AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0908290


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 28 sgRNAs with CRISPR-Local

Find 35 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CGCTTTACGCCCAATCATTC+CGG 0.287091 6_2:+9523473 None:intergenic
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 6_2:-9523610 Msa0908290:CDS
ACCTGTCCAGGGTTGAGCCC+TGG 0.327938 6_2:+9523416 None:intergenic
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 6_2:+9523510 None:intergenic
CCTGTCCAGGGTTGAGCCCT+GGG 0.363036 6_2:+9523417 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 6_2:-9523483 Msa0908290:CDS
ACCGTCATTGTTTCTTCTCC+AGG 0.384151 6_2:+9523564 Msa0908300:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 6_2:-9523492 Msa0908290:CDS
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 6_2:+9523426 None:intergenic
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 6_2:-9523434 Msa0908290:CDS
CCACGCGGCATTGCTCCGTC+AGG 0.484232 6_2:+9523620 Msa0908300:CDS
CCCAGGGCTCAACCCTGGAC+AGG 0.508220 6_2:-9523417 Msa0908290:CDS
AAGCGTTATCCGGAATGATT+GGG 0.511219 6_2:-9523482 Msa0908290:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 6_2:-9523635 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 6_2:-9523520 Msa0908290:CDS
CAAATCCCAGGGCTCAACCC+TGG 0.557720 6_2:-9523422 Msa0908290:CDS
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 6_2:-9523603 Msa0908290:CDS
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 6_2:-9523433 Msa0908290:CDS
AGGGCTCAACCCTGGACAGG+TGG 0.567008 6_2:-9523414 Msa0908290:CDS
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 6_2:-9523602 Msa0908290:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 6_2:-9523462 Msa0908290:CDS
TCCTGGAGAAGAAACAATGA+CGG 0.628601 6_2:-9523565 Msa0908290:intron
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 6_2:-9523465 Msa0908290:CDS
GACGGAGCAATGCCGCGTGG+AGG 0.640730 6_2:-9523617 Msa0908290:CDS
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 6_2:-9523509 Msa0908290:CDS
AAAAGAAGTTCATGACCCGT+AGG 0.653857 6_2:+9523587 Msa0908300:CDS
CCTGACGGAGCAATGCCGCG+TGG 0.711882 6_2:-9523620 Msa0908290:CDS
TTGCATCCTCTGTCTTACCG+CGG 0.760348 6_2:+9523503 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG - chr6_2:9523475-9523494 Msa0908290:CDS 35.0%
AAAAGAAGTTCATGACCCGT+AGG + chr6_2:9523448-9523467 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG - chr6_2:9523467-9523486 Msa0908290:CDS 40.0%
GAAGAAACAATGACGGTATC+TGG - chr6_2:9523474-9523493 Msa0908290:CDS 40.0%
AGAAACAATGACGGTATCTG+GGG - chr6_2:9523476-9523495 Msa0908290:CDS 40.0%
AAGCGTTATCCGGAATGATT+GGG - chr6_2:9523550-9523569 Msa0908290:intron 40.0%
! GGGTCATGAACTTCTTTTCC+TGG - chr6_2:9523450-9523469 Msa0908290:CDS 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG + chr6_2:9523471-9523490 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG - chr6_2:9523488-9523507 Msa0908290:CDS 45.0%
CAAGCGTTATCCGGAATGAT+TGG - chr6_2:9523549-9523568 Msa0908290:intron 45.0%
! TAGTTTTCACCACCTGTCCA+GGG + chr6_2:9523630-9523649 Msa0908300:CDS 45.0%
TTGCATCCTCTGTCTTACCG+CGG + chr6_2:9523532-9523551 None:intergenic 50.0%
CAGAGGATGCAAGCGTTATC+CGG - chr6_2:9523540-9523559 Msa0908290:intron 50.0%
CGCTTTACGCCCAATCATTC+CGG + chr6_2:9523562-9523581 Msa0908300:CDS 50.0%
! ATTGGGCGTAAAGCGTCTGT+AGG - chr6_2:9523567-9523586 Msa0908290:CDS 50.0%
TAAGTTCGCCGTCAAATCCC+AGG - chr6_2:9523598-9523617 Msa0908290:CDS 50.0%
AAGTTCGCCGTCAAATCCCA+GGG - chr6_2:9523599-9523618 Msa0908290:CDS 50.0%
! GTAGTTTTCACCACCTGTCC+AGG + chr6_2:9523631-9523650 Msa0908300:CDS 50.0%
CAATGCCGCGTGGAGGTAAA+AGG - chr6_2:9523422-9523441 Msa0908290:CDS 55.0%
! GTAGGCCTTTTACCTCCACG+CGG + chr6_2:9523430-9523449 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG - chr6_2:9523429-9523448 Msa0908290:CDS 55.0%
CGTGGAGGTAAAAGGCCTAC+GGG - chr6_2:9523430-9523449 Msa0908290:CDS 55.0%
GGTTGAGCCCTGGGATTTGA+CGG + chr6_2:9523609-9523628 Msa0908300:CDS 55.0%
TAACTCTGTGCCAGCAGCCG+CGG - chr6_2:9523512-9523531 Msa0908290:CDS 60.0%
! GGGCGTAAAGCGTCTGTAGG+TGG - chr6_2:9523570-9523589 Msa0908290:CDS 60.0%
CAAATCCCAGGGCTCAACCC+TGG - chr6_2:9523610-9523629 Msa0908290:CDS 60.0%
CTCTGTCTTACCGCGGCTGC+TGG + chr6_2:9523525-9523544 None:intergenic 65.0%
CAGCAGCCGCGGTAAGACAG+AGG - chr6_2:9523523-9523542 Msa0908290:CDS 65.0%
CCTGTCCAGGGTTGAGCCCT+GGG + chr6_2:9523618-9523637 Msa0908300:CDS 65.0%
ACCTGTCCAGGGTTGAGCCC+TGG + chr6_2:9523619-9523638 Msa0908300:CDS 65.0%
AGGGCTCAACCCTGGACAGG+TGG - chr6_2:9523618-9523637 Msa0908290:CDS 65.0%
CCACGCGGCATTGCTCCGTC+AGG + chr6_2:9523415-9523434 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG - chr6_2:9523412-9523431 Msa0908290:CDS 70.0%
GACGGAGCAATGCCGCGTGG+AGG - chr6_2:9523415-9523434 Msa0908290:CDS 70.0%
CCCAGGGCTCAACCCTGGAC+AGG - chr6_2:9523615-9523634 Msa0908290:CDS 70.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 9523401 9523653 9523401 ID=Msa0908290;Name=Msa0908290
chr6_2 mRNA 9523401 9523653 9523401 ID=Msa0908290-mRNA-1;Parent=Msa0908290;Name=Msa0908290-mRNA-1;_AED=0.42;_eAED=0.47;_QI=0|0|0|1|1|1|2|0|78
chr6_2 exon 9523566 9523653 9523566 ID=Msa0908290-mRNA-1:exon:2298;Parent=Msa0908290-mRNA-1
chr6_2 exon 9523401 9523549 9523401 ID=Msa0908290-mRNA-1:exon:2297;Parent=Msa0908290-mRNA-1
chr6_2 CDS 9523566 9523653 9523566 ID=Msa0908290-mRNA-1:cds;Parent=Msa0908290-mRNA-1
chr6_2 CDS 9523401 9523549 9523401 ID=Msa0908290-mRNA-1:cds;Parent=Msa0908290-mRNA-1
Gene Sequence

>Msa0908290

ATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTAAAAGGCCTACGGGTCATGAACTTCTTTTCCTGGAGAAGAAACAATGACGCATCGGCTAACTCTGTGCCAGCAGCCGCGGTAAGACAGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGCTTTTTAAGTTCGCCGTCAAATCCCAGGGCTCAACCCTGGACAGGTGGTGAAAACTACTAA

Protein sequence

>Msa0908290

MGESLTEQCRVEVKGLRVMNFFSWRRNNDASANSVPAAAVRQRMQALSGMIGRKASVGGFLSSPSNPRAQPWTGGENY*