AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0084940


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0084940 MtrunA17_Chr1g0199621 95.890 73 3 0 2 74 51 123 1.37e-45 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0084940 AT4G14145.1 71.831 71 20 0 2 72 62 132 1.94e-32 109

Find 32 sgRNAs with CRISPR-Local

Find 39 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCCATGTCTGTAGAAATTT+TGG 0.049430 1_2:+64731317 Msa0084940:three_prime_UTR
TTTGGCTTGTATGCATTTAC+TGG 0.178736 1_2:-64730946 None:intergenic
CGCCTGTCTTCATTTGGTTT+TGG 0.185654 1_2:-64731121 None:intergenic
ATTTGGTTCTACTTTAATAA+TGG 0.299141 1_2:+64731387 Msa0084940:three_prime_UTR
AACAGTAGAAGGTACATATT+TGG 0.303280 1_2:+64731370 Msa0084940:three_prime_UTR
TCGTCCAATGAAATCTTCTT+TGG 0.304726 1_2:-64730964 None:intergenic
TACCCTTGAAATGTCCTTGC+TGG 0.322269 1_2:-64730866 None:intergenic
GAATATCTCACTGTCGTTAT+GGG 0.324524 1_2:+64731272 Msa0084940:three_prime_UTR
TGAATATCTCACTGTCGTTA+TGG 0.337770 1_2:+64731271 Msa0084940:three_prime_UTR
TAGACTCGCCTGTCTTCATT+TGG 0.388375 1_2:-64731127 None:intergenic
CAAGCTAAATTCAAATTTGA+AGG 0.396627 1_2:+64731185 Msa0084940:three_prime_UTR
AATTCATCTGCAAGATGAAC+TGG 0.405412 1_2:-64731217 None:intergenic
CAAGCCAAAGAAGATTTCAT+TGG 0.416946 1_2:+64730960 Msa0084940:CDS
TTCAAGGGTAAAAGATGATA+AGG 0.431721 1_2:+64730879 Msa0084940:CDS
TTCATTGGACGATGAGCTAA+AGG 0.458241 1_2:+64730975 Msa0084940:CDS
CTTCAAATTTGAATTTAGCT+TGG 0.461085 1_2:-64731184 None:intergenic
TTCCCAGCAAGGACATTTCA+AGG 0.462275 1_2:+64730863 Msa0084940:CDS
GGTAAAAGATGATAAGGAAT+GGG 0.482081 1_2:+64730885 Msa0084940:CDS
GTCGTTATGGGAGAGGTAGT+TGG 0.482430 1_2:+64731284 Msa0084940:three_prime_UTR
AGAAAAGCACTGTCTAGAAC+AGG 0.493707 1_2:+64730922 Msa0084940:CDS
TCGTTATGGGAGAGGTAGTT+GGG 0.498380 1_2:+64731285 Msa0084940:three_prime_UTR
ACCCTTGAAATGTCCTTGCT+GGG 0.503980 1_2:-64730865 None:intergenic
GGGTAAAAGATGATAAGGAA+TGG 0.518508 1_2:+64730884 Msa0084940:CDS
TTGCACATCAGAAGAAGGAC+GGG 0.532167 1_2:-64730828 None:intergenic
TTCCAAAACCAAATGAAGAC+AGG 0.541017 1_2:+64731119 Msa0084940:CDS
ACTGTAAGGTGAACAGTAGA+AGG 0.543622 1_2:+64731359 Msa0084940:three_prime_UTR
TCTCACTGTCGTTATGGGAG+AGG 0.578593 1_2:+64731277 Msa0084940:three_prime_UTR
ATGCATTGCACATCAGAAGA+AGG 0.596498 1_2:-64730833 None:intergenic
GCATCTGTGTCTTCCCAGCA+AGG 0.597148 1_2:+64730852 Msa0084940:CDS
ACCCAAAATTTCTACAGACA+TGG 0.597759 1_2:-64731319 None:intergenic
TCCCAGCAAGGACATTTCAA+GGG 0.618279 1_2:+64730864 Msa0084940:CDS
ATTGCACATCAGAAGAAGGA+CGG 0.635753 1_2:-64730829 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATTTAATTTTTATTTGTTGT+TGG + chr1_2:64731046-64731065 Msa0084940:intron 10.0%
!!! ATTTTTATTTGTTGTTGGAT+AGG + chr1_2:64731051-64731070 Msa0084940:intron 20.0%
!!! ATTTGGTTCTACTTTAATAA+TGG + chr1_2:64731387-64731406 Msa0084940:three_prime_UTR 20.0%
! ACATTAAATTGCTAATGACA+GGG - chr1_2:64731009-64731028 None:intergenic 25.0%
! TACATTAAATTGCTAATGAC+AGG - chr1_2:64731010-64731029 None:intergenic 25.0%
! CTTCAAATTTGAATTTAGCT+TGG - chr1_2:64731187-64731206 None:intergenic 25.0%
! CAAGCTAAATTCAAATTTGA+AGG + chr1_2:64731185-64731204 Msa0084940:three_prime_UTR 25.0%
!!! AAGGATTTTTAAGTACTGTA+AGG + chr1_2:64731345-64731364 Msa0084940:three_prime_UTR 25.0%
TTCAAGGGTAAAAGATGATA+AGG + chr1_2:64730879-64730898 Msa0084940:CDS 30.0%
GGTAAAAGATGATAAGGAAT+GGG + chr1_2:64730885-64730904 Msa0084940:CDS 30.0%
! TCCATGTCTGTAGAAATTTT+GGG + chr1_2:64731318-64731337 Msa0084940:three_prime_UTR 30.0%
!! TGTAGAAATTTTGGGTATCA+AGG + chr1_2:64731326-64731345 Msa0084940:three_prime_UTR 30.0%
! AACAGTAGAAGGTACATATT+TGG + chr1_2:64731370-64731389 Msa0084940:three_prime_UTR 30.0%
GGGTAAAAGATGATAAGGAA+TGG + chr1_2:64730884-64730903 Msa0084940:CDS 35.0%
!! TTTGGCTTGTATGCATTTAC+TGG - chr1_2:64730949-64730968 None:intergenic 35.0%
CAAGCCAAAGAAGATTTCAT+TGG + chr1_2:64730960-64730979 Msa0084940:CDS 35.0%
TCGTCCAATGAAATCTTCTT+TGG - chr1_2:64730967-64730986 None:intergenic 35.0%
ATAGGCTTTGCAACAAAAAG+TGG + chr1_2:64731069-64731088 Msa0084940:intron 35.0%
TTCCAAAACCAAATGAAGAC+AGG + chr1_2:64731119-64731138 Msa0084940:CDS 35.0%
AATTCATCTGCAAGATGAAC+TGG - chr1_2:64731220-64731239 None:intergenic 35.0%
TGAATATCTCACTGTCGTTA+TGG + chr1_2:64731271-64731290 Msa0084940:three_prime_UTR 35.0%
GAATATCTCACTGTCGTTAT+GGG + chr1_2:64731272-64731291 Msa0084940:three_prime_UTR 35.0%
! CTCCATGTCTGTAGAAATTT+TGG + chr1_2:64731317-64731336 Msa0084940:three_prime_UTR 35.0%
ACCCAAAATTTCTACAGACA+TGG - chr1_2:64731322-64731341 None:intergenic 35.0%
ATGCATTGCACATCAGAAGA+AGG - chr1_2:64730836-64730855 None:intergenic 40.0%
!! AGAAAAGCACTGTCTAGAAC+AGG + chr1_2:64730922-64730941 Msa0084940:CDS 40.0%
TTCATTGGACGATGAGCTAA+AGG + chr1_2:64730975-64730994 Msa0084940:CDS 40.0%
ACTGTAAGGTGAACAGTAGA+AGG + chr1_2:64731359-64731378 Msa0084940:three_prime_UTR 40.0%
TTCCCAGCAAGGACATTTCA+AGG + chr1_2:64730863-64730882 Msa0084940:CDS 45.0%
TCCCAGCAAGGACATTTCAA+GGG + chr1_2:64730864-64730883 Msa0084940:CDS 45.0%
ACCCTTGAAATGTCCTTGCT+GGG - chr1_2:64730868-64730887 None:intergenic 45.0%
TACCCTTGAAATGTCCTTGC+TGG - chr1_2:64730869-64730888 None:intergenic 45.0%
!! CGCCTGTCTTCATTTGGTTT+TGG - chr1_2:64731124-64731143 None:intergenic 45.0%
TAGACTCGCCTGTCTTCATT+TGG - chr1_2:64731130-64731149 None:intergenic 45.0%
TCGTTATGGGAGAGGTAGTT+GGG + chr1_2:64731285-64731304 Msa0084940:three_prime_UTR 45.0%
!! AACAAATAAAAATTAAATTA+TGG - chr1_2:64731044-64731063 None:intergenic 5.0%
TCTCACTGTCGTTATGGGAG+AGG + chr1_2:64731277-64731296 Msa0084940:three_prime_UTR 50.0%
GTCGTTATGGGAGAGGTAGT+TGG + chr1_2:64731284-64731303 Msa0084940:three_prime_UTR 50.0%
GCATCTGTGTCTTCCCAGCA+AGG + chr1_2:64730852-64730871 Msa0084940:CDS 55.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 64730831 64731416 64730831 ID=Msa0084940;Name=Msa0084940
chr1_2 mRNA 64730831 64731416 64730831 ID=Msa0084940-mRNA-1;Parent=Msa0084940;Name=Msa0084940-mRNA-1;_AED=0.00;_eAED=0.00;_QI=19|1|1|1|1|1|2|266|74
chr1_2 exon 64730831 64730996 64730831 ID=Msa0084940-mRNA-1:exon:21845;Parent=Msa0084940-mRNA-1
chr1_2 exon 64731073 64731416 64731073 ID=Msa0084940-mRNA-1:exon:21846;Parent=Msa0084940-mRNA-1
chr1_2 five_prime_UTR 64730831 64730849 64730831 ID=Msa0084940-mRNA-1:five_prime_utr;Parent=Msa0084940-mRNA-1
chr1_2 CDS 64730850 64730996 64730850 ID=Msa0084940-mRNA-1:cds;Parent=Msa0084940-mRNA-1
chr1_2 CDS 64731073 64731150 64731073 ID=Msa0084940-mRNA-1:cds;Parent=Msa0084940-mRNA-1
chr1_2 three_prime_UTR 64731151 64731416 64731151 ID=Msa0084940-mRNA-1:three_prime_utr;Parent=Msa0084940-mRNA-1
Gene Sequence

>Msa0084940

ATGCATCTGTGTCTTCCCAGCAAGGACATTTCAAGGGTAAAAGATGATAAGGAATGGGAAATAATTGAAGCAAGAAAAGCACTGTCTAGAACAGGACCAGTAAATGCATACAAGCCAAAGAAGATTTCATTGGACGATGAGCTAAAGGCTTTGCAACAAAAAGTGGACATTAATGACTACGAGTTCAAGAAAATTCCAAAACCAAATGAAGACAGGCGAGTCTAG

Protein sequence

>Msa0084940

MHLCLPSKDISRVKDDKEWEIIEARKALSRTGPVNAYKPKKISLDDELKALQQKVDINDYEFKKIPKPNEDRRV*