AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0789270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789270 MtrunA17_Chr3g0131581 100.000 110 0 0 1 110 163 272 4.39e-77 228
Msa0789270 MtrunA17_Chr8g0385691 85.455 110 16 0 1 110 143 252 1.47e-67 203
Msa0789270 MtrunA17_Chr8g0385681 82.569 109 19 0 1 109 146 254 9.96e-65 196
Msa0789270 MtrunA17_Chr1g0161441 42.453 106 61 0 4 109 132 237 7.85e-28 102
Msa0789270 MtrunA17_Chr1g0155071 35.577 104 64 2 1 101 137 240 8.71e-16 70.9
Msa0789270 MtrunA17_Chr7g0254621 28.155 103 72 1 1 101 138 240 2.32e-13 64.3
Msa0789270 MtrunA17_Chr3g0141821 39.362 94 53 3 10 100 211 303 1.62e-11 59.3
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789270 AT1G01630.1 78.182 110 24 0 1 110 146 255 9.15e-62 189
Msa0789270 AT1G14820.3 42.453 106 61 0 4 109 131 236 2.56e-24 93.2
Msa0789270 AT1G14820.2 42.453 106 61 0 4 109 118 223 2.75e-24 92.8
Msa0789270 AT1G14820.1 42.453 106 61 0 4 109 118 223 2.75e-24 92.8
Msa0789270 AT4G08690.2 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789270 AT4G08690.1 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789270 AT4G08690.3 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789270 AT1G75170.3 35.577 104 64 2 1 101 55 158 4.43e-13 62.8
Msa0789270 AT1G75170.2 35.455 110 62 3 1 104 138 244 1.06e-12 62.8
Msa0789270 AT1G75170.1 35.455 110 62 3 1 104 138 244 1.06e-12 62.8
Msa0789270 AT4G36640.2 31.776 107 70 2 1 104 75 181 4.46e-12 60.5
Msa0789270 AT4G36640.1 31.776 107 70 2 1 104 135 241 6.65e-12 60.5
Msa0789270 AT4G36640.3 31.776 107 70 2 1 104 135 241 6.65e-12 60.5
Msa0789270 AT4G36490.1 37.374 99 56 3 6 100 192 288 1.91e-11 59.7
Msa0789270 AT1G22180.3 31.068 103 69 2 1 101 75 177 1.96e-11 58.9
Msa0789270 AT1G22180.1 31.068 103 69 2 1 101 75 177 1.96e-11 58.9
Msa0789270 AT1G22180.2 31.068 103 69 2 1 101 140 242 3.25e-11 58.5
Msa0789270 AT1G22180.4 31.068 103 69 2 1 101 140 242 3.25e-11 58.5
Msa0789270 AT2G18180.3 36.364 99 57 3 6 100 124 220 3.47e-11 58.9
Msa0789270 AT2G18180.2 36.364 99 57 3 6 100 195 291 3.49e-11 58.9
Msa0789270 AT2G18180.1 36.364 99 57 3 6 100 195 291 3.53e-11 58.9
Msa0789270 AT2G18180.4 36.364 99 57 3 6 100 124 220 4.00e-11 58.5
Msa0789270 AT2G18180.5 36.364 99 57 3 6 100 97 193 4.13e-11 58.5
Msa0789270 AT4G34580.2 36.735 98 58 3 6 100 202 298 7.60e-11 57.8
Msa0789270 AT4G34580.1 36.735 98 58 3 6 100 202 298 7.60e-11 57.8

Find 31 sgRNAs with CRISPR-Local

Find 82 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTATCTATTGCAGACATTA+AGG 0.206776 5_2:-77145396 Msa0789270:CDS
TAAAAGTGTTACCTTCTTCT+TGG 0.260617 5_2:+77145214 None:intergenic
CTTACATGTTTATGAAAGTA+TGG 0.278705 5_2:-77145268 Msa0789270:CDS
GAATCTTGTATTGGAACTAA+TGG 0.319714 5_2:+77145009 None:intergenic
TTATTACAAGCAAATAAATA+AGG 0.338806 5_2:-77144977 Msa0789270:three_prime_UTR
AGTCAGCTCCCAGAGATATA+TGG 0.360943 5_2:-77145042 Msa0789270:CDS
TTTATCGTTGAGCCATTGTT+TGG 0.389709 5_2:+77145631 None:intergenic
ATTAATCAAGAATCTTGTAT+TGG 0.399694 5_2:+77145000 None:intergenic
CATACTTTCATAAACATGTA+AGG 0.403022 5_2:+77145269 None:intergenic
AACAACTTTCCCAGTCTCTC+TGG 0.415107 5_2:+77145305 None:intergenic
GTATCTATTGCAGACATTAA+GGG 0.415933 5_2:-77145395 Msa0789270:CDS
AGTTTGCCTCCATATATCTC+TGG 0.418208 5_2:+77145033 None:intergenic
TATTGCAGACATTAAGGGCT+GGG 0.457362 5_2:-77145390 Msa0789270:CDS
AGATTACTATCCAGAGAGAC+TGG 0.459793 5_2:-77145315 Msa0789270:CDS
TGGTATTGTCATCAATGAAA+GGG 0.492868 5_2:+77145234 None:intergenic
TTGGTATTGTCATCAATGAA+AGG 0.500676 5_2:+77145233 None:intergenic
CTATTGCAGACATTAAGGGC+TGG 0.521375 5_2:-77145391 Msa0789270:CDS
TGGATAGTAATCTTGTAGAA+TGG 0.535897 5_2:+77145325 None:intergenic
TAATGTGACAGGATGCCACC+AGG 0.550381 5_2:-77145431 Msa0789270:intron
TGATGACAATACCAAGAAGA+AGG 0.551378 5_2:-77145225 Msa0789270:intron
TATGCAAACAGCGACATTCG+CGG 0.552322 5_2:-77145365 Msa0789270:CDS
TATGTTGTTTATCCAAACAA+TGG 0.555294 5_2:-77145643 None:intergenic
AGCGACATTCGCGGTTACCT+CGG 0.560343 5_2:-77145356 Msa0789270:CDS
GTTTGCCTCCATATATCTCT+GGG 0.573143 5_2:+77145034 None:intergenic
ATTGCAGACATTAAGGGCTG+GGG 0.606164 5_2:-77145389 Msa0789270:CDS
TCATAAACATGTAAGGTGCA+TGG 0.614836 5_2:+77145276 None:intergenic
AATGTGACAGGATGCCACCA+GGG 0.634560 5_2:-77145430 Msa0789270:intron
GATTACTATCCAGAGAGACT+GGG 0.647177 5_2:-77145314 Msa0789270:CDS
CAGCTCCCAGAGATATATGG+AGG 0.670836 5_2:-77145039 Msa0789270:CDS
ATGTGACAGGATGCCACCAG+GGG 0.685775 5_2:-77145429 Msa0789270:intron
GTAGAATGGTTAGAGCACCG+AGG 0.822792 5_2:+77145339 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATATTTTTTGTGTTAC+AGG - chr5_2:77144912-77144931 Msa0789270:three_prime_UTR 15.0%
!!! TAAATATTTTTTGTGTTACA+GGG - chr5_2:77144913-77144932 Msa0789270:three_prime_UTR 15.0%
!! TTATTACAAGCAAATAAATA+AGG - chr5_2:77145548-77145567 Msa0789270:intron 15.0%
!!! ATAAATATTTTTTGTGTTAC+AGG - chr5_2:77144912-77144931 Msa0789270:three_prime_UTR 15.0%
!!! TAAATATTTTTTGTGTTACA+GGG - chr5_2:77144913-77144932 Msa0789270:three_prime_UTR 15.0%
!! TTATTACAAGCAAATAAATA+AGG - chr5_2:77145548-77145567 Msa0789270:intron 15.0%
!! ATGCATATACAGTTTATATT+TGG - chr5_2:77145024-77145043 Msa0789270:CDS 20.0%
!! ATTAATCAAGAATCTTGTAT+TGG + chr5_2:77145528-77145547 None:intergenic 20.0%
!! ATGCATATACAGTTTATATT+TGG - chr5_2:77145024-77145043 Msa0789270:CDS 20.0%
!! ATTAATCAAGAATCTTGTAT+TGG + chr5_2:77145528-77145547 None:intergenic 20.0%
! TGCATGAATTAATTAATGAG+TGG + chr5_2:77144986-77145005 None:intergenic 25.0%
! AAGTTTACAATTCTTCTTAC+TGG + chr5_2:77145060-77145079 None:intergenic 25.0%
! CATACTTTCATAAACATGTA+AGG + chr5_2:77145259-77145278 None:intergenic 25.0%
! CTTACATGTTTATGAAAGTA+TGG - chr5_2:77145257-77145276 Msa0789270:CDS 25.0%
! TTTGAAAATTGAGATGTTCT+AGG - chr5_2:77145373-77145392 Msa0789270:CDS 25.0%
! TGCATGAATTAATTAATGAG+TGG + chr5_2:77144986-77145005 None:intergenic 25.0%
! AAGTTTACAATTCTTCTTAC+TGG + chr5_2:77145060-77145079 None:intergenic 25.0%
! CATACTTTCATAAACATGTA+AGG + chr5_2:77145259-77145278 None:intergenic 25.0%
! CTTACATGTTTATGAAAGTA+TGG - chr5_2:77145257-77145276 Msa0789270:CDS 25.0%
! TTTGAAAATTGAGATGTTCT+AGG - chr5_2:77145373-77145392 Msa0789270:CDS 25.0%
TGTATCTATTGCAGACATTA+AGG - chr5_2:77145129-77145148 Msa0789270:intron 30.0%
GTATCTATTGCAGACATTAA+GGG - chr5_2:77145130-77145149 Msa0789270:intron 30.0%
TGGATAGTAATCTTGTAGAA+TGG + chr5_2:77145203-77145222 None:intergenic 30.0%
TGGTATTGTCATCAATGAAA+GGG + chr5_2:77145294-77145313 None:intergenic 30.0%
TTGGTATTGTCATCAATGAA+AGG + chr5_2:77145295-77145314 None:intergenic 30.0%
!! TAAAAGTGTTACCTTCTTCT+TGG + chr5_2:77145314-77145333 None:intergenic 30.0%
GAATCTTGTATTGGAACTAA+TGG + chr5_2:77145519-77145538 None:intergenic 30.0%
TGTATCTATTGCAGACATTA+AGG - chr5_2:77145129-77145148 Msa0789270:intron 30.0%
GTATCTATTGCAGACATTAA+GGG - chr5_2:77145130-77145149 Msa0789270:intron 30.0%
TGGATAGTAATCTTGTAGAA+TGG + chr5_2:77145203-77145222 None:intergenic 30.0%
TGGTATTGTCATCAATGAAA+GGG + chr5_2:77145294-77145313 None:intergenic 30.0%
TTGGTATTGTCATCAATGAA+AGG + chr5_2:77145295-77145314 None:intergenic 30.0%
!! TAAAAGTGTTACCTTCTTCT+TGG + chr5_2:77145314-77145333 None:intergenic 30.0%
GAATCTTGTATTGGAACTAA+TGG + chr5_2:77145519-77145538 None:intergenic 30.0%
TTTATCGTTGAGCCATTGTT+TGG + chr5_2:77144897-77144916 None:intergenic 35.0%
TCATAAACATGTAAGGTGCA+TGG + chr5_2:77145252-77145271 None:intergenic 35.0%
TGATGACAATACCAAGAAGA+AGG - chr5_2:77145300-77145319 Msa0789270:CDS 35.0%
TTTATCGTTGAGCCATTGTT+TGG + chr5_2:77144897-77144916 None:intergenic 35.0%
TCATAAACATGTAAGGTGCA+TGG + chr5_2:77145252-77145271 None:intergenic 35.0%
TGATGACAATACCAAGAAGA+AGG - chr5_2:77145300-77145319 Msa0789270:CDS 35.0%
AGCTTACCCAATAATGTGAC+AGG - chr5_2:77145083-77145102 Msa0789270:CDS 40.0%
TGGCATCCTGTCACATTATT+GGG + chr5_2:77145092-77145111 None:intergenic 40.0%
! GATACAAACTTTTCTTCCCC+TGG + chr5_2:77145115-77145134 None:intergenic 40.0%
TATTGCAGACATTAAGGGCT+GGG - chr5_2:77145135-77145154 Msa0789270:intron 40.0%
AGATTACTATCCAGAGAGAC+TGG - chr5_2:77145210-77145229 Msa0789270:intron 40.0%
GATTACTATCCAGAGAGACT+GGG - chr5_2:77145211-77145230 Msa0789270:intron 40.0%
GTTTGCCTCCATATATCTCT+GGG + chr5_2:77145494-77145513 None:intergenic 40.0%
AGTTTGCCTCCATATATCTC+TGG + chr5_2:77145495-77145514 None:intergenic 40.0%
AGCTTACCCAATAATGTGAC+AGG - chr5_2:77145083-77145102 Msa0789270:CDS 40.0%
TGGCATCCTGTCACATTATT+GGG + chr5_2:77145092-77145111 None:intergenic 40.0%
! GATACAAACTTTTCTTCCCC+TGG + chr5_2:77145115-77145134 None:intergenic 40.0%
TATTGCAGACATTAAGGGCT+GGG - chr5_2:77145135-77145154 Msa0789270:intron 40.0%
AGATTACTATCCAGAGAGAC+TGG - chr5_2:77145210-77145229 Msa0789270:intron 40.0%
GATTACTATCCAGAGAGACT+GGG - chr5_2:77145211-77145230 Msa0789270:intron 40.0%
GTTTGCCTCCATATATCTCT+GGG + chr5_2:77145494-77145513 None:intergenic 40.0%
AGTTTGCCTCCATATATCTC+TGG + chr5_2:77145495-77145514 None:intergenic 40.0%
GTGGCATCCTGTCACATTAT+TGG + chr5_2:77145093-77145112 None:intergenic 45.0%
! ACAAACTTTTCTTCCCCTGG+TGG + chr5_2:77145112-77145131 None:intergenic 45.0%
CTATTGCAGACATTAAGGGC+TGG - chr5_2:77145134-77145153 Msa0789270:intron 45.0%
ATTGCAGACATTAAGGGCTG+GGG - chr5_2:77145136-77145155 Msa0789270:intron 45.0%
TATGCAAACAGCGACATTCG+CGG - chr5_2:77145160-77145179 Msa0789270:intron 45.0%
AACAACTTTCCCAGTCTCTC+TGG + chr5_2:77145223-77145242 None:intergenic 45.0%
AGTCAGCTCCCAGAGATATA+TGG - chr5_2:77145483-77145502 Msa0789270:intron 45.0%
GTGGCATCCTGTCACATTAT+TGG + chr5_2:77145093-77145112 None:intergenic 45.0%
! ACAAACTTTTCTTCCCCTGG+TGG + chr5_2:77145112-77145131 None:intergenic 45.0%
CTATTGCAGACATTAAGGGC+TGG - chr5_2:77145134-77145153 Msa0789270:intron 45.0%
ATTGCAGACATTAAGGGCTG+GGG - chr5_2:77145136-77145155 Msa0789270:intron 45.0%
TATGCAAACAGCGACATTCG+CGG - chr5_2:77145160-77145179 Msa0789270:intron 45.0%
AACAACTTTCCCAGTCTCTC+TGG + chr5_2:77145223-77145242 None:intergenic 45.0%
AGTCAGCTCCCAGAGATATA+TGG - chr5_2:77145483-77145502 Msa0789270:intron 45.0%
TAATGTGACAGGATGCCACC+AGG - chr5_2:77145094-77145113 Msa0789270:CDS 50.0%
AATGTGACAGGATGCCACCA+GGG - chr5_2:77145095-77145114 Msa0789270:CDS 50.0%
!! GTAGAATGGTTAGAGCACCG+AGG + chr5_2:77145189-77145208 None:intergenic 50.0%
CAGCTCCCAGAGATATATGG+AGG - chr5_2:77145486-77145505 Msa0789270:intron 50.0%
TAATGTGACAGGATGCCACC+AGG - chr5_2:77145094-77145113 Msa0789270:CDS 50.0%
AATGTGACAGGATGCCACCA+GGG - chr5_2:77145095-77145114 Msa0789270:CDS 50.0%
!! GTAGAATGGTTAGAGCACCG+AGG + chr5_2:77145189-77145208 None:intergenic 50.0%
CAGCTCCCAGAGATATATGG+AGG - chr5_2:77145486-77145505 Msa0789270:intron 50.0%
ATGTGACAGGATGCCACCAG+GGG - chr5_2:77145096-77145115 Msa0789270:CDS 55.0%
AGCGACATTCGCGGTTACCT+CGG - chr5_2:77145169-77145188 Msa0789270:intron 55.0%
ATGTGACAGGATGCCACCAG+GGG - chr5_2:77145096-77145115 Msa0789270:CDS 55.0%
AGCGACATTCGCGGTTACCT+CGG - chr5_2:77145169-77145188 Msa0789270:intron 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 77144894 77145653 77144894 ID=Msa0789270;Name=Msa0789270
chr5_2 mRNA 77144894 77145653 77144894 ID=Msa0789270-mRNA-1;Parent=Msa0789270;Name=Msa0789270-mRNA-1;_AED=0.38;_eAED=0.38;_QI=78|1|1|1|0.5|0.66|3|111|110
chr5_2 exon 77144894 77145121 77144894 ID=Msa0789270-mRNA-1:exon:23494;Parent=Msa0789270-mRNA-1
chr5_2 exon 77145226 77145442 77145226 ID=Msa0789270-mRNA-1:exon:23493;Parent=Msa0789270-mRNA-1
chr5_2 exon 77145577 77145653 77145577 ID=Msa0789270-mRNA-1:exon:23492;Parent=Msa0789270-mRNA-1
chr5_2 five_prime_UTR 77145577 77145653 77145577 ID=Msa0789270-mRNA-1:five_prime_utr;Parent=Msa0789270-mRNA-1
chr5_2 five_prime_UTR 77145442 77145442 77145442 ID=Msa0789270-mRNA-1:five_prime_utr;Parent=Msa0789270-mRNA-1
chr5_2 CDS 77145226 77145441 77145226 ID=Msa0789270-mRNA-1:cds;Parent=Msa0789270-mRNA-1
chr5_2 CDS 77145005 77145121 77145005 ID=Msa0789270-mRNA-1:cds;Parent=Msa0789270-mRNA-1
chr5_2 three_prime_UTR 77144894 77145004 77144894 ID=Msa0789270-mRNA-1:three_prime_utr;Parent=Msa0789270-mRNA-1
Gene Sequence

>Msa0789270

ATGCCACCAGGGGAAGAAAAGTTTGTATCTATTGCAGACATTAAGGGCTGGGGATATGCAAACAGCGACATTCGCGGTTACCTCGGTGCTCTAACCATTCTACAAGATTACTATCCAGAGAGACTGGGAAAGTTGTTCATAGTCCATGCACCTTACATGTTTATGAAAGTATGGAAAATTATTTACCCTTTCATTGATGACAATACCAAGAAGAAGATAGTATTTGTTGAGAACAAGAAGCTGAAAGCAACATTGCTTGAAGAGATTGATGAGAGTCAGCTCCCAGAGATATATGGAGGCAAACTTCCATTAGTTCCAATACAAGATTCTTGA

Protein sequence

>Msa0789270

MPPGEEKFVSIADIKGWGYANSDIRGYLGALTILQDYYPERLGKLFIVHAPYMFMKVWKIIYPFIDDNTKKKIVFVENKKLKATLLEEIDESQLPEIYGGKLPLVPIQDS*