AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1302750


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1302750 MtrunA17_Chr4g0074391 82.328 232 1 1 5 236 3 194 4.59e-130 365
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1302750 AT5G13510.1 73.626 182 48 0 51 232 39 220 4.85e-102 295
Msa1302750 AT3G12370.1 59.589 146 57 1 68 211 15 160 9.57e-62 191

Find 50 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACAACGAGTTTCGTTGTTTC+AGG 0.234422 8_3:+65442892 None:intergenic
TCTTTCTGAAAATCTCTATA+AGG 0.284478 8_3:+65442745 None:intergenic
GATGGATAAACGGTGGGTTT+TGG 0.306620 8_3:+65443053 None:intergenic
GAAAAGTCCTTCTTCTGCTT+TGG 0.317270 8_3:-65442593 Msa1302750:CDS
GGGTGGGTTGAATGGATTAA+TGG 0.321323 8_3:+65443101 None:intergenic
CGAGATTTATGCTAATTTGT+TGG 0.337443 8_3:-65442623 Msa1302750:CDS
AGAACTTATCATGGTTCTTA+AGG 0.338473 8_3:-65442545 Msa1302750:CDS
GAAGCCTTTGTAGTTGATTC+CGG 0.344742 8_3:+65442951 None:intergenic
ATGGATTAATGGGTCGGGTT+AGG 0.372564 8_3:+65443112 None:intergenic
GAAGCTTGAAGAACAGGAAC+AGG 0.372574 8_3:-65442512 Msa1302750:CDS
TATGATGTGGGTGGGTTGAA+TGG 0.376194 8_3:+65443093 None:intergenic
GAGATTTATGCTAATTTGTT+GGG 0.387159 8_3:-65442622 Msa1302750:CDS
GCGTGAAATTGCGGCGTTGA+TGG 0.388449 8_3:+65443035 None:intergenic
GATTTGAAAAGATTGGGTTT+TGG 0.397872 8_3:+65443134 None:intergenic
GGGTTAGGATTTGAAAAGAT+TGG 0.402896 8_3:+65443127 None:intergenic
TCAAGTTTCTTAAACTCGTC+AGG 0.408323 8_3:+65442664 None:intergenic
AAGTTCTTGAAATTGTTTAA+CGG 0.413631 8_3:+65442927 None:intergenic
TTGGTTTGTATGATGTGGGT+GGG 0.413650 8_3:+65443085 None:intergenic
TATTAAGAAGCTTGAAGAAC+AGG 0.423944 8_3:-65442518 Msa1302750:CDS
GGTTAGGATTTGAAAAGATT+GGG 0.426249 8_3:+65443128 None:intergenic
GGTCTTGGTTTGTATGATGT+GGG 0.456359 8_3:+65443081 None:intergenic
TTTCTTTGTGCGTGAAATTG+CGG 0.473934 8_3:+65443026 None:intergenic
TTCTCTAGCAGGAGCTTGAA+TGG 0.482406 8_3:+65442564 None:intergenic
CTTGGTTTGTATGATGTGGG+TGG 0.491348 8_3:+65443084 None:intergenic
GGTTGAATGGATTAATGGGT+CGG 0.496024 8_3:+65443106 None:intergenic
TTGCGGCGTTGATGGATAAA+CGG 0.507344 8_3:+65443043 None:intergenic
GGGTCTTGGTTTGTATGATG+TGG 0.515588 8_3:+65443080 None:intergenic
TGCAGTTGCAGTAGCTTCCA+TGG 0.517404 8_3:+65443185 None:intergenic
AGCACTTGAAGGAACACAAT+GGG 0.519774 8_3:-65442845 Msa1302750:CDS
GGTGGGTTGAATGGATTAAT+GGG 0.520626 8_3:+65443102 None:intergenic
ACATTCATACCTGTCATACA+TGG 0.531583 8_3:+65442811 None:intergenic
TTGGTGTATAAAGCACTTGA+AGG 0.538624 8_3:-65442856 Msa1302750:CDS
TCCTGCTAGAGAACTTATCA+TGG 0.541437 8_3:-65442554 Msa1302750:CDS
GTTGAATGGATTAATGGGTC+GGG 0.546717 8_3:+65443107 None:intergenic
AATAGCAGAAGGAATCTCTT+CGG 0.548948 8_3:+65442771 None:intergenic
ACCATGATAAGTTCTCTAGC+AGG 0.549644 8_3:+65442553 None:intergenic
GGCGTTGATGGATAAACGGT+GGG 0.563964 8_3:+65443047 None:intergenic
CTATAAGGCTTAATAGCAGA+AGG 0.564004 8_3:+65442760 None:intergenic
GTAGTAACCAAAGCAGAAGA+AGG 0.565336 8_3:+65442586 None:intergenic
TGTAGTTGATTCCGGCGAGA+AGG 0.569893 8_3:+65442959 None:intergenic
ACGCTGAAACCATGTATGAC+AGG 0.579109 8_3:-65442820 Msa1302750:CDS
GCATAAATCTCGCCGCGTGT+CGG 0.580599 8_3:+65442634 None:intergenic
GAAAACTGTTACCTTCTCGC+CGG 0.589832 8_3:-65442970 Msa1302750:CDS
CGGCGTTGATGGATAAACGG+TGG 0.618873 8_3:+65443046 None:intergenic
CTTGAAACATTGCCGACACG+CGG 0.624834 8_3:-65442646 Msa1302750:CDS
AAGCTTGAAGAACAGGAACA+GGG 0.635295 8_3:-65442511 Msa1302750:CDS
CGTTGTTGCAAAGAACACAT+TGG 0.653227 8_3:-65442875 Msa1302750:CDS
AAGCACTTGAAGGAACACAA+TGG 0.664659 8_3:-65442846 Msa1302750:CDS
CTCGCCGGAATCAACTACAA+AGG 0.670751 8_3:-65442955 Msa1302750:CDS
GTATGACAGGTATGAATGTG+TGG 0.676357 8_3:-65442807 Msa1302750:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTTCTTGAAATTGTTTAA+CGG + chr8_3:65442754-65442773 None:intergenic 20.0%
!! TCTTTCTGAAAATCTCTATA+AGG + chr8_3:65442936-65442955 None:intergenic 25.0%
!!! GTTTTTGAAGGGAAATTTTA+TGG - chr8_3:65442990-65443009 Msa1302750:CDS 25.0%
!!! GAGATTTATGCTAATTTGTT+GGG - chr8_3:65443056-65443075 Msa1302750:CDS 25.0%
! GATTTGAAAAGATTGGGTTT+TGG + chr8_3:65442547-65442566 None:intergenic 30.0%
GGTTAGGATTTGAAAAGATT+GGG + chr8_3:65442553-65442572 None:intergenic 30.0%
!! GTTTTCAAGCTGTTCTTTTA+CGG + chr8_3:65442694-65442713 None:intergenic 30.0%
! CTTGAAGAGAATGATTTTAC+TGG - chr8_3:65442963-65442982 Msa1302750:CDS 30.0%
! CGAGATTTATGCTAATTTGT+TGG - chr8_3:65443055-65443074 Msa1302750:CDS 30.0%
AGAACTTATCATGGTTCTTA+AGG - chr8_3:65443133-65443152 Msa1302750:CDS 30.0%
TATTAAGAAGCTTGAAGAAC+AGG - chr8_3:65443160-65443179 Msa1302750:CDS 30.0%
!! TTGAAAAGATTGGGTTTTGG+TGG + chr8_3:65442544-65442563 None:intergenic 35.0%
GGGTTAGGATTTGAAAAGAT+TGG + chr8_3:65442554-65442573 None:intergenic 35.0%
TTTCTTTGTGCGTGAAATTG+CGG + chr8_3:65442655-65442674 None:intergenic 35.0%
! TTGGTGTATAAAGCACTTGA+AGG - chr8_3:65442822-65442841 Msa1302750:CDS 35.0%
ACATTCATACCTGTCATACA+TGG + chr8_3:65442870-65442889 None:intergenic 35.0%
AATAGCAGAAGGAATCTCTT+CGG + chr8_3:65442910-65442929 None:intergenic 35.0%
CTATAAGGCTTAATAGCAGA+AGG + chr8_3:65442921-65442940 None:intergenic 35.0%
!!! TTTACTGGTGCTGTTTTTGA+AGG - chr8_3:65442978-65442997 Msa1302750:CDS 35.0%
!!! TTACTGGTGCTGTTTTTGAA+GGG - chr8_3:65442979-65442998 Msa1302750:CDS 35.0%
TCAAGTTTCTTAAACTCGTC+AGG + chr8_3:65443017-65443036 None:intergenic 35.0%
!! AAAGATTGGGTTTTGGTGGA+TGG + chr8_3:65442540-65442559 None:intergenic 40.0%
!! GTTGAATGGATTAATGGGTC+GGG + chr8_3:65442574-65442593 None:intergenic 40.0%
!! GGTTGAATGGATTAATGGGT+CGG + chr8_3:65442575-65442594 None:intergenic 40.0%
!! GGTGGGTTGAATGGATTAAT+GGG + chr8_3:65442579-65442598 None:intergenic 40.0%
!! TTGGTTTGTATGATGTGGGT+GGG + chr8_3:65442596-65442615 None:intergenic 40.0%
!! GGTCTTGGTTTGTATGATGT+GGG + chr8_3:65442600-65442619 None:intergenic 40.0%
!!! AAACGGTGGGTTTTGGAAAT+GGG + chr8_3:65442621-65442640 None:intergenic 40.0%
!!! TAAACGGTGGGTTTTGGAAA+TGG + chr8_3:65442622-65442641 None:intergenic 40.0%
! GAAGCCTTTGTAGTTGATTC+CGG + chr8_3:65442730-65442749 None:intergenic 40.0%
! ACAACGAGTTTCGTTGTTTC+AGG + chr8_3:65442789-65442808 None:intergenic 40.0%
CGTTGTTGCAAAGAACACAT+TGG - chr8_3:65442803-65442822 Msa1302750:CDS 40.0%
AAGCACTTGAAGGAACACAA+TGG - chr8_3:65442832-65442851 Msa1302750:CDS 40.0%
AGCACTTGAAGGAACACAAT+GGG - chr8_3:65442833-65442852 Msa1302750:CDS 40.0%
GTATGACAGGTATGAATGTG+TGG - chr8_3:65442871-65442890 Msa1302750:CDS 40.0%
GAAAAGTCCTTCTTCTGCTT+TGG - chr8_3:65443085-65443104 Msa1302750:CDS 40.0%
GTAGTAACCAAAGCAGAAGA+AGG + chr8_3:65443095-65443114 None:intergenic 40.0%
TCCTGCTAGAGAACTTATCA+TGG - chr8_3:65443124-65443143 Msa1302750:CDS 40.0%
ACCATGATAAGTTCTCTAGC+AGG + chr8_3:65443128-65443147 None:intergenic 40.0%
AAGCTTGAAGAACAGGAACA+GGG - chr8_3:65443167-65443186 Msa1302750:CDS 40.0%
! ATGGATTAATGGGTCGGGTT+AGG + chr8_3:65442569-65442588 None:intergenic 45.0%
!! GGGTGGGTTGAATGGATTAA+TGG + chr8_3:65442580-65442599 None:intergenic 45.0%
!! TATGATGTGGGTGGGTTGAA+TGG + chr8_3:65442588-65442607 None:intergenic 45.0%
!! CTTGGTTTGTATGATGTGGG+TGG + chr8_3:65442597-65442616 None:intergenic 45.0%
!! GGGTCTTGGTTTGTATGATG+TGG + chr8_3:65442601-65442620 None:intergenic 45.0%
!!! TGGGTTTTGGAAATGGGTCT+TGG + chr8_3:65442615-65442634 None:intergenic 45.0%
!! GATGGATAAACGGTGGGTTT+TGG + chr8_3:65442628-65442647 None:intergenic 45.0%
!! TTGCGGCGTTGATGGATAAA+CGG + chr8_3:65442638-65442657 None:intergenic 45.0%
GAAAACTGTTACCTTCTCGC+CGG - chr8_3:65442708-65442727 Msa1302750:CDS 45.0%
ACGCTGAAACCATGTATGAC+AGG - chr8_3:65442858-65442877 Msa1302750:CDS 45.0%
TTCTCTAGCAGGAGCTTGAA+TGG + chr8_3:65443117-65443136 None:intergenic 45.0%
GAAGCTTGAAGAACAGGAAC+AGG - chr8_3:65443166-65443185 Msa1302750:CDS 45.0%
!! GGCGTTGATGGATAAACGGT+GGG + chr8_3:65442634-65442653 None:intergenic 50.0%
! TGTAGTTGATTCCGGCGAGA+AGG + chr8_3:65442722-65442741 None:intergenic 50.0%
CTCGCCGGAATCAACTACAA+AGG - chr8_3:65442723-65442742 Msa1302750:CDS 50.0%
CTTGAAACATTGCCGACACG+CGG - chr8_3:65443032-65443051 Msa1302750:CDS 50.0%
!! CGGCGTTGATGGATAAACGG+TGG + chr8_3:65442635-65442654 None:intergenic 55.0%
! GCGTGAAATTGCGGCGTTGA+TGG + chr8_3:65442646-65442665 None:intergenic 55.0%
GCATAAATCTCGCCGCGTGT+CGG + chr8_3:65443047-65443066 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr8_3 gene 65442495 65443205 65442495 ID=Msa1302750;Name=Msa1302750
chr8_3 mRNA 65442495 65443205 65442495 ID=Msa1302750-mRNA-1;Parent=Msa1302750;Name=Msa1302750-mRNA-1;_AED=0.08;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|236
chr8_3 exon 65442495 65443205 65442495 ID=Msa1302750-mRNA-1:exon:19879;Parent=Msa1302750-mRNA-1
chr8_3 CDS 65442495 65443205 65442495 ID=Msa1302750-mRNA-1:cds;Parent=Msa1302750-mRNA-1
Gene Sequence

>Msa1302750

ATGGAAGCTACTGCAACTGCAACTCTACTCAGCTTTTCACTTCCATCCACCAAAACCCAATCTTTTCAAATCCTAACCCGACCCATTAATCCATTCAACCCACCCACATCATACAAACCAAGACCCATTTCCAAAACCCACCGTTTATCCATCAACGCCGCAATTTCACGCACAAAGAAAGAAGAAACAGTTGAAACCGTAAAAGAACAGCTTGAAAACTGTTACCTTCTCGCCGGAATCAACTACAAAGGCTTCACCGTTAAACAATTTCAAGAACTTAGAAAAACTCTTCCTGAAACAACGAAACTCGTTGTTGCAAAGAACACATTGGTGTATAAAGCACTTGAAGGAACACAATGGGAGACGCTGAAACCATGTATGACAGGTATGAATGTGTGGTTGTTTGTTCATACCGAAGAGATTCCTTCTGCTATTAAGCCTTATAGAGATTTTCAGAAAGAGAAGAAGCTTGAAGAGAATGATTTTACTGGTGCTGTTTTTGAAGGGAAATTTTATGGTCCTGACGAGTTTAAGAAACTTGAAACATTGCCGACACGCGGCGAGATTTATGCTAATTTGTTGGGTTCTTTGAAAAGTCCTTCTTCTGCTTTGGTTACTACCATTCAAGCTCCTGCTAGAGAACTTATCATGGTTCTTAAGGCACATATTAAGAAGCTTGAAGAACAGGAACAGGGTAGTGCTGTTCTATAG

Protein sequence

>Msa1302750

MEATATATLLSFSLPSTKTQSFQILTRPINPFNPPTSYKPRPISKTHRLSINAAISRTKKEETVETVKEQLENCYLLAGINYKGFTVKQFQELRKTLPETTKLVVAKNTLVYKALEGTQWETLKPCMTGMNVWLFVHTEEIPSAIKPYRDFQKEKKLEENDFTGAVFEGKFYGPDEFKKLETLPTRGEIYANLLGSLKSPSSALVTTIQAPARELIMVLKAHIKKLEEQEQGSAVL*