AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0520700


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 23 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATGTCATGAAGCGATTT+TGG 0.142839 3_4:-73234926 None:intergenic
TTTAAAGAGGTTTCAATTAT+TGG 0.165386 3_4:+73234396 Msa0520700:CDS
CTTTGTGGTCGTCTCCCTTC+AGG 0.311368 3_4:-73234473 None:intergenic
GTTAAGGTTGTTGCTGGTTG+TGG 0.329970 3_4:+73234441 Msa0520700:CDS
GTGGTTGTTAAGGTTGTTGC+TGG 0.335193 3_4:+73234435 Msa0520700:CDS
TTCTGTGAATGTGGTTGTTA+AGG 0.361374 3_4:+73234425 Msa0520700:CDS
TTAAGGTTGTTGCTGGTTGT+GGG 0.373170 3_4:+73234442 Msa0520700:CDS
TTGTTGCTGGTTGTGGGAGG+TGG 0.374353 3_4:+73234448 Msa0520700:CDS
TCATCTTGCTCCCACCTTTG+TGG 0.374883 3_4:-73234488 None:intergenic
GATCAGAACAATTACGATGA+AGG 0.448729 3_4:-73235009 None:intergenic
TTGTGGGAGGTGGAGCCTGA+AGG 0.457754 3_4:+73234458 Msa0520700:CDS
AATGAAGGTAAGCCATGCTT+TGG 0.472531 3_4:+73234365 None:intergenic
CCAAATTCTAACTCAGCGAT+TGG 0.480896 3_4:-73235060 None:intergenic
ATCAGAACAATTACGATGAA+GGG 0.495680 3_4:-73235008 None:intergenic
TTTGGTTCACACATTTAAAG+AGG 0.508262 3_4:+73234383 Msa0520700:CDS
TGGTTGTGTTTCTGTGAATG+TGG 0.521498 3_4:+73234416 Msa0520700:CDS
AGGTTGTTGCTGGTTGTGGG+AGG 0.530134 3_4:+73234445 Msa0520700:CDS
TGTGGGAGGTGGAGCCTGAA+GGG 0.539977 3_4:+73234459 Msa0520700:CDS
TAAATGTGTGAACCAAAGCA+TGG 0.589815 3_4:-73234377 None:intergenic
AAGGGAGACGACCACAAAGG+TGG 0.595825 3_4:+73234477 Msa0520700:CDS
TTCTAACTCAGCGATTGGAA+CGG 0.608058 3_4:-73235055 None:intergenic
AGGGAGACGACCACAAAGGT+GGG 0.637230 3_4:+73234478 Msa0520700:CDS
CTGAAGGGAGACGACCACAA+AGG 0.700107 3_4:+73234474 Msa0520700:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAAAAAACTTTTTCTTTTTT+CGG - chr3_4:73234806-73234825 None:intergenic 15.0%
!! TTTAAAGAGGTTTCAATTAT+TGG + chr3_4:73234396-73234415 Msa0520700:CDS 20.0%
!! AACAATCTAACTATTTATCT+TGG + chr3_4:73234578-73234597 Msa0520700:intron 20.0%
!! ACAATCTAACTATTTATCTT+GGG + chr3_4:73234579-73234598 Msa0520700:intron 20.0%
!!! TTTTGAAGGCATATAAAAGT+GGG - chr3_4:73234650-73234669 None:intergenic 25.0%
!!! TTTTTGAAGGCATATAAAAG+TGG - chr3_4:73234651-73234670 None:intergenic 25.0%
!!! AATGACAACGCAATTTTAAT+TGG + chr3_4:73234689-73234708 Msa0520700:intron 25.0%
! TTTGGTTCACACATTTAAAG+AGG + chr3_4:73234383-73234402 Msa0520700:CDS 30.0%
ATCAGAACAATTACGATGAA+GGG - chr3_4:73235011-73235030 None:intergenic 30.0%
TAAATGTGTGAACCAAAGCA+TGG - chr3_4:73234380-73234399 None:intergenic 35.0%
TTCTGTGAATGTGGTTGTTA+AGG + chr3_4:73234425-73234444 Msa0520700:CDS 35.0%
GAAGCTATTGAGATCATATG+TGG + chr3_4:73234527-73234546 Msa0520700:intron 35.0%
TATTTATCTTGGGTGACTCA+TGG + chr3_4:73234589-73234608 Msa0520700:intron 35.0%
!!! GTTAGGAACGGATTTTTTGA+AGG - chr3_4:73234664-73234683 None:intergenic 35.0%
TGTCATTGTCATGTTAGGAA+CGG - chr3_4:73234676-73234695 None:intergenic 35.0%
! CTATGTCATGAAGCGATTTT+GGG - chr3_4:73234928-73234947 None:intergenic 35.0%
GATCAGAACAATTACGATGA+AGG - chr3_4:73235012-73235031 None:intergenic 35.0%
! TGGTTGTGTTTCTGTGAATG+TGG + chr3_4:73234416-73234435 Msa0520700:CDS 40.0%
! TTAAGGTTGTTGCTGGTTGT+GGG + chr3_4:73234442-73234461 Msa0520700:CDS 40.0%
GGAGCAAGATGAGAAAAGTT+TGG + chr3_4:73234499-73234518 Msa0520700:intron 40.0%
GTGGCATTTAACATGGGAAA+GGG - chr3_4:73234628-73234647 None:intergenic 40.0%
AAGTGGGTGGCATTTAACAT+GGG - chr3_4:73234634-73234653 None:intergenic 40.0%
AAAGTGGGTGGCATTTAACA+TGG - chr3_4:73234635-73234654 None:intergenic 40.0%
! TGAAGGCATATAAAAGTGGG+TGG - chr3_4:73234647-73234666 None:intergenic 40.0%
TGCGTTGTCATTGTCATGTT+AGG - chr3_4:73234681-73234700 None:intergenic 40.0%
! GCTATGTCATGAAGCGATTT+TGG - chr3_4:73234929-73234948 None:intergenic 40.0%
GTGGTTGTTAAGGTTGTTGC+TGG + chr3_4:73234435-73234454 Msa0520700:CDS 45.0%
! GTTAAGGTTGTTGCTGGTTG+TGG + chr3_4:73234441-73234460 Msa0520700:CDS 45.0%
GGTGGCATTTAACATGGGAA+AGG - chr3_4:73234629-73234648 None:intergenic 45.0%
TCATCTTGCTCCCACCTTTG+TGG - chr3_4:73234491-73234510 None:intergenic 50.0%
! AGGTTGTTGCTGGTTGTGGG+AGG + chr3_4:73234445-73234464 Msa0520700:CDS 55.0%
! TTGTTGCTGGTTGTGGGAGG+TGG + chr3_4:73234448-73234467 Msa0520700:CDS 55.0%
CTTTGTGGTCGTCTCCCTTC+AGG - chr3_4:73234476-73234495 None:intergenic 55.0%
CTGAAGGGAGACGACCACAA+AGG + chr3_4:73234474-73234493 Msa0520700:CDS 55.0%
AAGGGAGACGACCACAAAGG+TGG + chr3_4:73234477-73234496 Msa0520700:CDS 55.0%
AGGGAGACGACCACAAAGGT+GGG + chr3_4:73234478-73234497 Msa0520700:CDS 55.0%
TTGTGGGAGGTGGAGCCTGA+AGG + chr3_4:73234458-73234477 Msa0520700:CDS 60.0%
TGTGGGAGGTGGAGCCTGAA+GGG + chr3_4:73234459-73234478 Msa0520700:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 73234366 73235075 73234366 ID=Msa0520700;Name=Msa0520700
chr3_4 mRNA 73234366 73235075 73234366 ID=Msa0520700-mRNA-1;Parent=Msa0520700;Name=Msa0520700-mRNA-1;_AED=0.43;_eAED=0.74;_QI=0|0|0|1|1|1|2|0|103
chr3_4 exon 73234366 73234515 73234366 ID=Msa0520700-mRNA-1:exon:20485;Parent=Msa0520700-mRNA-1
chr3_4 exon 73234914 73235075 73234914 ID=Msa0520700-mRNA-1:exon:20486;Parent=Msa0520700-mRNA-1
chr3_4 CDS 73234366 73234515 73234366 ID=Msa0520700-mRNA-1:cds;Parent=Msa0520700-mRNA-1
chr3_4 CDS 73234914 73235075 73234914 ID=Msa0520700-mRNA-1:cds;Parent=Msa0520700-mRNA-1
Gene Sequence

>Msa0520700

ATGAAGGTAAGCCATGCTTTGGTTCACACATTTAAAGAGGTTTCAATTATTGGTTGTGTTTCTGTGAATGTGGTTGTTAAGGTTGTTGCTGGTTGTGGGAGGTGGAGCCTGAAGGGAGACGACCACAAAGGTGGGAGCAAGATGAGAAAAAAGCGCTTTATCCCAAAATCGCTTCATGACATAGCTTCATCAGTTTCATCTCAATCACTCTCACATCTTCATCTCAATCGCTCTTCTTCACAATCCCTTCATCGTAATTGTTCTGATCAAATTCTTCATCGCAATCTCATTCCGTTCCAATCGCTGAGTTAG

Protein sequence

>Msa0520700

MKVSHALVHTFKEVSIIGCVSVNVVVKVVAGCGRWSLKGDDHKGGSKMRKKRFIPKSLHDIASSVSSQSLSHLHLNRSSSQSLHRNCSDQILHRNLIPFQSLS*