AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0789290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0789290 MtrunA17_Chr3g0131581 100.000 110 0 0 1 110 163 272 4.39e-77 228
Msa0789290 MtrunA17_Chr8g0385691 85.455 110 16 0 1 110 143 252 1.47e-67 203
Msa0789290 MtrunA17_Chr8g0385681 82.569 109 19 0 1 109 146 254 9.96e-65 196
Msa0789290 MtrunA17_Chr1g0161441 42.453 106 61 0 4 109 132 237 7.85e-28 102
Msa0789290 MtrunA17_Chr1g0155071 35.577 104 64 2 1 101 137 240 8.71e-16 70.9
Msa0789290 MtrunA17_Chr7g0254621 28.155 103 72 1 1 101 138 240 2.32e-13 64.3
Msa0789290 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
Msa0789290 AT1G01630.1 78.182 110 24 0 1 110 146 255 9.15e-62 189
Msa0789290 AT1G14820.3 42.453 106 61 0 4 109 131 236 2.56e-24 93.2
Msa0789290 AT1G14820.2 42.453 106 61 0 4 109 118 223 2.75e-24 92.8
Msa0789290 AT1G14820.1 42.453 106 61 0 4 109 118 223 2.75e-24 92.8
Msa0789290 AT4G08690.2 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789290 AT4G08690.1 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789290 AT4G08690.3 32.353 102 67 1 1 100 137 238 2.84e-14 67.0
Msa0789290 AT1G75170.3 35.577 104 64 2 1 101 55 158 4.43e-13 62.8
Msa0789290 AT1G75170.2 35.455 110 62 3 1 104 138 244 1.06e-12 62.8
Msa0789290 AT1G75170.1 35.455 110 62 3 1 104 138 244 1.06e-12 62.8
Msa0789290 AT4G36640.2 31.776 107 70 2 1 104 75 181 4.46e-12 60.5
Msa0789290 AT4G36640.1 31.776 107 70 2 1 104 135 241 6.65e-12 60.5
Msa0789290 AT4G36640.3 31.776 107 70 2 1 104 135 241 6.65e-12 60.5
Msa0789290 AT4G36490.1 37.374 99 56 3 6 100 192 288 1.91e-11 59.7
Msa0789290 AT1G22180.3 31.068 103 69 2 1 101 75 177 1.96e-11 58.9
Msa0789290 AT1G22180.1 31.068 103 69 2 1 101 75 177 1.96e-11 58.9
Msa0789290 AT1G22180.2 31.068 103 69 2 1 101 140 242 3.25e-11 58.5
Msa0789290 AT1G22180.4 31.068 103 69 2 1 101 140 242 3.25e-11 58.5
Msa0789290 AT2G18180.3 36.364 99 57 3 6 100 124 220 3.47e-11 58.9
Msa0789290 AT2G18180.2 36.364 99 57 3 6 100 195 291 3.49e-11 58.9
Msa0789290 AT2G18180.1 36.364 99 57 3 6 100 195 291 3.53e-11 58.9
Msa0789290 AT2G18180.4 36.364 99 57 3 6 100 124 220 4.00e-11 58.5
Msa0789290 AT2G18180.5 36.364 99 57 3 6 100 97 193 4.13e-11 58.5
Msa0789290 AT4G34580.2 36.735 98 58 3 6 100 202 298 7.60e-11 57.8
Msa0789290 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:-77153599 Msa0789290:CDS
TAAAAGTGTTACCTTCTTCT+TGG 0.260617 5_2:+77153417 None:intergenic
CTTACATGTTTATGAAAGTA+TGG 0.278705 5_2:-77153471 Msa0789290:CDS
GAATCTTGTATTGGAACTAA+TGG 0.319714 5_2:+77153212 None:intergenic
TTATTACAAGCAAATAAATA+AGG 0.338806 5_2:-77153180 Msa0789290:three_prime_UTR
AGTCAGCTCCCAGAGATATA+TGG 0.360943 5_2:-77153245 Msa0789290:CDS
TTTATCGTTGAGCCATTGTT+TGG 0.389709 5_2:+77153834 None:intergenic
ATTAATCAAGAATCTTGTAT+TGG 0.399694 5_2:+77153203 None:intergenic
CATACTTTCATAAACATGTA+AGG 0.403022 5_2:+77153472 None:intergenic
AACAACTTTCCCAGTCTCTC+TGG 0.415107 5_2:+77153508 None:intergenic
GTATCTATTGCAGACATTAA+GGG 0.415933 5_2:-77153598 Msa0789290:CDS
AGTTTGCCTCCATATATCTC+TGG 0.418208 5_2:+77153236 None:intergenic
TATTGCAGACATTAAGGGCT+GGG 0.457362 5_2:-77153593 Msa0789290:CDS
AGATTACTATCCAGAGAGAC+TGG 0.459793 5_2:-77153518 Msa0789290:CDS
TGGTATTGTCATCAATGAAA+GGG 0.492868 5_2:+77153437 None:intergenic
TTGGTATTGTCATCAATGAA+AGG 0.500676 5_2:+77153436 None:intergenic
CTATTGCAGACATTAAGGGC+TGG 0.521375 5_2:-77153594 Msa0789290:CDS
TGGATAGTAATCTTGTAGAA+TGG 0.535897 5_2:+77153528 None:intergenic
TAATGTGACAGGATGCCACC+AGG 0.550381 5_2:-77153634 Msa0789290:intron
TGATGACAATACCAAGAAGA+AGG 0.551378 5_2:-77153428 Msa0789290:intron
TATGCAAACAGCGACATTCG+CGG 0.552322 5_2:-77153568 Msa0789290:CDS
TATGTTGTTTATCCAAACAA+TGG 0.555294 5_2:-77153846 None:intergenic
AGCGACATTCGCGGTTACCT+CGG 0.560343 5_2:-77153559 Msa0789290:CDS
GTTTGCCTCCATATATCTCT+GGG 0.573143 5_2:+77153237 None:intergenic
ATTGCAGACATTAAGGGCTG+GGG 0.606164 5_2:-77153592 Msa0789290:CDS
TCATAAACATGTAAGGTGCA+TGG 0.614836 5_2:+77153479 None:intergenic
AATGTGACAGGATGCCACCA+GGG 0.634560 5_2:-77153633 Msa0789290:intron
GATTACTATCCAGAGAGACT+GGG 0.647177 5_2:-77153517 Msa0789290:CDS
CAGCTCCCAGAGATATATGG+AGG 0.670836 5_2:-77153242 Msa0789290:CDS
ATGTGACAGGATGCCACCAG+GGG 0.685775 5_2:-77153632 Msa0789290:intron
GTAGAATGGTTAGAGCACCG+AGG 0.822792 5_2:+77153542 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATAAATATTTTTTGTGTTAC+AGG - chr5_2:77153115-77153134 Msa0789290:three_prime_UTR 15.0%
!!! TAAATATTTTTTGTGTTACA+GGG - chr5_2:77153116-77153135 Msa0789290:three_prime_UTR 15.0%
!! TTATTACAAGCAAATAAATA+AGG - chr5_2:77153751-77153770 Msa0789290:intron 15.0%
!!! ATAAATATTTTTTGTGTTAC+AGG - chr5_2:77153115-77153134 Msa0789290:three_prime_UTR 15.0%
!!! TAAATATTTTTTGTGTTACA+GGG - chr5_2:77153116-77153135 Msa0789290:three_prime_UTR 15.0%
!! TTATTACAAGCAAATAAATA+AGG - chr5_2:77153751-77153770 Msa0789290:intron 15.0%
!! ATGCATATACAGTTTATATT+TGG - chr5_2:77153227-77153246 Msa0789290:CDS 20.0%
!! ATTAATCAAGAATCTTGTAT+TGG + chr5_2:77153731-77153750 None:intergenic 20.0%
!! ATGCATATACAGTTTATATT+TGG - chr5_2:77153227-77153246 Msa0789290:CDS 20.0%
!! ATTAATCAAGAATCTTGTAT+TGG + chr5_2:77153731-77153750 None:intergenic 20.0%
! TGCATGAATTAATTAATGAG+TGG + chr5_2:77153189-77153208 None:intergenic 25.0%
! AAGTTTACAATTCTTCTTAC+TGG + chr5_2:77153263-77153282 None:intergenic 25.0%
! CATACTTTCATAAACATGTA+AGG + chr5_2:77153462-77153481 None:intergenic 25.0%
! CTTACATGTTTATGAAAGTA+TGG - chr5_2:77153460-77153479 Msa0789290:CDS 25.0%
! TTTGAAAATTGAGATGTTCT+AGG - chr5_2:77153576-77153595 Msa0789290:CDS 25.0%
! TGCATGAATTAATTAATGAG+TGG + chr5_2:77153189-77153208 None:intergenic 25.0%
! AAGTTTACAATTCTTCTTAC+TGG + chr5_2:77153263-77153282 None:intergenic 25.0%
! CATACTTTCATAAACATGTA+AGG + chr5_2:77153462-77153481 None:intergenic 25.0%
! CTTACATGTTTATGAAAGTA+TGG - chr5_2:77153460-77153479 Msa0789290:CDS 25.0%
! TTTGAAAATTGAGATGTTCT+AGG - chr5_2:77153576-77153595 Msa0789290:CDS 25.0%
TGTATCTATTGCAGACATTA+AGG - chr5_2:77153332-77153351 Msa0789290:intron 30.0%
GTATCTATTGCAGACATTAA+GGG - chr5_2:77153333-77153352 Msa0789290:intron 30.0%
TGGATAGTAATCTTGTAGAA+TGG + chr5_2:77153406-77153425 None:intergenic 30.0%
TGGTATTGTCATCAATGAAA+GGG + chr5_2:77153497-77153516 None:intergenic 30.0%
TTGGTATTGTCATCAATGAA+AGG + chr5_2:77153498-77153517 None:intergenic 30.0%
!! TAAAAGTGTTACCTTCTTCT+TGG + chr5_2:77153517-77153536 None:intergenic 30.0%
GAATCTTGTATTGGAACTAA+TGG + chr5_2:77153722-77153741 None:intergenic 30.0%
TGTATCTATTGCAGACATTA+AGG - chr5_2:77153332-77153351 Msa0789290:intron 30.0%
GTATCTATTGCAGACATTAA+GGG - chr5_2:77153333-77153352 Msa0789290:intron 30.0%
TGGATAGTAATCTTGTAGAA+TGG + chr5_2:77153406-77153425 None:intergenic 30.0%
TGGTATTGTCATCAATGAAA+GGG + chr5_2:77153497-77153516 None:intergenic 30.0%
TTGGTATTGTCATCAATGAA+AGG + chr5_2:77153498-77153517 None:intergenic 30.0%
!! TAAAAGTGTTACCTTCTTCT+TGG + chr5_2:77153517-77153536 None:intergenic 30.0%
GAATCTTGTATTGGAACTAA+TGG + chr5_2:77153722-77153741 None:intergenic 30.0%
TTTATCGTTGAGCCATTGTT+TGG + chr5_2:77153100-77153119 None:intergenic 35.0%
TCATAAACATGTAAGGTGCA+TGG + chr5_2:77153455-77153474 None:intergenic 35.0%
TGATGACAATACCAAGAAGA+AGG - chr5_2:77153503-77153522 Msa0789290:CDS 35.0%
TTTATCGTTGAGCCATTGTT+TGG + chr5_2:77153100-77153119 None:intergenic 35.0%
TCATAAACATGTAAGGTGCA+TGG + chr5_2:77153455-77153474 None:intergenic 35.0%
TGATGACAATACCAAGAAGA+AGG - chr5_2:77153503-77153522 Msa0789290:CDS 35.0%
AGCTTACCCAATAATGTGAC+AGG - chr5_2:77153286-77153305 Msa0789290:CDS 40.0%
TGGCATCCTGTCACATTATT+GGG + chr5_2:77153295-77153314 None:intergenic 40.0%
! GATACAAACTTTTCTTCCCC+TGG + chr5_2:77153318-77153337 None:intergenic 40.0%
TATTGCAGACATTAAGGGCT+GGG - chr5_2:77153338-77153357 Msa0789290:intron 40.0%
AGATTACTATCCAGAGAGAC+TGG - chr5_2:77153413-77153432 Msa0789290:intron 40.0%
GATTACTATCCAGAGAGACT+GGG - chr5_2:77153414-77153433 Msa0789290:intron 40.0%
GTTTGCCTCCATATATCTCT+GGG + chr5_2:77153697-77153716 None:intergenic 40.0%
AGTTTGCCTCCATATATCTC+TGG + chr5_2:77153698-77153717 None:intergenic 40.0%
AGCTTACCCAATAATGTGAC+AGG - chr5_2:77153286-77153305 Msa0789290:CDS 40.0%
TGGCATCCTGTCACATTATT+GGG + chr5_2:77153295-77153314 None:intergenic 40.0%
! GATACAAACTTTTCTTCCCC+TGG + chr5_2:77153318-77153337 None:intergenic 40.0%
TATTGCAGACATTAAGGGCT+GGG - chr5_2:77153338-77153357 Msa0789290:intron 40.0%
AGATTACTATCCAGAGAGAC+TGG - chr5_2:77153413-77153432 Msa0789290:intron 40.0%
GATTACTATCCAGAGAGACT+GGG - chr5_2:77153414-77153433 Msa0789290:intron 40.0%
GTTTGCCTCCATATATCTCT+GGG + chr5_2:77153697-77153716 None:intergenic 40.0%
AGTTTGCCTCCATATATCTC+TGG + chr5_2:77153698-77153717 None:intergenic 40.0%
GTGGCATCCTGTCACATTAT+TGG + chr5_2:77153296-77153315 None:intergenic 45.0%
! ACAAACTTTTCTTCCCCTGG+TGG + chr5_2:77153315-77153334 None:intergenic 45.0%
CTATTGCAGACATTAAGGGC+TGG - chr5_2:77153337-77153356 Msa0789290:intron 45.0%
ATTGCAGACATTAAGGGCTG+GGG - chr5_2:77153339-77153358 Msa0789290:intron 45.0%
TATGCAAACAGCGACATTCG+CGG - chr5_2:77153363-77153382 Msa0789290:intron 45.0%
AACAACTTTCCCAGTCTCTC+TGG + chr5_2:77153426-77153445 None:intergenic 45.0%
AGTCAGCTCCCAGAGATATA+TGG - chr5_2:77153686-77153705 Msa0789290:intron 45.0%
GTGGCATCCTGTCACATTAT+TGG + chr5_2:77153296-77153315 None:intergenic 45.0%
! ACAAACTTTTCTTCCCCTGG+TGG + chr5_2:77153315-77153334 None:intergenic 45.0%
CTATTGCAGACATTAAGGGC+TGG - chr5_2:77153337-77153356 Msa0789290:intron 45.0%
ATTGCAGACATTAAGGGCTG+GGG - chr5_2:77153339-77153358 Msa0789290:intron 45.0%
TATGCAAACAGCGACATTCG+CGG - chr5_2:77153363-77153382 Msa0789290:intron 45.0%
AACAACTTTCCCAGTCTCTC+TGG + chr5_2:77153426-77153445 None:intergenic 45.0%
AGTCAGCTCCCAGAGATATA+TGG - chr5_2:77153686-77153705 Msa0789290:intron 45.0%
TAATGTGACAGGATGCCACC+AGG - chr5_2:77153297-77153316 Msa0789290:CDS 50.0%
AATGTGACAGGATGCCACCA+GGG - chr5_2:77153298-77153317 Msa0789290:CDS 50.0%
!! GTAGAATGGTTAGAGCACCG+AGG + chr5_2:77153392-77153411 None:intergenic 50.0%
CAGCTCCCAGAGATATATGG+AGG - chr5_2:77153689-77153708 Msa0789290:intron 50.0%
TAATGTGACAGGATGCCACC+AGG - chr5_2:77153297-77153316 Msa0789290:CDS 50.0%
AATGTGACAGGATGCCACCA+GGG - chr5_2:77153298-77153317 Msa0789290:CDS 50.0%
!! GTAGAATGGTTAGAGCACCG+AGG + chr5_2:77153392-77153411 None:intergenic 50.0%
CAGCTCCCAGAGATATATGG+AGG - chr5_2:77153689-77153708 Msa0789290:intron 50.0%
ATGTGACAGGATGCCACCAG+GGG - chr5_2:77153299-77153318 Msa0789290:CDS 55.0%
AGCGACATTCGCGGTTACCT+CGG - chr5_2:77153372-77153391 Msa0789290:intron 55.0%
ATGTGACAGGATGCCACCAG+GGG - chr5_2:77153299-77153318 Msa0789290:CDS 55.0%
AGCGACATTCGCGGTTACCT+CGG - chr5_2:77153372-77153391 Msa0789290:intron 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 77153097 77153856 77153097 ID=Msa0789290;Name=Msa0789290
chr5_2 mRNA 77153097 77153856 77153097 ID=Msa0789290-mRNA-1;Parent=Msa0789290;Name=Msa0789290-mRNA-1;_AED=0.38;_eAED=0.38;_QI=78|1|1|1|0.5|0.66|3|111|110
chr5_2 exon 77153097 77153324 77153097 ID=Msa0789290-mRNA-1:exon:23488;Parent=Msa0789290-mRNA-1
chr5_2 exon 77153429 77153645 77153429 ID=Msa0789290-mRNA-1:exon:23487;Parent=Msa0789290-mRNA-1
chr5_2 exon 77153780 77153856 77153780 ID=Msa0789290-mRNA-1:exon:23486;Parent=Msa0789290-mRNA-1
chr5_2 five_prime_UTR 77153780 77153856 77153780 ID=Msa0789290-mRNA-1:five_prime_utr;Parent=Msa0789290-mRNA-1
chr5_2 five_prime_UTR 77153645 77153645 77153645 ID=Msa0789290-mRNA-1:five_prime_utr;Parent=Msa0789290-mRNA-1
chr5_2 CDS 77153429 77153644 77153429 ID=Msa0789290-mRNA-1:cds;Parent=Msa0789290-mRNA-1
chr5_2 CDS 77153208 77153324 77153208 ID=Msa0789290-mRNA-1:cds;Parent=Msa0789290-mRNA-1
chr5_2 three_prime_UTR 77153097 77153207 77153097 ID=Msa0789290-mRNA-1:three_prime_utr;Parent=Msa0789290-mRNA-1
Gene Sequence

>Msa0789290

ATGCCACCAGGGGAAGAAAAGTTTGTATCTATTGCAGACATTAAGGGCTGGGGATATGCAAACAGCGACATTCGCGGTTACCTCGGTGCTCTAACCATTCTACAAGATTACTATCCAGAGAGACTGGGAAAGTTGTTCATAGTCCATGCACCTTACATGTTTATGAAAGTATGGAAAATTATTTACCCTTTCATTGATGACAATACCAAGAAGAAGATAGTATTTGTTGAGAACAAGAAGCTGAAAGCAACATTGCTTGAAGAGATTGATGAGAGTCAGCTCCCAGAGATATATGGAGGCAAACTTCCATTAGTTCCAATACAAGATTCTTGA

Protein sequence

>Msa0789290

MPPGEEKFVSIADIKGWGYANSDIRGYLGALTILQDYYPERLGKLFIVHAPYMFMKVWKIIYPFIDDNTKKKIVFVENKKLKATLLEEIDESQLPEIYGGKLPLVPIQDS*