AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086200 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086200 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086200 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1086200 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1086200 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1086200 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1086200 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
Msa1086200 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:-87230332 Msa1086200:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 7_2:-87230898 Msa1086200:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 7_2:-87230897 Msa1086200:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 7_2:+87230458 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 7_2:-87230694 Msa1086200:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 7_2:+87230528 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 7_2:-87230331 Msa1086200:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 7_2:-87230858 Msa1086200:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 7_2:+87230807 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 7_2:+87230451 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 7_2:-87230271 Msa1086200:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 7_2:+87230579 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 7_2:-87230857 Msa1086200:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 7_2:+87230580 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 7_2:+87230420 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 7_2:+87230682 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 7_2:-87230715 Msa1086200:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 7_2:+87230325 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 7_2:+87230331 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 7_2:+87230787 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 7_2:-87230906 Msa1086200:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 7_2:-87230260 Msa1086200:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 7_2:+87230743 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 7_2:+87230469 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 7_2:-87230922 Msa1086200:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 7_2:+87230421 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 7_2:-87230727 Msa1086200:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 7_2:+87230473 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 7_2:-87230616 Msa1086200:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 7_2:+87230270 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 7_2:+87230463 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 7_2:-87230787 Msa1086200:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 7_2:+87230775 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 7_2:-87230535 Msa1086200:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 7_2:-87230896 Msa1086200:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 7_2:+87230343 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 7_2:-87230256 Msa1086200:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 7_2:-87230707 Msa1086200:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 7_2:-87230708 Msa1086200:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 7_2:-87230316 Msa1086200:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 7_2:+87230768 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 7_2:+87230691 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 7_2:-87230536 Msa1086200:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 7_2:+87230843 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 7_2:+87230601 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - chr7_2:87230553-87230572 Msa1086200:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - chr7_2:87230597-87230616 Msa1086200:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + chr7_2:87230636-87230655 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + chr7_2:87230637-87230656 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + chr7_2:87230765-87230784 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - chr7_2:87230316-87230335 Msa1086200:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + chr7_2:87230448-87230467 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + chr7_2:87230534-87230553 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + chr7_2:87230594-87230613 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - chr7_2:87230708-87230727 Msa1086200:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - chr7_2:87230307-87230326 Msa1086200:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - chr7_2:87230315-87230334 Msa1086200:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - chr7_2:87230317-87230336 Msa1086200:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - chr7_2:87230356-87230375 Msa1086200:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - chr7_2:87230558-87230577 Msa1086200:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - chr7_2:87230559-87230578 Msa1086200:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - chr7_2:87230693-87230712 Msa1086200:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - chr7_2:87230698-87230717 Msa1086200:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + chr7_2:87230753-87230772 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + chr7_2:87230758-87230777 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + chr7_2:87230795-87230814 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + chr7_2:87230796-87230815 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - chr7_2:87230798-87230817 Msa1086200:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + chr7_2:87230891-87230910 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - chr7_2:87230897-87230916 Msa1086200:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - chr7_2:87230957-87230976 Msa1086200:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - chr7_2:87230355-87230374 Msa1086200:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + chr7_2:87230409-87230428 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - chr7_2:87230498-87230517 Msa1086200:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - chr7_2:87230560-87230579 Msa1086200:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + chr7_2:87230688-87230707 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + chr7_2:87230873-87230892 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - chr7_2:87230881-87230900 Msa1086200:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - chr7_2:87230882-87230901 Msa1086200:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - chr7_2:87230932-87230951 Msa1086200:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - chr7_2:87230953-87230972 Msa1086200:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - chr7_2:87230291-87230310 Msa1086200:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + chr7_2:87230373-87230392 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - chr7_2:87230677-87230696 Msa1086200:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - chr7_2:87230678-87230697 Msa1086200:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + chr7_2:87230743-87230762 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + chr7_2:87230747-87230766 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + chr7_2:87230885-87230904 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + chr7_2:87230441-87230460 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + chr7_2:87230473-87230492 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + chr7_2:87230485-87230504 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - chr7_2:87230486-87230505 Msa1086200:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - chr7_2:87230505-87230524 Msa1086200:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - chr7_2:87230506-87230525 Msa1086200:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + chr7_2:87230525-87230544 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - chr7_2:87230942-87230961 Msa1086200:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + chr7_2:87230946-87230965 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + chr7_2:87230429-87230448 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - chr7_2:87230426-87230445 Msa1086200:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + chr7_2:87230615-87230634 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - chr7_2:87230519-87230538 Msa1086200:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - chr7_2:87230574-87230593 Msa1086200:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87230246 87230989 87230246 ID=Msa1086200;Name=Msa1086200
chr7_2 mRNA 87230246 87230989 87230246 ID=Msa1086200-mRNA-1;Parent=Msa1086200;Name=Msa1086200-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
chr7_2 exon 87230246 87230989 87230246 ID=Msa1086200-mRNA-1:exon:23728;Parent=Msa1086200-mRNA-1
chr7_2 CDS 87230246 87230989 87230246 ID=Msa1086200-mRNA-1:cds;Parent=Msa1086200-mRNA-1
Gene Sequence

>Msa1086200

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1086200

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*