7 192 7.28e-58 181
Msa0672680 AT2G14560.3 49.733 187 88 3 15 196 67 252 1.26e-56 180
Msa0672680 AT5G01750.1 52.532 158 67 4 6 156 16 172 1.09e-52 167
Msa0672680 AT2G14560.2 51.351 148 66 3 15 157 7 153 5.50e-45 147
Msa0672680 AT2G14560.4 51.351 148 66 3 15 157 67 213 1.06e-43 146
Msa0672680 AT1G33840.2 47.973 148 71 3 15 157 27 173 1.04e-40 137
Msa0672680 AT3G16900.1 33.500 200 108 6 1 195 1 180 1.33e-34 121
Msa0672680 AT3G56180.2 26.633 199 137 4 2 193 5 201 6.41e-22 89.4
Msa0672680 AT3G15810.1 30.909 165 103 4 39 197 45 204 9.34e-22 89.0
Msa0672680 AT3G56180.1 26.131 199 136 5 2 193 5 199 1.25e-19 83.2
Msa0672680 AT1G80120.1 30.357 168 103 5 39 197 31 193 4.38e-16 73.9
Msa0672680 AT3G10986.1 24.737 190 131 6 15 193 4 192 2.58e-12 63.5
Msa0672680 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_4:+17996926 Msa0672680:CDS
GTGTTCAAAGTGTTGCGTTT+GGG 0.407302 4_4:+17996905 Msa0672680:CDS
CTTCTTTAGTATTACTAGCT+AGG 0.413877 4_4:-17996644 None:intergenic
CTGTTGACCTATCAATTGTA+AGG 0.415763 4_4:+17996228 Msa0672680:CDS
AGTGTTCAAAGTGTTGCGTT+TGG 0.433678 4_4:+17996904 Msa0672680:CDS
TGACATTCCTTACAATTGAT+AGG 0.450507 4_4:-17996235 None:intergenic
GTAAGAGACTGTGATCATAA+AGG 0.456930 4_4:-17996322 None:intergenic
TGTGATCATAAAGGAATTTG+AGG 0.464343 4_4:-17996313 None:intergenic
CGATCTTGTGTTGTTTATGC+TGG 0.470752 4_4:+17996705 Msa0672680:CDS
GAAAGATAATCTCACGGTTA+GGG 0.472008 4_4:+17996927 Msa0672680:CDS
CAATGACGGGACATGATAGA+TGG 0.479331 4_4:+17996526 Msa0672680:CDS
TTGATTGTAGATGCATAAGA+AGG 0.480843 4_4:+17996879 Msa0672680:intron
ATGAATGCATAGTCAATGTT+GGG 0.488228 4_4:-17996955 None:intergenic
ATCTCATCACATTGTTGCCC+AGG 0.500173 4_4:+17996731 Msa0672680:CDS
GATGAATGCATAGTCAATGT+TGG 0.514312 4_4:-17996956 None:intergenic
AATTATGAGAGTGGTATCAT+TGG 0.521876 4_4:+17996182 Msa0672680:CDS
TTTCTTATACAGGCAATGAC+GGG 0.543853 4_4:+17996513 Msa0672680:intron
AGTCTCTTACTTGATGCAGC+TGG 0.550594 4_4:+17996335 Msa0672680:CDS
TGTCATGACGCTGCGACGAA+AGG 0.555705 4_4:+17996367 Msa0672680:CDS
ATTGATAGGTCAACAGAATG+AGG 0.558385 4_4:-17996221 None:intergenic
ACTCTCATAATTTGCTGCAG+AGG 0.575251 4_4:-17996171 None:intergenic
GAATGAGGAACACGATATTG+AGG 0.585084 4_4:-17996206 None:intergenic
TCTGCAGCAAATTATGAGAG+TGG 0.622628 4_4:+17996173 Msa0672680:CDS
TTTGATCTTTGTTTGAAACA+TGG 0.637933 4_4:-17996610 None:intergenic
GTTTGGGAAAGATAATCTCA+CGG 0.663482 4_4:+17996921 Msa0672680:CDS
CATTGACTATGCATTCATCG+TGG 0.756924 4_4:+17996960 Msa0672680:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAAAAATTGCATTATTAA+TGG - chr4_4:17996811-17996830 None:intergenic 10.0%
!! TAAAAAAATTGCATTATTAA+TGG - chr4_4:17996811-17996830 None:intergenic 10.0%
!! ACGGTAAAATTTTCTTATAC+AGG + chr4_4:17996503-17996522 Msa0672680:intron 25.0%
!! TTTGATCTTTGTTTGAAACA+TGG - chr4_4:17996613-17996632 None:intergenic 25.0%
!! AGAAGATACTAGTGATTTTA+AGG + chr4_4:17996662-17996681 Msa0672680:CDS 25.0%
!! TAAACTTGCTTCTATAGAAA+GGG - chr4_4:17996763-17996782 None:intergenic 25.0%
!! ATAAACTTGCTTCTATAGAA+AGG - chr4_4:17996764-17996783 None:intergenic 25.0%
!! ACGGTAAAATTTTCTTATAC+AGG + chr4_4:17996503-17996522 Msa0672680:intron 25.0%
!! TTTGATCTTTGTTTGAAACA+TGG - chr4_4:17996613-17996632 None:intergenic 25.0%
!! AGAAGATACTAGTGATTTTA+AGG + chr4_4:17996662-17996681 Msa0672680:CDS 25.0%
!! TAAACTTGCTTCTATAGAAA+GGG - chr4_4:17996763-17996782 None:intergenic 25.0%
!! ATAAACTTGCTTCTATAGAA+AGG - chr4_4:17996764-17996783 None:intergenic 25.0%
AATTATGAGAGTGGTATCAT+TGG + chr4_4:17996182-17996201 Msa0672680:CDS 30.0%
TGACATTCCTTACAATTGAT+AGG - chr4_4:17996238-17996257 None:intergenic 30.0%
! TTCACAGTCACAGATTTTAA+TGG + chr4_4:17996275-17996294 Msa0672680:CDS 30.0%
TGTGATCATAAAGGAATTTG+AGG - chr4_4:17996316-17996335 None:intergenic 30.0%
CAAAAATGATCAAAATACGC+AGG - chr4_4:17996418-17996437 None:intergenic 30.0%
! TTTTCTTATACAGGCAATGA+CGG + chr4_4:17996512-17996531 Msa0672680:intron 30.0%
CTTCTTTAGTATTACTAGCT+AGG - chr4_4:17996647-17996666 None:intergenic 30.0%
!!! ACTAGTGATTTTAAGGTCAA+AGG + chr4_4:17996669-17996688 Msa0672680:CDS 30.0%
!!! ATTTTAAGGTCAAAGGAAGT+TGG + chr4_4:17996676-17996695 Msa0672680:CDS 30.0%
TTGATTGTAGATGCATAAGA+AGG + chr4_4:17996879-17996898 Msa0672680:intron 30.0%
ATGAATGCATAGTCAATGTT+GGG - chr4_4:17996958-17996977 None:intergenic 30.0%
AATTATGAGAGTGGTATCAT+TGG + chr4_4:17996182-17996201 Msa0672680:CDS 30.0%
TGACATTCCTTACAATTGAT+AGG - chr4_4:17996238-17996257 None:intergenic 30.0%
! TTCACAGTCACAGATTTTAA+TGG + chr4_4:17996275-17996294 Msa0672680:CDS 30.0%
TGTGATCATAAAGGAATTTG+AGG - chr4_4:17996316-17996335 None:intergenic 30.0%
CAAAAATGATCAAAATACGC+AGG - chr4_4:17996418-17996437 None:intergenic 30.0%
! TTTTCTTATACAGGCAATGA+CGG + chr4_4:17996512-17996531 Msa0672680:intron 30.0%
CTTCTTTAGTATTACTAGCT+AGG - chr4_4:17996647-17996666 None:intergenic 30.0%
!!! ACTAGTGATTTTAAGGTCAA+AGG + chr4_4:17996669-17996688 Msa0672680:CDS 30.0%
!!! ATTTTAAGGTCAAAGGAAGT+TGG + chr4_4:17996676-17996695 Msa0672680:CDS 30.0%
TTGATTGTAGATGCATAAGA+AGG + chr4_4:17996879-17996898 Msa0672680:intron 30.0%
ATGAATGCATAGTCAATGTT+GGG - chr4_4:17996958-17996977 None:intergenic 30.0%
ATTGATAGGTCAACAGAATG+AGG - chr4_4:17996224-17996243 None:intergenic 35.0%
CTGTTGACCTATCAATTGTA+AGG + chr4_4:17996228-17996247 Msa0672680:CDS 35.0%
GTAAGAGACTGTGATCATAA+AGG - chr4_4:17996325-17996344 None:intergenic 35.0%
TTTCTTATACAGGCAATGAC+GGG + chr4_4:17996513-17996532 Msa0672680:intron 35.0%
GTTTGGGAAAGATAATCTCA+CGG + chr4_4:17996921-17996940 Msa0672680:CDS 35.0%
GAAAGATAATCTCACGGTTA+GGG + chr4_4:17996927-17996946 Msa0672680:CDS 35.0%
GATGAATGCATAGTCAATGT+TGG - chr4_4:17996959-17996978 None:intergenic 35.0%
ATTGATAGGTCAACAGAATG+AGG - chr4_4:17996224-17996243 None:intergenic 35.0%
CTGTTGACCTATCAATTGTA+AGG + chr4_4:17996228-17996247 Msa0672680:CDS 35.0%
GTAAGAGACTGTGATCATAA+AGG - chr4_4:17996325-17996344 None:intergenic 35.0%
TTTCTTATACAGGCAATGAC+GGG + chr4_4:17996513-17996532 Msa0672680:intron 35.0%
GTTTGGGAAAGATAATCTCA+CGG + chr4_4:17996921-17996940 Msa0672680:CDS 35.0%
GAAAGATAATCTCACGGTTA+GGG + chr4_4:17996927-17996946 Msa0672680:CDS 35.0%
GATGAATGCATAGTCAATGT+TGG - chr4_4:17996959-17996978 None:intergenic 35.0%
!! ACTCTCATAATTTGCTGCAG+AGG - chr4_4:17996174-17996193 None:intergenic 40.0%
TCTGCAGCAAATTATGAGAG+TGG + chr4_4:17996173-17996192 Msa0672680:CDS 40.0%
GAATGAGGAACACGATATTG+AGG - chr4_4:17996209-17996228 None:intergenic 40.0%
!! AGCTTTTCGAGGTGAAAGTA+CGG + chr4_4:17996551-17996570 Msa0672680:CDS 40.0%
!! CGATCTTGTGTTGTTTATGC+TGG + chr4_4:17996705-17996724 Msa0672680:CDS 40.0%
TATAGAAAGGGTCCTTACCT+GGG - chr4_4:17996751-17996770 None:intergenic 40.0%
!! AGTGTTCAAAGTGTTGCGTT+TGG + chr4_4:17996904-17996923 Msa0672680:CDS 40.0%
!! GTGTTCAAAGTGTTGCGTTT+GGG + chr4_4:17996905-17996924 Msa0672680:CDS 40.0%
GGAAAGATAATCTCACGGTT+AGG + chr4_4:17996926-17996945 Msa0672680:CDS 40.0%
! CATTGACTATGCATTCATCG+TGG + chr4_4:17996960-17996979 Msa0672680:CDS 40.0%
! GTTGTTGTCGTGTTTTGTCT+TGG - chr4_4:17997014-17997033 None:intergenic 40.0%
!! ACTCTCATAATTTGCTGCAG+AGG - chr4_4:17996174-17996193 None:intergenic 40.0%
TCTGCAGCAAATTATGAGAG+TGG + chr4_4:17996173-17996192 Msa0672680:CDS 40.0%
GAATGAGGAACACGATATTG+AGG - chr4_4:17996209-17996228 None:intergenic 40.0%
!! AGCTTTTCGAGGTGAAAGTA+CGG + chr4_4:17996551-17996570 Msa0672680:CDS 40.0%
!! CGATCTTGTGTTGTTTATGC+TGG + chr4_4:17996705-17996724 Msa0672680:CDS 40.0%
TATAGAAAGGGTCCTTACCT+GGG - chr4_4:17996751-17996770 None:intergenic 40.0%
!! AGTGTTCAAAGTGTTGCGTT+TGG + chr4_4:17996904-17996923 Msa0672680:CDS 40.0%
!! GTGTTCAAAGTGTTGCGTTT+GGG + chr4_4:17996905-17996924 Msa0672680:CDS 40.0%
GGAAAGATAATCTCACGGTT+AGG + chr4_4:17996926-17996945 Msa0672680:CDS 40.0%
! CATTGACTATGCATTCATCG+TGG + chr4_4:17996960-17996979 Msa0672680:CDS 40.0%
! GTTGTTGTCGTGTTTTGTCT+TGG - chr4_4:17997014-17997033 None:intergenic 40.0%
AGTCTCTTACTTGATGCAGC+TGG + chr4_4:17996335-17996354 Msa0672680:CDS 45.0%
! CAATGACGGGACATGATAGA+TGG + chr4_4:17996526-17996545 Msa0672680:CDS 45.0%
! GATAGATGGCAAGCTTTTCG+AGG + chr4_4:17996540-17996559 Msa0672680:CDS 45.0%
!! TTTTCGAGGTGAAAGTACGG+AGG + chr4_4:17996554-17996573 Msa0672680:CDS 45.0%
ATCTCATCACATTGTTGCCC+AGG + chr4_4:17996731-17996750 Msa0672680:CDS 45.0%
ATCACATTGTTGCCCAGGTA+AGG + chr4_4:17996736-17996755 Msa0672680:intron 45.0%
CTATAGAAAGGGTCCTTACC+TGG - chr4_4:17996752-17996771 None:intergenic 45.0%
AGTCTCTTACTTGATGCAGC+TGG + chr4_4:17996335-17996354 Msa0672680:CDS 45.0%
! CAATGACGGGACATGATAGA+TGG + chr4_4:17996526-17996545 Msa0672680:CDS 45.0%
! GATAGATGGCAAGCTTTTCG+AGG + chr4_4:17996540-17996559 Msa0672680:CDS 45.0%
!! TTTTCGAGGTGAAAGTACGG+AGG + chr4_4:17996554-17996573 Msa0672680:CDS 45.0%
ATCTCATCACATTGTTGCCC+AGG + chr4_4:17996731-17996750 Msa0672680:CDS 45.0%
ATCACATTGTTGCCCAGGTA+AGG + chr4_4:17996736-17996755 Msa0672680:intron 45.0%
CTATAGAAAGGGTCCTTACC+TGG - chr4_4:17996752-17996771 None:intergenic 45.0%
!!! AGATTAATATTTTATTTAAA+CGG + chr4_4:17996484-17996503 Msa0672680:intron 5.0%
!!! AGATTAATATTTTATTTAAA+CGG + chr4_4:17996484-17996503 Msa0672680:intron 5.0%
TGTCATGACGCTGCGACGAA+AGG + chr4_4:17996367-17996386 Msa0672680:CDS 55.0%
TGTCATGACGCTGCGACGAA+AGG + chr4_4:17996367-17996386 Msa0672680:CDS 55.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 17996155 17997038 17996155 ID=Msa0672680;Name=Msa0672680
chr4_4 mRNA 17996155 17997038 17996155 ID=Msa0672680-mRNA-1;Parent=Msa0672680;Name=Msa0672680-mRNA-1;_AED=0.13;_eAED=0.13;_QI=0|0|0|1|1|1|3|0|203
chr4_4 exon 17996155 17996388 17996155 ID=Msa0672680-mRNA-1:exon:5257;Parent=Msa0672680-mRNA-1
chr4_4 exon 17996525 17996752 17996525 ID=Msa0672680-mRNA-1:exon:5258;Parent=Msa0672680-mRNA-1
chr4_4 exon 17996889 17997038 17996889 ID=Msa0672680-mRNA-1:exon:5259;Parent=Msa0672680-mRNA-1
chr4_4 CDS 17996155 17996388 17996155 ID=Msa0672680-mRNA-1:cds;Parent=Msa0672680-mRNA-1
chr4_4 CDS 17996525 17996752 17996525 ID=Msa0672680-mRNA-1:cds;Parent=Msa0672680-mRNA-1
chr4_4 CDS 17996889 17997038 17996889 ID=Msa0672680-mRNA-1:cds;Parent=Msa0672680-mRNA-1
Gene Sequence

>Msa0672680

ATGAAAAGAGTACAATCCTCTGCAGCAAATTATGAGAGTGGTATCATTGGTCCTCAATATCGTGTTCCTCATTCTGTTGACCTATCAATTGTAAGGAATGTCACAACATTAACTGATAATTTCACAGTCACAGATTTTAATGGCAAAATCTTTTTCAACCTCAAATTCCTTTATGATCACAGTCTCTTACTTGATGCAGCTGGAAAATCTGTTGTCATGACGCTGCGACGAAAGGCAATGACGGGACATGATAGATGGCAAGCTTTTCGAGGTGAAAGTACGGAGGTGAAAGATTTGATATTTAGCGTAAAGCGATCAACCATGTTTCAAACAAAGATCAAATTAGATGTGTTCCTAGCTAGTAATACTAAAGAAGATACTAGTGATTTTAAGGTCAAAGGAAGTTGGTTAGAGCGATCTTGTGTTGTTTATGCTGGTGAATCTCATCACATTGTTGCCCAGATGCATAAGAAGGAGAGTGTTCAAAGTGTTGCGTTTGGGAAAGATAATCTCACGGTTAGGGTGTATCCCAACATTGACTATGCATTCATCGTGGCAGTGATGTTGATTCTTGACGAAATTAACCAAGACAAAACACGACAACAACAGTAG

Protein sequence

>Msa0672680

MKRVQSSAANYESGIIGPQYRVPHSVDLSIVRNVTTLTDNFTVTDFNGKIFFNLKFLYDHSLLLDAAGKSVVMTLRRKAMTGHDRWQAFRGESTEVKDLIFSVKRSTMFQTKIKLDVFLASNTKEDTSDFKVKGSWLERSCVVYAGESHHIVAQMHKKESVQSVAFGKDNLTVRVYPNIDYAFIVAVMLILDEINQDKTRQQQ*