AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1354920


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1354920 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1354920 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1354920 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1354920 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1354920 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1354920 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1354920 MtrunA17_Chr6g0460191 74.468 94 24 0 154 247 8 101 1.73e-28 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1354920 ATCG00150.1 91.165 249 20 1 1 247 1 249 1.75e-151 422

Find 45 sgRNAs with CRISPR-Local

Find 57 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTATACCTGTTATGTTTC+TGG 0.052609 tig0014543:-587965 Msa1354920:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 tig0014543:-588531 Msa1354920:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 tig0014543:-588530 Msa1354920:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 tig0014543:+588091 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 tig0014543:-588327 Msa1354920:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 tig0014543:+588161 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 tig0014543:-587964 Msa1354920:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 tig0014543:-588491 Msa1354920:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 tig0014543:+588440 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 tig0014543:+588084 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 tig0014543:-587904 Msa1354920:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 tig0014543:+588212 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 tig0014543:-588490 Msa1354920:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 tig0014543:+588213 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 tig0014543:+588053 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 tig0014543:+588315 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 tig0014543:-588348 Msa1354920:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 tig0014543:+587958 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 tig0014543:+587964 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 tig0014543:+588420 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 tig0014543:-588539 Msa1354920:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 tig0014543:-587893 Msa1354920:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 tig0014543:+588376 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 tig0014543:+588102 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 tig0014543:-588555 Msa1354920:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 tig0014543:+588054 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 tig0014543:-588360 Msa1354920:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 tig0014543:+588106 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 tig0014543:-588249 Msa1354920:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 tig0014543:+587903 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 tig0014543:+588096 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 tig0014543:-588420 Msa1354920:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 tig0014543:+588408 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 tig0014543:-588168 Msa1354920:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 tig0014543:-588529 Msa1354920:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 tig0014543:+587976 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 tig0014543:-587889 Msa1354920:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 tig0014543:-588340 Msa1354920:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 tig0014543:-588341 Msa1354920:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 tig0014543:-587949 Msa1354920:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 tig0014543:+588401 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 tig0014543:+588324 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 tig0014543:-588169 Msa1354920:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 tig0014543:+588476 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 tig0014543:+588234 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - tig0014543:588186-588205 Msa1354920:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - tig0014543:588230-588249 Msa1354920:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + tig0014543:588269-588288 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + tig0014543:588270-588289 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + tig0014543:588398-588417 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - tig0014543:587949-587968 Msa1354920:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + tig0014543:588081-588100 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + tig0014543:588167-588186 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + tig0014543:588227-588246 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - tig0014543:588341-588360 Msa1354920:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - tig0014543:587940-587959 Msa1354920:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - tig0014543:587948-587967 Msa1354920:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - tig0014543:587950-587969 Msa1354920:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - tig0014543:587989-588008 Msa1354920:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - tig0014543:588191-588210 Msa1354920:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - tig0014543:588192-588211 Msa1354920:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - tig0014543:588326-588345 Msa1354920:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - tig0014543:588331-588350 Msa1354920:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + tig0014543:588386-588405 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + tig0014543:588391-588410 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + tig0014543:588428-588447 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + tig0014543:588429-588448 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - tig0014543:588431-588450 Msa1354920:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + tig0014543:588524-588543 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - tig0014543:588530-588549 Msa1354920:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - tig0014543:588590-588609 Msa1354920:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - tig0014543:587988-588007 Msa1354920:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + tig0014543:588042-588061 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - tig0014543:588131-588150 Msa1354920:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - tig0014543:588193-588212 Msa1354920:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + tig0014543:588321-588340 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + tig0014543:588506-588525 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - tig0014543:588514-588533 Msa1354920:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - tig0014543:588515-588534 Msa1354920:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - tig0014543:588565-588584 Msa1354920:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - tig0014543:588586-588605 Msa1354920:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - tig0014543:587924-587943 Msa1354920:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + tig0014543:588006-588025 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - tig0014543:588310-588329 Msa1354920:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - tig0014543:588311-588330 Msa1354920:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + tig0014543:588376-588395 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + tig0014543:588380-588399 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + tig0014543:588518-588537 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + tig0014543:588074-588093 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + tig0014543:588106-588125 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + tig0014543:588118-588137 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - tig0014543:588119-588138 Msa1354920:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - tig0014543:588138-588157 Msa1354920:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - tig0014543:588139-588158 Msa1354920:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + tig0014543:588158-588177 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - tig0014543:588575-588594 Msa1354920:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + tig0014543:588579-588598 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + tig0014543:588062-588081 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - tig0014543:588059-588078 Msa1354920:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + tig0014543:588248-588267 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - tig0014543:588152-588171 Msa1354920:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - tig0014543:588207-588226 Msa1354920:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 587879 588622 587879 ID=Msa1354920;Name=Msa1354920
tig0014543 mRNA 587879 588622 587879 ID=Msa1354920-mRNA-1;Parent=Msa1354920;Name=Msa1354920-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
tig0014543 exon 587879 588622 587879 ID=Msa1354920-mRNA-1:exon:9292;Parent=Msa1354920-mRNA-1
tig0014543 CDS 587879 588622 587879 ID=Msa1354920-mRNA-1:cds;Parent=Msa1354920-mRNA-1
Gene Sequence

>Msa1354920

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1354920

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*