AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0543270

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0543270 MtrunA17_Chr4g0023061 93.651 189 11 1 1 188 1 189 3.14e-119 335
Msa0543270 MtrunA17_Chr4g0023051 90.476 189 17 1 1 188 1 189 6.78e-113 319
Msa0543270 MtrunA17_Chr4g0022951 86.294 197 18 2 1 188 1 197 2.27e-109 310
Msa0543270 MtrunA17_Chr4g0022991 85.246 183 26 1 1 182 1 183 1.46e-100 288
Msa0543270 MtrunA17_Chr4g0023041 89.205 176 18 1 1 175 1 176 6.04e-100 286
Msa0543270 MtrunA17_Chr2g0323311 35.500 200 93 5 1 165 1 199 1.30e-23 93.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 37 sgRNAs with CRISPR-Local

Find 86 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTCCAAAATAATGCTCTTTA+TGG 0.186974 4_1:+29215679 None:intergenic
AAACACCACATATAGAAAAT+AGG 0.217188 4_1:+29216529 None:intergenic
AAAGAAATTCTTCAAGAGTT+TGG 0.226306 4_1:+29216468 None:intergenic
TCTCATAAGCTTAGTATTTA+CGG 0.283536 4_1:-29215849 Msa0543270:CDS
TTTATATGAAAGTTTGGTTT+TGG 0.315648 4_1:+29216562 None:intergenic
GACCATATAGCAACATCTTT+TGG 0.318622 4_1:+29215744 None:intergenic
TTAGTATTTACGGTGTGTTT+TGG 0.356630 4_1:-29215839 Msa0543270:CDS
TATGGTGTTGGAAACTATAT+TGG 0.360379 4_1:-29216288 Msa0543270:intron
GCTCGTTATAAAACTTGTTA+CGG 0.374404 4_1:-29216088 Msa0543270:CDS
CCCTTTACATCCATGTACTT+TGG 0.380899 4_1:+29215722 None:intergenic
TGTTACGGCTTTGATTGTTT+TGG 0.407040 4_1:-29216073 Msa0543270:CDS
AACACCACATATAGAAAATA+GGG 0.409892 4_1:+29216530 None:intergenic
TGCCAAAAGATGTTGCTATA+TGG 0.423316 4_1:-29215746 Msa0543270:CDS
TATTAAGATGCAACAATGTT+TGG 0.427570 4_1:+29216585 None:intergenic
TTGAGTTGCAAAGAGAGAAA+AGG 0.434179 4_1:+29215777 None:intergenic
TCCAAAGTACATGGATGTAA+AGG 0.456302 4_1:-29215723 Msa0543270:CDS
TGCAACAATGTTTGGTTGGT+GGG 0.470355 4_1:+29216593 None:intergenic
CCAAAGTACATGGATGTAAA+GGG 0.489055 4_1:-29215722 Msa0543270:CDS
AAAAGCTCCTCATGATGTAC+TGG 0.490686 4_1:+29216429 None:intergenic
TTTAAAAGTGATCAAAGCTA+TGG 0.495130 4_1:-29216306 Msa0543270:CDS
TCTCTAATATTGCGCTTCCT+CGG 0.504970 4_1:+29215909 None:intergenic
ATGTCATCTAGATCAACAAC+AGG 0.505619 4_1:+29216377 None:intergenic
TGTATAACTTCAAGCTAGCA+AGG 0.517140 4_1:+29216505 None:intergenic
TGAGTGGTGAGCAACAACTT+TGG 0.524133 4_1:+29216346 None:intergenic
CAAAGACGATTGAGTGGCGT+TGG 0.529377 4_1:+29216012 None:intergenic
AGTGATCAAAGCTATGGTGT+TGG 0.544417 4_1:-29216300 Msa0543270:CDS
TTTATCTTCAGATAGTTCAA+AGG 0.573345 4_1:-29215984 Msa0543270:CDS
AAGATGCAACAATGTTTGGT+TGG 0.580143 4_1:+29216589 None:intergenic
ATGCAACAATGTTTGGTTGG+TGG 0.581182 4_1:+29216592 None:intergenic
GCTATATGGTCCAAAGTACA+TGG 0.601132 4_1:-29215732 Msa0543270:CDS
TCAAAGAAAATGTCCACCAA+AGG 0.623053 4_1:-29215953 Msa0543270:CDS
GTATAACTTCAAGCTAGCAA+GGG 0.634869 4_1:+29216506 None:intergenic
CTGTACGTTTGTTCTTTGAG+TGG 0.647000 4_1:+29216330 None:intergenic
ACTTGTCAAAGACGATTGAG+TGG 0.668519 4_1:+29216006 None:intergenic
AGTACATGGATGTAAAGGGT+CGG 0.669346 4_1:-29215718 Msa0543270:CDS
TACACAACCAGTACATCATG+AGG 0.683592 4_1:-29216436 Msa0543270:exon
CATGAGAAAGAAACTAGCCG+AGG 0.686816 4_1:-29215926 Msa0543270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATATGAAAGTTTGGTTT+TGG + chr4_1:29215725-29215744 None:intergenic 20.0%
!!! CTCTTTTTTATATGAAAGTT+TGG + chr4_1:29215731-29215750 None:intergenic 20.0%
!! AAAAACTTTGTGCTATAAAA+AGG + chr4_1:29216135-29216154 None:intergenic 20.0%
!!! TTTATATGAAAGTTTGGTTT+TGG + chr4_1:29215725-29215744 None:intergenic 20.0%
!!! CTCTTTTTTATATGAAAGTT+TGG + chr4_1:29215731-29215750 None:intergenic 20.0%
!! AAAAACTTTGTGCTATAAAA+AGG + chr4_1:29216135-29216154 None:intergenic 20.0%
! TATTAAGATGCAACAATGTT+TGG + chr4_1:29215702-29215721 None:intergenic 25.0%
! AACACCACATATAGAAAATA+GGG + chr4_1:29215757-29215776 None:intergenic 25.0%
! AAACACCACATATAGAAAAT+AGG + chr4_1:29215758-29215777 None:intergenic 25.0%
! AAAGAAATTCTTCAAGAGTT+TGG + chr4_1:29215819-29215838 None:intergenic 25.0%
! TTTAAAAGTGATCAAAGCTA+TGG - chr4_1:29215978-29215997 Msa0543270:CDS 25.0%
! TTTGTGCTATAAAAAGGAAA+TGG + chr4_1:29216129-29216148 None:intergenic 25.0%
! TTTATCTTCAGATAGTTCAA+AGG - chr4_1:29216300-29216319 Msa0543270:CDS 25.0%
! TCTCATAAGCTTAGTATTTA+CGG - chr4_1:29216435-29216454 Msa0543270:exon 25.0%
! TATTAAGATGCAACAATGTT+TGG + chr4_1:29215702-29215721 None:intergenic 25.0%
! AACACCACATATAGAAAATA+GGG + chr4_1:29215757-29215776 None:intergenic 25.0%
! AAACACCACATATAGAAAAT+AGG + chr4_1:29215758-29215777 None:intergenic 25.0%
! AAAGAAATTCTTCAAGAGTT+TGG + chr4_1:29215819-29215838 None:intergenic 25.0%
! TTTAAAAGTGATCAAAGCTA+TGG - chr4_1:29215978-29215997 Msa0543270:CDS 25.0%
! TTTGTGCTATAAAAAGGAAA+TGG + chr4_1:29216129-29216148 None:intergenic 25.0%
! TTTATCTTCAGATAGTTCAA+AGG - chr4_1:29216300-29216319 Msa0543270:CDS 25.0%
! TCTCATAAGCTTAGTATTTA+CGG - chr4_1:29216435-29216454 Msa0543270:exon 25.0%
! GTTACCCTATTTTCTATATG+TGG - chr4_1:29215750-29215769 Msa0543270:CDS 30.0%
! TATGGTGTTGGAAACTATAT+TGG - chr4_1:29215996-29216015 Msa0543270:CDS 30.0%
!! GCTCGTTATAAAACTTGTTA+CGG - chr4_1:29216196-29216215 Msa0543270:intron 30.0%
! TTCTTTCTCATGTTTTCCTT+TGG + chr4_1:29216350-29216369 None:intergenic 30.0%
!! TGAGTTTTATGCAATGTGTT+TGG - chr4_1:29216411-29216430 Msa0543270:CDS 30.0%
! TTAGTATTTACGGTGTGTTT+TGG - chr4_1:29216445-29216464 Msa0543270:five_prime_UTR 30.0%
! TAGTATTTACGGTGTGTTTT+GGG - chr4_1:29216446-29216465 Msa0543270:five_prime_UTR 30.0%
! GTTACCCTATTTTCTATATG+TGG - chr4_1:29215750-29215769 Msa0543270:CDS 30.0%
! TATGGTGTTGGAAACTATAT+TGG - chr4_1:29215996-29216015 Msa0543270:CDS 30.0%
!! GCTCGTTATAAAACTTGTTA+CGG - chr4_1:29216196-29216215 Msa0543270:intron 30.0%
! TTCTTTCTCATGTTTTCCTT+TGG + chr4_1:29216350-29216369 None:intergenic 30.0%
!! TGAGTTTTATGCAATGTGTT+TGG - chr4_1:29216411-29216430 Msa0543270:CDS 30.0%
! TTAGTATTTACGGTGTGTTT+TGG - chr4_1:29216445-29216464 Msa0543270:five_prime_UTR 30.0%
! TAGTATTTACGGTGTGTTTT+GGG - chr4_1:29216446-29216465 Msa0543270:five_prime_UTR 30.0%
AAGATGCAACAATGTTTGGT+TGG + chr4_1:29215698-29215717 None:intergenic 35.0%
GTATAACTTCAAGCTAGCAA+GGG + chr4_1:29215781-29215800 None:intergenic 35.0%
TGTATAACTTCAAGCTAGCA+AGG + chr4_1:29215782-29215801 None:intergenic 35.0%
ATGTCATCTAGATCAACAAC+AGG + chr4_1:29215910-29215929 None:intergenic 35.0%
!! TGTTACGGCTTTGATTGTTT+TGG - chr4_1:29216211-29216230 Msa0543270:intron 35.0%
TCAAAGAAAATGTCCACCAA+AGG - chr4_1:29216331-29216350 Msa0543270:CDS 35.0%
! TTTCTCATGTTTTCCTTTGG+TGG + chr4_1:29216347-29216366 None:intergenic 35.0%
!!! GTGTGTTTTGGGAAACTATT+TGG - chr4_1:29216457-29216476 Msa0543270:five_prime_UTR 35.0%
! TTGAGTTGCAAAGAGAGAAA+AGG + chr4_1:29216510-29216529 None:intergenic 35.0%
TGCCAAAAGATGTTGCTATA+TGG - chr4_1:29216538-29216557 Msa0543270:five_prime_UTR 35.0%
! GACCATATAGCAACATCTTT+TGG + chr4_1:29216543-29216562 None:intergenic 35.0%
TCCAAAGTACATGGATGTAA+AGG - chr4_1:29216561-29216580 Msa0543270:five_prime_UTR 35.0%
CCAAAGTACATGGATGTAAA+GGG - chr4_1:29216562-29216581 Msa0543270:five_prime_UTR 35.0%
AAGATGCAACAATGTTTGGT+TGG + chr4_1:29215698-29215717 None:intergenic 35.0%
GTATAACTTCAAGCTAGCAA+GGG + chr4_1:29215781-29215800 None:intergenic 35.0%
TGTATAACTTCAAGCTAGCA+AGG + chr4_1:29215782-29215801 None:intergenic 35.0%
ATGTCATCTAGATCAACAAC+AGG + chr4_1:29215910-29215929 None:intergenic 35.0%
!! TGTTACGGCTTTGATTGTTT+TGG - chr4_1:29216211-29216230 Msa0543270:intron 35.0%
TCAAAGAAAATGTCCACCAA+AGG - chr4_1:29216331-29216350 Msa0543270:CDS 35.0%
! TTTCTCATGTTTTCCTTTGG+TGG + chr4_1:29216347-29216366 None:intergenic 35.0%
!!! GTGTGTTTTGGGAAACTATT+TGG - chr4_1:29216457-29216476 Msa0543270:five_prime_UTR 35.0%
! TTGAGTTGCAAAGAGAGAAA+AGG + chr4_1:29216510-29216529 None:intergenic 35.0%
TGCCAAAAGATGTTGCTATA+TGG - chr4_1:29216538-29216557 Msa0543270:five_prime_UTR 35.0%
! GACCATATAGCAACATCTTT+TGG + chr4_1:29216543-29216562 None:intergenic 35.0%
TCCAAAGTACATGGATGTAA+AGG - chr4_1:29216561-29216580 Msa0543270:five_prime_UTR 35.0%
CCAAAGTACATGGATGTAAA+GGG - chr4_1:29216562-29216581 Msa0543270:five_prime_UTR 35.0%
TACACAACCAGTACATCATG+AGG - chr4_1:29215848-29215867 Msa0543270:CDS 40.0%
AAAAGCTCCTCATGATGTAC+TGG + chr4_1:29215858-29215877 None:intergenic 40.0%
CTGTACGTTTGTTCTTTGAG+TGG + chr4_1:29215957-29215976 None:intergenic 40.0%
AGTGATCAAAGCTATGGTGT+TGG - chr4_1:29215984-29216003 Msa0543270:CDS 40.0%
ACTTGTCAAAGACGATTGAG+TGG + chr4_1:29216281-29216300 None:intergenic 40.0%
TCTCTAATATTGCGCTTCCT+CGG + chr4_1:29216378-29216397 None:intergenic 40.0%
GCTATATGGTCCAAAGTACA+TGG - chr4_1:29216552-29216571 Msa0543270:five_prime_UTR 40.0%
CCCTTTACATCCATGTACTT+TGG + chr4_1:29216565-29216584 None:intergenic 40.0%
AGTACATGGATGTAAAGGGT+CGG - chr4_1:29216566-29216585 Msa0543270:five_prime_UTR 40.0%
TACACAACCAGTACATCATG+AGG - chr4_1:29215848-29215867 Msa0543270:CDS 40.0%
AAAAGCTCCTCATGATGTAC+TGG + chr4_1:29215858-29215877 None:intergenic 40.0%
CTGTACGTTTGTTCTTTGAG+TGG + chr4_1:29215957-29215976 None:intergenic 40.0%
AGTGATCAAAGCTATGGTGT+TGG - chr4_1:29215984-29216003 Msa0543270:CDS 40.0%
ACTTGTCAAAGACGATTGAG+TGG + chr4_1:29216281-29216300 None:intergenic 40.0%
TCTCTAATATTGCGCTTCCT+CGG + chr4_1:29216378-29216397 None:intergenic 40.0%
GCTATATGGTCCAAAGTACA+TGG - chr4_1:29216552-29216571 Msa0543270:five_prime_UTR 40.0%
CCCTTTACATCCATGTACTT+TGG + chr4_1:29216565-29216584 None:intergenic 40.0%
AGTACATGGATGTAAAGGGT+CGG - chr4_1:29216566-29216585 Msa0543270:five_prime_UTR 40.0%
TGAGTGGTGAGCAACAACTT+TGG + chr4_1:29215941-29215960 None:intergenic 45.0%
CATGAGAAAGAAACTAGCCG+AGG - chr4_1:29216358-29216377 Msa0543270:CDS 45.0%
TGAGTGGTGAGCAACAACTT+TGG + chr4_1:29215941-29215960 None:intergenic 45.0%
CATGAGAAAGAAACTAGCCG+AGG - chr4_1:29216358-29216377 Msa0543270:CDS 45.0%
CAAAGACGATTGAGTGGCGT+TGG + chr4_1:29216275-29216294 None:intergenic 50.0%
CAAAGACGATTGAGTGGCGT+TGG + chr4_1:29216275-29216294 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_1 gene 29215693 29216613 29215693 ID=Msa0543270;Name=Msa0543270
chr4_1 mRNA 29215693 29216613 29215693 ID=Msa0543270-mRNA-1;Parent=Msa0543270;Name=Msa0543270-mRNA-1;_AED=0.01;_eAED=0.01;_QI=172|1|1|1|1|1|2|13|188
chr4_1 exon 29215693 29216119 29215693 ID=Msa0543270-mRNA-1:exon:7826;Parent=Msa0543270-mRNA-1
chr4_1 exon 29216289 29216613 29216289 ID=Msa0543270-mRNA-1:exon:7825;Parent=Msa0543270-mRNA-1
chr4_1 five_prime_UTR 29216442 29216613 29216442 ID=Msa0543270-mRNA-1:five_prime_utr;Parent=Msa0543270-mRNA-1
chr4_1 CDS 29216289 29216441 29216289 ID=Msa0543270-mRNA-1:cds;Parent=Msa0543270-mRNA-1
chr4_1 CDS 29215706 29216119 29215706 ID=Msa0543270-mRNA-1:cds;Parent=Msa0543270-mRNA-1
chr4_1 three_prime_UTR 29215693 29215705 29215693 ID=Msa0543270-mRNA-1:three_prime_utr;Parent=Msa0543270-mRNA-1
Gene Sequence

>Msa0543270

ATGAGGAGCTTTTCAAAGAGCAAATTCTCTCAATGTTTTCGTCCTGTTGTTGATCTAGATGACATACTTGAATCCAAAGTTGTTGCTCACCACTCAAAGAACAAACGTACAGTTTTAAAAGTGATCAAAGCTATGGTGTTGGAAACTATATTGAATAGAAGAGCTCGTTATAAAACTTGTTACGGCTTTGATTGTTTTGGTGTGTCAAAGCATAATTATTCGACGTATAAGAAAGTAACCAACGCCACTCAATCGTCTTTGACAAGTTTATCTTCAGATAGTTCAAAGGTATCACAATCAAAGAAAATGTCCACCAAAGGAAAACATGAGAAAGAAACTAGCCGAGGAAGCGCAATATTAGAGAAGCAAAAGAAGTTTGAGTTTTATGCAATGTGTTTGGTTCTCATAAGCTTAGTATTTACGGTGTGTTTTGGGAAACTATTTGGAATTTTTTTGACTTCAATATGCATCTTCCTTTTCTCTCTTTGCAACTCAAACTATAGCTGCCAAAAGATGTTGCTATATGGTCCAAAGTACATGGATGTAAAGGGTCGGTATAGAAAGTGA
Protein sequence

>Msa0543270

MRSFSKSKFSQCFRPVVDLDDILESKVVAHHSKNKRTVLKVIKAMVLETILNRRARYKTCYGFDCFGVSKHNYSTYKKVTNATQSSLTSLSSDSSKVSQSKKMSTKGKHEKETSRGSAILEKQKKFEFYAMCLVLISLVFTVCFGKLFGIFLTSICIFLFSLCNSNYSCQKMLLYGPKYMDVKGRYRK*