AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086090 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086090 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086090 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086090 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1086090 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1086090 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1086090 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
Msa1086090 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:-87118330 Msa1086090:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 7_2:-87118896 Msa1086090:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 7_2:-87118895 Msa1086090:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 7_2:+87118456 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 7_2:-87118692 Msa1086090:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 7_2:+87118526 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 7_2:-87118329 Msa1086090:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 7_2:-87118856 Msa1086090:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 7_2:+87118805 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 7_2:+87118449 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 7_2:-87118269 Msa1086090:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 7_2:+87118577 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 7_2:-87118855 Msa1086090:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 7_2:+87118578 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 7_2:+87118418 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 7_2:+87118680 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 7_2:-87118713 Msa1086090:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 7_2:+87118323 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 7_2:+87118329 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 7_2:+87118785 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 7_2:-87118904 Msa1086090:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 7_2:-87118258 Msa1086090:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 7_2:+87118741 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 7_2:+87118467 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 7_2:-87118920 Msa1086090:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 7_2:+87118419 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 7_2:-87118725 Msa1086090:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 7_2:+87118471 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 7_2:-87118614 Msa1086090:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 7_2:+87118268 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 7_2:+87118461 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 7_2:-87118785 Msa1086090:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 7_2:+87118773 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 7_2:-87118533 Msa1086090:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 7_2:-87118894 Msa1086090:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 7_2:+87118341 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 7_2:-87118254 Msa1086090:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 7_2:-87118705 Msa1086090:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 7_2:-87118706 Msa1086090:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 7_2:-87118314 Msa1086090:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 7_2:+87118766 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 7_2:+87118689 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 7_2:-87118534 Msa1086090:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 7_2:+87118841 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 7_2:+87118599 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr7_2:87118551-87118570 Msa1086090:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr7_2:87118595-87118614 Msa1086090:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr7_2:87118634-87118653 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr7_2:87118635-87118654 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr7_2:87118763-87118782 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr7_2:87118314-87118333 Msa1086090:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr7_2:87118446-87118465 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr7_2:87118532-87118551 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr7_2:87118592-87118611 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr7_2:87118706-87118725 Msa1086090:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr7_2:87118305-87118324 Msa1086090:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr7_2:87118313-87118332 Msa1086090:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr7_2:87118315-87118334 Msa1086090:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr7_2:87118354-87118373 Msa1086090:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr7_2:87118556-87118575 Msa1086090:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr7_2:87118557-87118576 Msa1086090:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr7_2:87118691-87118710 Msa1086090:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr7_2:87118696-87118715 Msa1086090:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr7_2:87118751-87118770 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr7_2:87118756-87118775 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr7_2:87118793-87118812 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr7_2:87118794-87118813 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr7_2:87118796-87118815 Msa1086090:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr7_2:87118889-87118908 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr7_2:87118895-87118914 Msa1086090:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr7_2:87118955-87118974 Msa1086090:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr7_2:87118353-87118372 Msa1086090:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr7_2:87118407-87118426 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr7_2:87118496-87118515 Msa1086090:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr7_2:87118558-87118577 Msa1086090:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr7_2:87118686-87118705 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr7_2:87118871-87118890 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr7_2:87118879-87118898 Msa1086090:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr7_2:87118880-87118899 Msa1086090:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr7_2:87118930-87118949 Msa1086090:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr7_2:87118951-87118970 Msa1086090:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr7_2:87118289-87118308 Msa1086090:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr7_2:87118371-87118390 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr7_2:87118675-87118694 Msa1086090:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr7_2:87118676-87118695 Msa1086090:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr7_2:87118741-87118760 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr7_2:87118745-87118764 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr7_2:87118883-87118902 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr7_2:87118439-87118458 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr7_2:87118471-87118490 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr7_2:87118483-87118502 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr7_2:87118484-87118503 Msa1086090:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr7_2:87118503-87118522 Msa1086090:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr7_2:87118504-87118523 Msa1086090:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr7_2:87118523-87118542 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr7_2:87118940-87118959 Msa1086090:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr7_2:87118944-87118963 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr7_2:87118427-87118446 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr7_2:87118424-87118443 Msa1086090:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr7_2:87118613-87118632 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr7_2:87118517-87118536 Msa1086090:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr7_2:87118572-87118591 Msa1086090:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87118244 87118987 87118244 ID=Msa1086090;Name=Msa1086090
chr7_2 mRNA 87118244 87118987 87118244 ID=Msa1086090-mRNA-1;Parent=Msa1086090;Name=Msa1086090-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr7_2 exon 87118244 87118987 87118244 ID=Msa1086090-mRNA-1:exon:23696;Parent=Msa1086090-mRNA-1
chr7_2 CDS 87118244 87118987 87118244 ID=Msa1086090-mRNA-1:cds;Parent=Msa1086090-mRNA-1
Gene Sequence

>Msa1086090

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1086090

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*