AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1355090


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1355090 MtrunA17_Chr4g0016701 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1355090 MtrunA17_CPg0492981 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1355090 MtrunA17_Chr4g0015611 98.785 247 1 1 1 247 1 245 1.77e-175 482
Msa1355090 MtrunA17_Chr3g0088491 92.661 218 11 1 30 247 2 214 1.10e-129 365
Msa1355090 MtrunA17_Chr7g0275151 73.494 166 11 1 82 247 2 134 1.65e-76 228
Msa1355090 MtrunA17_Chr4g0060751 67.273 165 8 1 83 247 11 129 1.10e-64 197
Msa1355090 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
Msa1355090 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:-713471 Msa1355090:CDS
CAACATTTCTATTGGCAAAT+AGG 0.196864 tig0014543:-714037 Msa1355090:CDS
AACATTTCTATTGGCAAATA+GGG 0.237546 tig0014543:-714036 Msa1355090:CDS
CTAAGATGTTAATCGGTAAA+AGG 0.238850 tig0014543:+713597 None:intergenic
GGTCCGTGGGTTCCGTTTAT+TGG 0.248543 tig0014543:-713833 Msa1355090:CDS
TGAAATACCCGCATAGAAAT+AGG 0.255569 tig0014543:+713667 None:intergenic
CCTATACCTGTTATGTTTCT+GGG 0.293135 tig0014543:-713470 Msa1355090:CDS
CTCAAGTACTTATTACCTCT+TGG 0.341108 tig0014543:-713997 Msa1355090:CDS
CGGATTTCTAACAACTAGAA+TGG 0.400438 tig0014543:+713946 None:intergenic
AAATCTTCTAAGATGTTAAT+CGG 0.412258 tig0014543:+713590 None:intergenic
ACCTTAGCTGCGGCTTATAT+AGG 0.418344 tig0014543:-713410 Msa1355090:CDS
AGTAGTATTTATATCATTTG+TGG 0.424401 tig0014543:+713718 None:intergenic
TCAAGTACTTATTACCTCTT+GGG 0.428139 tig0014543:-713996 Msa1355090:CDS
GTAGTATTTATATCATTTGT+GGG 0.434707 tig0014543:+713719 None:intergenic
AAGTCGAAAACTAAGTGATA+AGG 0.438506 tig0014543:+713559 None:intergenic
AGAAACAAAGTTCCAATAAA+CGG 0.439134 tig0014543:+713821 None:intergenic
ACTCAGATTGGAGAAGAATA+TGG 0.441550 tig0014543:-713854 Msa1355090:CDS
AATAATCCCAGAAACATAAC+AGG 0.443207 tig0014543:+713464 None:intergenic
CCCAGAAACATAACAGGTAT+AGG 0.450475 tig0014543:+713470 None:intergenic
CCGGACGTTGGAATAGTTTG+CGG 0.455395 tig0014543:+713926 None:intergenic
AAGTAGGTCAACATTTCTAT+TGG 0.460455 tig0014543:-714045 Msa1355090:CDS
GGCTTATATAGGTGAATCTA+TGG 0.463562 tig0014543:-713399 Msa1355090:CDS
TCACGTCTCGGATGAATTCA+AGG 0.477047 tig0014543:+713882 None:intergenic
ATCGGTAAAAGGATTGGAGT+TGG 0.490463 tig0014543:+713608 None:intergenic
GATATATCTGCTGTCGAAGT+AGG 0.493921 tig0014543:-714061 Msa1355090:CDS
AGTCGAAAACTAAGTGATAA+GGG 0.500280 tig0014543:+713560 None:intergenic
GACGTGAGCAAAACTCAGAT+TGG 0.510359 tig0014543:-713866 Msa1355090:CDS
GTAAAAGGATTGGAGTTGGT+TGG 0.515104 tig0014543:+713612 None:intergenic
AAAATTATAAAGTTACCTCA+TGG 0.526541 tig0014543:-713755 Msa1355090:CDS
ACCTATATAAGCCGCAGCTA+AGG 0.529655 tig0014543:+713409 None:intergenic
ATGTTAATCGGTAAAAGGAT+TGG 0.530907 tig0014543:+713602 None:intergenic
CCGCAAACTATTCCAACGTC+CGG 0.541897 tig0014543:-713926 Msa1355090:CDS
AAGAAATTCTGACCGGACGT+TGG 0.546490 tig0014543:+713914 None:intergenic
TCAGTAGCCTATTTCTATGC+GGG 0.553188 tig0014543:-713674 Msa1355090:CDS
ACATTTCTATTGGCAAATAG+GGG 0.561596 tig0014543:-714035 Msa1355090:CDS
ACAGGTATAGGAACTACTAA+AGG 0.585481 tig0014543:+713482 None:intergenic
TATATAGGTGAATCTATGGA+AGG 0.605539 tig0014543:-713395 Msa1355090:CDS
TGGAGAAGAATATGGTCCGT+GGG 0.620080 tig0014543:-713846 Msa1355090:CDS
TTGGAGAAGAATATGGTCCG+TGG 0.620994 tig0014543:-713847 Msa1355090:CDS
TTTCTGGGATTATTTACAAG+CGG 0.630473 tig0014543:-713455 Msa1355090:CDS
ATATTCAAAGAAATTCTGAC+CGG 0.632509 tig0014543:+713907 None:intergenic
GTTCCAATAAACGGAACCCA+CGG 0.647484 tig0014543:+713830 None:intergenic
GTCAGTAGCCTATTTCTATG+CGG 0.655321 tig0014543:-713675 Msa1355090:CDS
GATAGCAATTACAACCCAAG+AGG 0.659110 tig0014543:+713982 None:intergenic
GGTGCAGCTAATTCTCCATG+AGG 0.714976 tig0014543:+713740 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATTTATTTTTGTTTCGAAT+TGG - tig0014543:713692-713711 Msa1355090:CDS 15.0%
!! AAAATTATAAAGTTACCTCA+TGG - tig0014543:713736-713755 Msa1355090:CDS 20.0%
!! GTAGTATTTATATCATTTGT+GGG + tig0014543:713775-713794 None:intergenic 20.0%
!! AGTAGTATTTATATCATTTG+TGG + tig0014543:713776-713795 None:intergenic 20.0%
!!! AAATCTTCTAAGATGTTAAT+CGG + tig0014543:713904-713923 None:intergenic 20.0%
! AACATTTCTATTGGCAAATA+GGG - tig0014543:713455-713474 Msa1355090:CDS 25.0%
! ATATTCAAAGAAATTCTGAC+CGG + tig0014543:713587-713606 None:intergenic 25.0%
! AGAAACAAAGTTCCAATAAA+CGG + tig0014543:713673-713692 None:intergenic 25.0%
!! GGTAACTTTATAATTTTCCA+AGG + tig0014543:713733-713752 None:intergenic 25.0%
!!! AAAAAAGGATTGGCTTATTT+TGG - tig0014543:713847-713866 Msa1355090:CDS 25.0%
AAGTAGGTCAACATTTCTAT+TGG - tig0014543:713446-713465 Msa1355090:CDS 30.0%
CAACATTTCTATTGGCAAAT+AGG - tig0014543:713454-713473 Msa1355090:CDS 30.0%
ACATTTCTATTGGCAAATAG+GGG - tig0014543:713456-713475 Msa1355090:CDS 30.0%
TCAAGTACTTATTACCTCTT+GGG - tig0014543:713495-713514 Msa1355090:CDS 30.0%
!! ATTTTTGTTTCGAATTGGTC+AGG - tig0014543:713697-713716 Msa1355090:CDS 30.0%
!! TTTTTGTTTCGAATTGGTCA+GGG - tig0014543:713698-713717 Msa1355090:CDS 30.0%
TATGCGGGTATTTCAAAAAA+AGG - tig0014543:713832-713851 Msa1355090:CDS 30.0%
GGGTATTTCAAAAAAAGGAT+TGG - tig0014543:713837-713856 Msa1355090:CDS 30.0%
ATGTTAATCGGTAAAAGGAT+TGG + tig0014543:713892-713911 None:intergenic 30.0%
CTAAGATGTTAATCGGTAAA+AGG + tig0014543:713897-713916 None:intergenic 30.0%
AGTCGAAAACTAAGTGATAA+GGG + tig0014543:713934-713953 None:intergenic 30.0%
AAGTCGAAAACTAAGTGATA+AGG + tig0014543:713935-713954 None:intergenic 30.0%
!! TCACTTAGTTTTCGACTTTT+CGG - tig0014543:713937-713956 Msa1355090:CDS 30.0%
AATAATCCCAGAAACATAAC+AGG + tig0014543:714030-714049 None:intergenic 30.0%
!! TTTCTGGGATTATTTACAAG+CGG - tig0014543:714036-714055 Msa1355090:CDS 30.0%
TATATAGGTGAATCTATGGA+AGG - tig0014543:714096-714115 Msa1355090:CDS 30.0%
CTCAAGTACTTATTACCTCT+TGG - tig0014543:713494-713513 Msa1355090:CDS 35.0%
CGGATTTCTAACAACTAGAA+TGG + tig0014543:713548-713567 None:intergenic 35.0%
ACTCAGATTGGAGAAGAATA+TGG - tig0014543:713637-713656 Msa1355090:CDS 35.0%
!! TTTTGTTTCGAATTGGTCAG+GGG - tig0014543:713699-713718 Msa1355090:CDS 35.0%
TGAAATACCCGCATAGAAAT+AGG + tig0014543:713827-713846 None:intergenic 35.0%
ACAGGTATAGGAACTACTAA+AGG + tig0014543:714012-714031 None:intergenic 35.0%
TCCTATACCTGTTATGTTTC+TGG - tig0014543:714020-714039 Msa1355090:CDS 35.0%
CCTATACCTGTTATGTTTCT+GGG - tig0014543:714021-714040 Msa1355090:CDS 35.0%
!! TATTTTTGCTACCTTAGCTG+CGG - tig0014543:714071-714090 Msa1355090:CDS 35.0%
GGCTTATATAGGTGAATCTA+TGG - tig0014543:714092-714111 Msa1355090:CDS 35.0%
GATATATCTGCTGTCGAAGT+AGG - tig0014543:713430-713449 Msa1355090:CDS 40.0%
GATAGCAATTACAACCCAAG+AGG + tig0014543:713512-713531 None:intergenic 40.0%
!! GTCAGTAGCCTATTTCTATG+CGG - tig0014543:713816-713835 Msa1355090:CDS 40.0%
!! TCAGTAGCCTATTTCTATGC+GGG - tig0014543:713817-713836 Msa1355090:CDS 40.0%
! GTAAAAGGATTGGAGTTGGT+TGG + tig0014543:713882-713901 None:intergenic 40.0%
ATCGGTAAAAGGATTGGAGT+TGG + tig0014543:713886-713905 None:intergenic 40.0%
CCCAGAAACATAACAGGTAT+AGG + tig0014543:714024-714043 None:intergenic 40.0%
AAGAAATTCTGACCGGACGT+TGG + tig0014543:713580-713599 None:intergenic 45.0%
TCACGTCTCGGATGAATTCA+AGG + tig0014543:713612-713631 None:intergenic 45.0%
! TCTGAGTTTTGCTCACGTCT+CGG + tig0014543:713624-713643 None:intergenic 45.0%
GACGTGAGCAAAACTCAGAT+TGG - tig0014543:713625-713644 Msa1355090:CDS 45.0%
TTGGAGAAGAATATGGTCCG+TGG - tig0014543:713644-713663 Msa1355090:CDS 45.0%
TGGAGAAGAATATGGTCCGT+GGG - tig0014543:713645-713664 Msa1355090:CDS 45.0%
GTTCCAATAAACGGAACCCA+CGG + tig0014543:713664-713683 None:intergenic 45.0%
ACCTTAGCTGCGGCTTATAT+AGG - tig0014543:714081-714100 Msa1355090:CDS 45.0%
ACCTATATAAGCCGCAGCTA+AGG + tig0014543:714085-714104 None:intergenic 45.0%
CCGGACGTTGGAATAGTTTG+CGG + tig0014543:713568-713587 None:intergenic 50.0%
CCGCAAACTATTCCAACGTC+CGG - tig0014543:713565-713584 Msa1355090:CDS 50.0%
GGTGCAGCTAATTCTCCATG+AGG + tig0014543:713754-713773 None:intergenic 50.0%
GGTCCGTGGGTTCCGTTTAT+TGG - tig0014543:713658-713677 Msa1355090:CDS 55.0%
! GGTCAGGGGCTCTTTTGCCT+TGG - tig0014543:713713-713732 Msa1355090:CDS 60.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 713385 714128 713385 ID=Msa1355090;Name=Msa1355090
tig0014543 mRNA 713385 714128 713385 ID=Msa1355090-mRNA-1;Parent=Msa1355090;Name=Msa1355090-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|247
tig0014543 exon 713385 714128 713385 ID=Msa1355090-mRNA-1:exon:9291;Parent=Msa1355090-mRNA-1
tig0014543 CDS 713385 714128 713385 ID=Msa1355090-mRNA-1:cds;Parent=Msa1355090-mRNA-1
Gene Sequence

>Msa1355090

ATGAATGTTCTATTATGTTACATCAACACATTAAACAGATTCTATGATATATCTGCTGTCGAAGTAGGTCAACATTTCTATTGGCAAATAGGGGATTTTCAAGTGCATGCTCAAGTACTTATTACCTCTTGGGTTGTAATTGCTATCTTATTAATTTCAACCATTCTAGTTGTTAGAAATCCGCAAACTATTCCAACGTCCGGTCAGAATTTCTTTGAATATGTCCTTGAATTCATCCGAGACGTGAGCAAAACTCAGATTGGAGAAGAATATGGTCCGTGGGTTCCGTTTATTGGAACTTTGTTTCTATTTATTTTTGTTTCGAATTGGTCAGGGGCTCTTTTGCCTTGGAAAATTATAAAGTTACCTCATGGAGAATTAGCTGCACCCACAAATGATATAAATACTACTGTTGCATTAGCTTTACTTACGTCAGTAGCCTATTTCTATGCGGGTATTTCAAAAAAAGGATTGGCTTATTTTGGTAAATACATCCAACCAACTCCAATCCTTTTACCGATTAACATCTTAGAAGATTTCACAAAACCCTTATCACTTAGTTTTCGACTTTTCGGAAATATATTAGCTGATGAATTAGTAGTTGTTGTTCTTGTTTCGTTAGTACCTTTAGTAGTTCCTATACCTGTTATGTTTCTGGGATTATTTACAAGCGGTATTCAAGCTCTTATTTTTGCTACCTTAGCTGCGGCTTATATAGGTGAATCTATGGAAGGCCATCATTGA

Protein sequence

>Msa1355090

MNVLLCYINTLNRFYDISAVEVGQHFYWQIGDFQVHAQVLITSWVVIAILLISTILVVRNPQTIPTSGQNFFEYVLEFIRDVSKTQIGEEYGPWVPFIGTLFLFIFVSNWSGALLPWKIIKLPHGELAAPTNDINTTVALALLTSVAYFYAGISKKGLAYFGKYIQPTPILLPINILEDFTKPLSLSFRLFGNILADELVVVVLVSLVPLVVPIPVMFLGLFTSGIQALIFATLAAAYIGESMEGHH*