AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086900


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086900 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086900 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086900 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086900 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1086900 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1086900 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1086900 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
Msa1086900 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 7_2:-87611027 Msa1086900:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 7_2:-87611593 Msa1086900:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 7_2:-87611592 Msa1086900:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 7_2:+87611153 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 7_2:-87611389 Msa1086900:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 7_2:+87611223 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 7_2:-87611026 Msa1086900:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 7_2:-87611553 Msa1086900:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 7_2:+87611502 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 7_2:+87611146 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 7_2:-87610966 Msa1086900:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 7_2:+87611274 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 7_2:-87611552 Msa1086900:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 7_2:+87611275 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 7_2:+87611115 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 7_2:+87611377 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 7_2:-87611410 Msa1086900:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 7_2:+87611020 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 7_2:+87611026 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 7_2:+87611482 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 7_2:-87611601 Msa1086900:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 7_2:-87610955 Msa1086900:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 7_2:+87611438 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 7_2:+87611164 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 7_2:-87611617 Msa1086900:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 7_2:+87611116 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 7_2:-87611422 Msa1086900:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 7_2:+87611168 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 7_2:-87611311 Msa1086900:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 7_2:+87610965 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 7_2:+87611158 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 7_2:-87611482 Msa1086900:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 7_2:+87611470 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 7_2:-87611230 Msa1086900:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 7_2:-87611591 Msa1086900:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 7_2:+87611038 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 7_2:-87610951 Msa1086900:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 7_2:-87611402 Msa1086900:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 7_2:-87611403 Msa1086900:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 7_2:-87611011 Msa1086900:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 7_2:+87611463 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 7_2:+87611386 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 7_2:-87611231 Msa1086900:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 7_2:+87611538 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 7_2:+87611296 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr7_2:87611248-87611267 Msa1086900:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr7_2:87611292-87611311 Msa1086900:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr7_2:87611331-87611350 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr7_2:87611332-87611351 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr7_2:87611460-87611479 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr7_2:87611011-87611030 Msa1086900:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr7_2:87611143-87611162 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr7_2:87611229-87611248 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr7_2:87611289-87611308 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr7_2:87611403-87611422 Msa1086900:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr7_2:87611002-87611021 Msa1086900:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr7_2:87611010-87611029 Msa1086900:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr7_2:87611012-87611031 Msa1086900:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr7_2:87611051-87611070 Msa1086900:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr7_2:87611253-87611272 Msa1086900:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr7_2:87611254-87611273 Msa1086900:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr7_2:87611388-87611407 Msa1086900:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr7_2:87611393-87611412 Msa1086900:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr7_2:87611448-87611467 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr7_2:87611453-87611472 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr7_2:87611490-87611509 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr7_2:87611491-87611510 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr7_2:87611493-87611512 Msa1086900:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr7_2:87611586-87611605 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr7_2:87611592-87611611 Msa1086900:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr7_2:87611652-87611671 Msa1086900:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr7_2:87611050-87611069 Msa1086900:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr7_2:87611104-87611123 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr7_2:87611193-87611212 Msa1086900:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr7_2:87611255-87611274 Msa1086900:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr7_2:87611383-87611402 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr7_2:87611568-87611587 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr7_2:87611576-87611595 Msa1086900:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr7_2:87611577-87611596 Msa1086900:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr7_2:87611627-87611646 Msa1086900:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr7_2:87611648-87611667 Msa1086900:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr7_2:87610986-87611005 Msa1086900:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr7_2:87611068-87611087 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr7_2:87611372-87611391 Msa1086900:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr7_2:87611373-87611392 Msa1086900:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr7_2:87611438-87611457 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr7_2:87611442-87611461 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr7_2:87611580-87611599 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr7_2:87611136-87611155 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr7_2:87611168-87611187 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr7_2:87611180-87611199 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr7_2:87611181-87611200 Msa1086900:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr7_2:87611200-87611219 Msa1086900:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr7_2:87611201-87611220 Msa1086900:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr7_2:87611220-87611239 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr7_2:87611637-87611656 Msa1086900:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr7_2:87611641-87611660 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr7_2:87611124-87611143 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr7_2:87611121-87611140 Msa1086900:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr7_2:87611310-87611329 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr7_2:87611214-87611233 Msa1086900:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr7_2:87611269-87611288 Msa1086900:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87610941 87611684 87610941 ID=Msa1086900;Name=Msa1086900
chr7_2 mRNA 87610941 87611684 87610941 ID=Msa1086900-mRNA-1;Parent=Msa1086900;Name=Msa1086900-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr7_2 exon 87610941 87611684 87610941 ID=Msa1086900-mRNA-1:exon:23930;Parent=Msa1086900-mRNA-1
chr7_2 CDS 87610941 87611684 87610941 ID=Msa1086900-mRNA-1:cds;Parent=Msa1086900-mRNA-1
Gene Sequence

>Msa1086900

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1086900

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*