AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0902760


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0902760 MtrunA17_Chr4g0068191 98.333 60 1 0 1 60 1 60 5.94e-38 119
Msa0902760 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
Msa0902760 AT3G06680.1 85.000 60 9 0 1 60 23 82 3.09e-31 103
Msa0902760 AT3G06700.1 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa0902760 AT3G06700.2 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa0902760 AT3G06700.3 85.000 60 9 0 1 60 1 60 4.99e-31 102
Msa0902760 AT3G06680.2 85.000 60 9 0 1 60 1 60 6.78e-31 102
Msa0902760 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 6_1:-102529427 Msa0902760:five_prime_UTR
GCTGCATCTTTGGAAGAATT+AGG 0.286020 6_1:-102529417 Msa0902760:five_prime_UTR
AAACCCTACAGTTTATATTT+CGG 0.332398 6_1:+102528730 None:intergenic
GAAGTGTGACGATGCCTCTT+TGG 0.332537 6_1:+102529308 None:intergenic
CAATGCTTATGCCTGAGTTT+AGG 0.346762 6_1:-102528912 Msa0902760:three_prime_UTR
ACTTGTGACTTGATTTAGTT+TGG 0.352767 6_1:-102528753 Msa0902760:three_prime_UTR
AGTAAAGTGTCGATCTCTAA+TGG 0.363459 6_1:-102529103 Msa0902760:exon
GGGGTATATATATGTGTGTT+GGG 0.369747 6_1:+102529460 None:intergenic
GTAAAGTGTCGATCTCTAAT+GGG 0.392517 6_1:-102529102 Msa0902760:exon
CTCTGGTTCCTCAAGAACTT+TGG 0.404366 6_1:+102529173 None:intergenic
TCTTGTGAGCTTTGTAAGAC+TGG 0.419661 6_1:+102529345 None:intergenic
TATGCTTCCTTGCATACCTC+TGG 0.420261 6_1:+102529156 None:intergenic
AAGTGTTTGTTTGAAGTTGA+AGG 0.438744 6_1:-102528787 Msa0902760:three_prime_UTR
AGGGGTATATATATGTGTGT+TGG 0.464991 6_1:+102529459 None:intergenic
TTCTTCCAAAGATGCAGCTA+GGG 0.475876 6_1:+102529422 None:intergenic
ATCGTCACACTTCAACCAAA+GGG 0.488627 6_1:-102529298 Msa0902760:CDS
ATGATGAATACATACCCCTT+TGG 0.493133 6_1:+102529283 None:intergenic
AGTGTTTGTTTGAAGTTGAA+GGG 0.501632 6_1:-102528786 Msa0902760:three_prime_UTR
ATTCTTCCAAAGATGCAGCT+AGG 0.530379 6_1:+102529421 None:intergenic
TCTTACAAAGCTCACAAGAA+TGG 0.532217 6_1:-102529341 Msa0902760:CDS
GTGTTTGTTTGAAGTTGAAG+GGG 0.550371 6_1:-102528785 Msa0902760:three_prime_UTR
AGAATTGTGTGCCTAAACTC+AGG 0.570831 6_1:+102528901 None:intergenic
GGTTTATCGAATTTCAGAGA+TGG 0.592629 6_1:-102529396 Msa0902760:exon
CATCGTCACACTTCAACCAA+AGG 0.595920 6_1:-102529299 Msa0902760:CDS
TGATGCTCAAAATGAGCCGT+GGG 0.596386 6_1:-102528864 Msa0902760:three_prime_UTR
AGATGGATCCAAAGTTCTTG+AGG 0.596761 6_1:-102529181 Msa0902760:CDS
TTGATGCTCAAAATGAGCCG+TGG 0.600460 6_1:-102528865 Msa0902760:three_prime_UTR
TGAGGAACCAGAGGTATGCA+AGG 0.624057 6_1:-102529163 Msa0902760:CDS
TGTTTGTTTGAAGTTGAAGG+GGG 0.627059 6_1:-102528784 Msa0902760:three_prime_UTR
GGGTATATATATGTGTGTTG+GGG 0.642368 6_1:+102529461 None:intergenic
CAAAGTTCTTGAGGAACCAG+AGG 0.651910 6_1:-102529172 Msa0902760:CDS
TTTGTAAGACTGGTTGTGAG+CGG 0.659865 6_1:+102529355 None:intergenic
TAAAGTGTCGATCTCTAATG+GGG 0.672667 6_1:-102529101 Msa0902760:three_prime_UTR
TCGTCACACTTCAACCAAAG+GGG 0.708509 6_1:-102529297 Msa0902760:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAAGAAAAATATAATCCCA+CGG + chr6_1:102529355-102529374 None:intergenic 20.0%
!!! TATGTTCGAAAGTATTTTGA+TGG - chr6_1:102529181-102529200 Msa0902760:CDS 25.0%
TTGTGATTGATTACTGTAGA+TGG - chr6_1:102529002-102529021 Msa0902760:three_prime_UTR 30.0%
! AGGAAGCATAACAAGAAAAA+TGG - chr6_1:102529057-102529076 Msa0902760:three_prime_UTR 30.0%
! AGTACTCTGTTAGCATTTTT+GGG - chr6_1:102529227-102529246 Msa0902760:intron 30.0%
! ATCATTTTCGATTGTGTGAT+TGG - chr6_1:102529379-102529398 Msa0902760:CDS 30.0%
! AAGTGTTTGTTTGAAGTTGA+AGG - chr6_1:102529413-102529432 Msa0902760:five_prime_UTR 30.0%
! AGTGTTTGTTTGAAGTTGAA+GGG - chr6_1:102529414-102529433 Msa0902760:five_prime_UTR 30.0%
ACTTGTGACTTGATTTAGTT+TGG - chr6_1:102529447-102529466 Msa0902760:five_prime_UTR 30.0%
GGGGTATATATATGTGTGTT+GGG + chr6_1:102528743-102528762 None:intergenic 35.0%
! AGGGGTATATATATGTGTGT+TGG + chr6_1:102528744-102528763 None:intergenic 35.0%
!!! TAGGGTTTTGTTTAGAGAGA+GGG + chr6_1:102528763-102528782 None:intergenic 35.0%
GGTTTATCGAATTTCAGAGA+TGG - chr6_1:102528804-102528823 Msa0902760:three_prime_UTR 35.0%
TCTTACAAAGCTCACAAGAA+TGG - chr6_1:102528859-102528878 Msa0902760:three_prime_UTR 35.0%
ATGATGAATACATACCCCTT+TGG + chr6_1:102528920-102528939 None:intergenic 35.0%
!! AGTAAAGTGTCGATCTCTAA+TGG - chr6_1:102529097-102529116 Msa0902760:three_prime_UTR 35.0%
!! GTAAAGTGTCGATCTCTAAT+GGG - chr6_1:102529098-102529117 Msa0902760:three_prime_UTR 35.0%
!! TAAAGTGTCGATCTCTAATG+GGG - chr6_1:102529099-102529118 Msa0902760:three_prime_UTR 35.0%
! CAGTACTCTGTTAGCATTTT+TGG - chr6_1:102529226-102529245 Msa0902760:intron 35.0%
! GTGTTTGTTTGAAGTTGAAG+GGG - chr6_1:102529415-102529434 Msa0902760:five_prime_UTR 35.0%
! TGTTTGTTTGAAGTTGAAGG+GGG - chr6_1:102529416-102529435 Msa0902760:five_prime_UTR 35.0%
!!! AGGGTTTTGTTTAGAGAGAG+GGG + chr6_1:102528762-102528781 None:intergenic 40.0%
!!! CTAGGGTTTTGTTTAGAGAG+AGG + chr6_1:102528764-102528783 None:intergenic 40.0%
TTCTTCCAAAGATGCAGCTA+GGG + chr6_1:102528781-102528800 None:intergenic 40.0%
ATTCTTCCAAAGATGCAGCT+AGG + chr6_1:102528782-102528801 None:intergenic 40.0%
! GCTGCATCTTTGGAAGAATT+AGG - chr6_1:102528783-102528802 Msa0902760:three_prime_UTR 40.0%
! TTTGTAAGACTGGTTGTGAG+CGG + chr6_1:102528848-102528867 None:intergenic 40.0%
! TCTTGTGAGCTTTGTAAGAC+TGG + chr6_1:102528858-102528877 None:intergenic 40.0%
ATGGCATCAAAAAGCCAAAG+AGG - chr6_1:102528878-102528897 Msa0902760:three_prime_UTR 40.0%
ATCGTCACACTTCAACCAAA+GGG - chr6_1:102528902-102528921 Msa0902760:three_prime_UTR 40.0%
AGATGGATCCAAAGTTCTTG+AGG - chr6_1:102529019-102529038 Msa0902760:three_prime_UTR 40.0%
CAATGCTTATGCCTGAGTTT+AGG - chr6_1:102529288-102529307 Msa0902760:intron 40.0%
AGAATTGTGTGCCTAAACTC+AGG + chr6_1:102529302-102529321 None:intergenic 40.0%
CAAAACCCTAGCTGCATCTT+TGG - chr6_1:102528773-102528792 Msa0902760:three_prime_UTR 45.0%
CATCGTCACACTTCAACCAA+AGG - chr6_1:102528901-102528920 Msa0902760:three_prime_UTR 45.0%
TCGTCACACTTCAACCAAAG+GGG - chr6_1:102528903-102528922 Msa0902760:three_prime_UTR 45.0%
! CTCTGGTTCCTCAAGAACTT+TGG + chr6_1:102529030-102529049 None:intergenic 45.0%
CAAAGTTCTTGAGGAACCAG+AGG - chr6_1:102529028-102529047 Msa0902760:three_prime_UTR 45.0%
TATGCTTCCTTGCATACCTC+TGG + chr6_1:102529047-102529066 None:intergenic 45.0%
TTGATGCTCAAAATGAGCCG+TGG - chr6_1:102529335-102529354 Msa0902760:CDS 45.0%
TGATGCTCAAAATGAGCCGT+GGG - chr6_1:102529336-102529355 Msa0902760:CDS 45.0%
! TTGTTTGAAGTTGAAGGGGG+AGG - chr6_1:102529419-102529438 Msa0902760:five_prime_UTR 45.0%
! TGTTTGAAGTTGAAGGGGGA+GGG - chr6_1:102529420-102529439 Msa0902760:five_prime_UTR 45.0%
GAAGTGTGACGATGCCTCTT+TGG + chr6_1:102528895-102528914 None:intergenic 50.0%
! TGAGGAACCAGAGGTATGCA+AGG - chr6_1:102529037-102529056 Msa0902760:three_prime_UTR 50.0%
! GTTTGAAGTTGAAGGGGGAG+GGG - chr6_1:102529421-102529440 Msa0902760:five_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 102528740 102529482 102528740 ID=Msa0902760;Name=Msa0902760
chr6_1 mRNA 102528740 102529482 102528740 ID=Msa0902760-mRNA-1;Parent=Msa0902760;Name=Msa0902760-mRNA-1;_AED=0.36;_eAED=0.36;_QI=83|1|1|1|1|1|2|381|60
chr6_1 exon 102528740 102529201 102528740 ID=Msa0902760-mRNA-1:exon:18026;Parent=Msa0902760-mRNA-1
chr6_1 exon 102529298 102529482 102529298 ID=Msa0902760-mRNA-1:exon:18025;Parent=Msa0902760-mRNA-1
chr6_1 five_prime_UTR 102529400 102529482 102529400 ID=Msa0902760-mRNA-1:five_prime_utr;Parent=Msa0902760-mRNA-1
chr6_1 CDS 102529298 102529399 102529298 ID=Msa0902760-mRNA-1:cds;Parent=Msa0902760-mRNA-1
chr6_1 CDS 102529121 102529201 102529121 ID=Msa0902760-mRNA-1:cds;Parent=Msa0902760-mRNA-1
chr6_1 three_prime_UTR 102528740 102529120 102528740 ID=Msa0902760-mRNA-1:three_prime_utr;Parent=Msa0902760-mRNA-1
Gene Sequence

>Msa0902760

ATGGCGAAATCGAAGAATCACACCGCTCACAACCAGTCTTACAAAGCTCACAAGAATGGCATCAAAAAGCCAAAGAGGCATCGTCACACTTCAACCAAAGGGATGGATCCAAAGTTCTTGAGGAACCAGAGGTATGCAAGGAAGCATAACAAGAAAAATGGTGAAATTGCAGAAGAAGAGTAA

Protein sequence

>Msa0902760

MAKSKNHTAHNQSYKAHKNGIKKPKRHRHTSTKGMDPKFLRNQRYARKHNKKNGEIAEEE*