AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1093530


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1093530 MtrunA17_Chr4g0068191 98.333 60 1 0 1 60 1 60 5.94e-38 119
Msa1093530 MtrunA17_Chr4g0068181 95.000 60 3 0 1 60 1 60 4.02e-37 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1093530 AT3G06680.1 85.000 60 9 0 1 60 23 82 3.09e-31 103
Msa1093530 AT3G06700.1 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa1093530 AT3G06700.2 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa1093530 AT3G06700.3 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa1093530 AT3G06680.2 85.000 60 9 0 1 60 1 60 6.78e-31 102
Msa1093530 AT3G06680.3 85.000 60 9 0 1 60 1 60 6.78e-31 102

Find 34 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAAAACCCTAGCTGCATCTT+TGG 0.221573 7_3:-13464810 Msa1093530:five_prime_UTR
GCTGCATCTTTGGAAGAATT+AGG 0.286020 7_3:-13464800 Msa1093530:five_prime_UTR
AAACCCTACAGTTTATATTT+CGG 0.332398 7_3:+13464113 None:intergenic
GAAGTGTGACGATGCCTCTT+TGG 0.332537 7_3:+13464691 None:intergenic
CAATGCTTATGCCTGAGTTT+AGG 0.346762 7_3:-13464295 Msa1093530:three_prime_UTR
ACTTGTGACTTGATTTAGTT+TGG 0.352767 7_3:-13464136 Msa1093530:three_prime_UTR
AGTAAAGTGTCGATCTCTAA+TGG 0.363459 7_3:-13464486 Msa1093530:exon
GGGGTATATATATGTGTGTT+GGG 0.369747 7_3:+13464843 None:intergenic
GTAAAGTGTCGATCTCTAAT+GGG 0.392517 7_3:-13464485 Msa1093530:exon
CTCTGGTTCCTCAAGAACTT+TGG 0.404366 7_3:+13464556 None:intergenic
TCTTGTGAGCTTTGTAAGAC+TGG 0.419661 7_3:+13464728 None:intergenic
TATGCTTCCTTGCATACCTC+TGG 0.420261 7_3:+13464539 None:intergenic
AAGTGTTTGTTTGAAGTTGA+AGG 0.438744 7_3:-13464170 Msa1093530:three_prime_UTR
AGGGGTATATATATGTGTGT+TGG 0.464991 7_3:+13464842 None:intergenic
TTCTTCCAAAGATGCAGCTA+GGG 0.475876 7_3:+13464805 None:intergenic
ATCGTCACACTTCAACCAAA+GGG 0.488627 7_3:-13464681 Msa1093530:CDS
ATGATGAATACATACCCCTT+TGG 0.493133 7_3:+13464666 None:intergenic
AGTGTTTGTTTGAAGTTGAA+GGG 0.501632 7_3:-13464169 Msa1093530:three_prime_UTR
ATTCTTCCAAAGATGCAGCT+AGG 0.530379 7_3:+13464804 None:intergenic
TCTTACAAAGCTCACAAGAA+TGG 0.532217 7_3:-13464724 Msa1093530:CDS
GTGTTTGTTTGAAGTTGAAG+GGG 0.550371 7_3:-13464168 Msa1093530:three_prime_UTR
AGAATTGTGTGCCTAAACTC+AGG 0.570831 7_3:+13464284 None:intergenic
GGTTTATCGAATTTCAGAGA+TGG 0.592629 7_3:-13464779 Msa1093530:exon
CATCGTCACACTTCAACCAA+AGG 0.595920 7_3:-13464682 Msa1093530:CDS
TGATGCTCAAAATGAGCCGT+GGG 0.596386 7_3:-13464247 Msa1093530:three_prime_UTR
AGATGGATCCAAAGTTCTTG+AGG 0.596761 7_3:-13464564 Msa1093530:CDS
TTGATGCTCAAAATGAGCCG+TGG 0.600460 7_3:-13464248 Msa1093530:three_prime_UTR
TGAGGAACCAGAGGTATGCA+AGG 0.624057 7_3:-13464546 Msa1093530:CDS
TGTTTGTTTGAAGTTGAAGG+GGG 0.627059 7_3:-13464167 Msa1093530:three_prime_UTR
GGGTATATATATGTGTGTTG+GGG 0.642368 7_3:+13464844 None:intergenic
CAAAGTTCTTGAGGAACCAG+AGG 0.651910 7_3:-13464555 Msa1093530:CDS
TTTGTAAGACTGGTTGTGAG+CGG 0.659865 7_3:+13464738 None:intergenic
TAAAGTGTCGATCTCTAATG+GGG 0.672667 7_3:-13464484 Msa1093530:three_prime_UTR
TCGTCACACTTCAACCAAAG+GGG 0.708509 7_3:-13464680 Msa1093530:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAAATATAATCCCA+CGG + chr7_3:13464738-13464757 None:intergenic 20.0%
!!! TATGTTCGAAAGTATTTTGA+TGG - chr7_3:13464564-13464583 Msa1093530:CDS 25.0%
TTGTGATTGATTACTGTAGA+TGG - chr7_3:13464385-13464404 Msa1093530:three_prime_UTR 30.0%
! AGGAAGCATAACAAGAAAAA+TGG - chr7_3:13464440-13464459 Msa1093530:three_prime_UTR 30.0%
! AGTACTCTGTTAGCATTTTT+GGG - chr7_3:13464610-13464629 Msa1093530:intron 30.0%
! ATCATTTTCGATTGTGTGAT+TGG - chr7_3:13464762-13464781 Msa1093530:CDS 30.0%
! AAGTGTTTGTTTGAAGTTGA+AGG - chr7_3:13464796-13464815 Msa1093530:five_prime_UTR 30.0%
! AGTGTTTGTTTGAAGTTGAA+GGG - chr7_3:13464797-13464816 Msa1093530:five_prime_UTR 30.0%
ACTTGTGACTTGATTTAGTT+TGG - chr7_3:13464830-13464849 Msa1093530:five_prime_UTR 30.0%
GGGGTATATATATGTGTGTT+GGG + chr7_3:13464126-13464145 None:intergenic 35.0%
! AGGGGTATATATATGTGTGT+TGG + chr7_3:13464127-13464146 None:intergenic 35.0%
!!! TAGGGTTTTGTTTAGAGAGA+GGG + chr7_3:13464146-13464165 None:intergenic 35.0%
GGTTTATCGAATTTCAGAGA+TGG - chr7_3:13464187-13464206 Msa1093530:three_prime_UTR 35.0%
TCTTACAAAGCTCACAAGAA+TGG - chr7_3:13464242-13464261 Msa1093530:three_prime_UTR 35.0%
ATGATGAATACATACCCCTT+TGG + chr7_3:13464303-13464322 None:intergenic 35.0%
!! AGTAAAGTGTCGATCTCTAA+TGG - chr7_3:13464480-13464499 Msa1093530:three_prime_UTR 35.0%
!! GTAAAGTGTCGATCTCTAAT+GGG - chr7_3:13464481-13464500 Msa1093530:three_prime_UTR 35.0%
!! TAAAGTGTCGATCTCTAATG+GGG - chr7_3:13464482-13464501 Msa1093530:three_prime_UTR 35.0%
! CAGTACTCTGTTAGCATTTT+TGG - chr7_3:13464609-13464628 Msa1093530:intron 35.0%
! GTGTTTGTTTGAAGTTGAAG+GGG - chr7_3:13464798-13464817 Msa1093530:five_prime_UTR 35.0%
! TGTTTGTTTGAAGTTGAAGG+GGG - chr7_3:13464799-13464818 Msa1093530:five_prime_UTR 35.0%
!!! AGGGTTTTGTTTAGAGAGAG+GGG + chr7_3:13464145-13464164 None:intergenic 40.0%
!!! CTAGGGTTTTGTTTAGAGAG+AGG + chr7_3:13464147-13464166 None:intergenic 40.0%
TTCTTCCAAAGATGCAGCTA+GGG + chr7_3:13464164-13464183 None:intergenic 40.0%
ATTCTTCCAAAGATGCAGCT+AGG + chr7_3:13464165-13464184 None:intergenic 40.0%
! GCTGCATCTTTGGAAGAATT+AGG - chr7_3:13464166-13464185 Msa1093530:three_prime_UTR 40.0%
! TTTGTAAGACTGGTTGTGAG+CGG + chr7_3:13464231-13464250 None:intergenic 40.0%
! TCTTGTGAGCTTTGTAAGAC+TGG + chr7_3:13464241-13464260 None:intergenic 40.0%
ATGGCATCAAAAAGCCAAAG+AGG - chr7_3:13464261-13464280 Msa1093530:three_prime_UTR 40.0%
ATCGTCACACTTCAACCAAA+GGG - chr7_3:13464285-13464304 Msa1093530:three_prime_UTR 40.0%
AGATGGATCCAAAGTTCTTG+AGG - chr7_3:13464402-13464421 Msa1093530:three_prime_UTR 40.0%
CAATGCTTATGCCTGAGTTT+AGG - chr7_3:13464671-13464690 Msa1093530:intron 40.0%
AGAATTGTGTGCCTAAACTC+AGG + chr7_3:13464685-13464704 None:intergenic 40.0%
CAAAACCCTAGCTGCATCTT+TGG - chr7_3:13464156-13464175 Msa1093530:three_prime_UTR 45.0%
CATCGTCACACTTCAACCAA+AGG - chr7_3:13464284-13464303 Msa1093530:three_prime_UTR 45.0%
TCGTCACACTTCAACCAAAG+GGG - chr7_3:13464286-13464305 Msa1093530:three_prime_UTR 45.0%
! CTCTGGTTCCTCAAGAACTT+TGG + chr7_3:13464413-13464432 None:intergenic 45.0%
CAAAGTTCTTGAGGAACCAG+AGG - chr7_3:13464411-13464430 Msa1093530:three_prime_UTR 45.0%
TATGCTTCCTTGCATACCTC+TGG + chr7_3:13464430-13464449 None:intergenic 45.0%
TTGATGCTCAAAATGAGCCG+TGG - chr7_3:13464718-13464737 Msa1093530:CDS 45.0%
TGATGCTCAAAATGAGCCGT+GGG - chr7_3:13464719-13464738 Msa1093530:CDS 45.0%
! TTGTTTGAAGTTGAAGGGGG+AGG - chr7_3:13464802-13464821 Msa1093530:five_prime_UTR 45.0%
! TGTTTGAAGTTGAAGGGGGA+GGG - chr7_3:13464803-13464822 Msa1093530:five_prime_UTR 45.0%
GAAGTGTGACGATGCCTCTT+TGG + chr7_3:13464278-13464297 None:intergenic 50.0%
! TGAGGAACCAGAGGTATGCA+AGG - chr7_3:13464420-13464439 Msa1093530:three_prime_UTR 50.0%
! GTTTGAAGTTGAAGGGGGAG+GGG - chr7_3:13464804-13464823 Msa1093530:five_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr7_3 gene 13464123 13464865 13464123 ID=Msa1093530;Name=Msa1093530
chr7_3 mRNA 13464123 13464865 13464123 ID=Msa1093530-mRNA-1;Parent=Msa1093530;Name=Msa1093530-mRNA-1;_AED=0.36;_eAED=0.36;_QI=83|1|1|1|1|1|2|381|60
chr7_3 exon 13464123 13464584 13464123 ID=Msa1093530-mRNA-1:exon:3201;Parent=Msa1093530-mRNA-1
chr7_3 exon 13464681 13464865 13464681 ID=Msa1093530-mRNA-1:exon:3200;Parent=Msa1093530-mRNA-1
chr7_3 five_prime_UTR 13464783 13464865 13464783 ID=Msa1093530-mRNA-1:five_prime_utr;Parent=Msa1093530-mRNA-1
chr7_3 CDS 13464681 13464782 13464681 ID=Msa1093530-mRNA-1:cds;Parent=Msa1093530-mRNA-1
chr7_3 CDS 13464504 13464584 13464504 ID=Msa1093530-mRNA-1:cds;Parent=Msa1093530-mRNA-1
chr7_3 three_prime_UTR 13464123 13464503 13464123 ID=Msa1093530-mRNA-1:three_prime_utr;Parent=Msa1093530-mRNA-1
Gene Sequence

>Msa1093530

ATGGCGAAATCGAAGAATCACACCGCTCACAACCAGTCTTACAAAGCTCACAAGAATGGCATCAAAAAGCCAAAGAGGCATCGTCACACTTCAACCAAAGGGATGGATCCAAAGTTCTTGAGGAACCAGAGGTATGCAAGGAAGCATAACAAGAAAAATGGTGAAATTGCAGAAGAAGAGTAA

Protein sequence

>Msa1093530

MAKSKNHTAHNQSYKAHKNGIKKPKRHRHTSTKGMDPKFLRNQRYARKHNKKNGEIAEEE*