AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0383380


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0383380 MtrunA17_Chr3g0139181 85.470 117 17 0 22 138 1 117 1.28e-66 197
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0383380 AT2G24395.1 73.134 67 18 0 69 135 61 127 2.19e-32 111

Find 39 sgRNAs with CRISPR-Local

Find 92 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATTTCCTTCATTCAATTA+AGG 0.229113 3_1:-86278411 Msa0383380:three_prime_UTR
CGACGGTAGATACGGTTGTT+AGG 0.341305 3_1:+86278661 None:intergenic
CCTACGACTGTGTCTGTAAC+TGG 0.344862 3_1:+86278846 None:intergenic
ATATGATGCCTACTGCTATA+AGG 0.354942 3_1:+86278811 None:intergenic
GGAGGAGAGAAGAGGATTAA+TGG 0.361525 3_1:-86278911 Msa0383380:CDS
GAGATGATGAATTAATTAAT+AGG 0.374694 3_1:+86278437 None:intergenic
ATAGGAGAATCGTTGAAATC+AGG 0.450197 3_1:+86278455 None:intergenic
GACGGTAGATACGGTTGTTA+GGG 0.453240 3_1:+86278662 None:intergenic
GAAGGGAGGGTGAGAATAAA+CGG 0.455974 3_1:+86278874 None:intergenic
TCTCTCCTCCCACGATGGAT+CGG 0.506919 3_1:+86278924 None:intergenic
GTATTGTTCCTTATAGCAGT+AGG 0.522666 3_1:-86278819 Msa0383380:CDS
AAGGACATCGACGGTAGATA+CGG 0.533599 3_1:+86278653 None:intergenic
AAAGCACCTTAATTGAATGA+AGG 0.534547 3_1:+86278405 None:intergenic
TACAGACACAGTCGTAGGCT+TGG 0.536423 3_1:-86278841 Msa0383380:CDS
TCAAGTGAGCAGTTAAATGA+AGG 0.542638 3_1:+86278278 None:intergenic
CACGATAAAGTGTGTGAAGG+TGG 0.544142 3_1:-86278779 Msa0383380:CDS
GATAAGGAGGAGAAGAAATG+AGG 0.556274 3_1:-86278972 None:intergenic
TGTGAACCTTGCAATGGAAA+AGG 0.558985 3_1:-86278733 Msa0383380:CDS
TTGCAATGGAAAAGGATGGT+TGG 0.588776 3_1:-86278725 Msa0383380:CDS
GTAACTGGAAATTGAAGGGA+GGG 0.598428 3_1:+86278861 None:intergenic
TGTCTGTAACTGGAAATTGA+AGG 0.607601 3_1:+86278856 None:intergenic
CCTCTTCTCTCCTCCCACGA+TGG 0.612788 3_1:+86278919 None:intergenic
ATCATGTGTGAACCTTGCAA+TGG 0.614562 3_1:-86278739 Msa0383380:CDS
GTATTCTACTCTACATACAT+TGG 0.617882 3_1:+86278304 None:intergenic
CCATCGTGGGAGGAGAGAAG+AGG 0.627180 3_1:-86278919 Msa0383380:CDS
TAACGTACGGCTTTGCACGA+AGG 0.629237 3_1:+86278634 None:intergenic
CTCAACCGATCCATCGTGGG+AGG 0.631725 3_1:-86278929 Msa0383380:CDS
GTCTGTAACTGGAAATTGAA+GGG 0.632329 3_1:+86278857 None:intergenic
CCAGTTACAGACACAGTCGT+AGG 0.638479 3_1:-86278846 Msa0383380:CDS
TTCACTCAACCGATCCATCG+TGG 0.640322 3_1:-86278933 Msa0383380:CDS
TCACTCAACCGATCCATCGT+GGG 0.647997 3_1:-86278932 Msa0383380:CDS
TACGCATGCATGTGATTGTG+AGG 0.649817 3_1:+86278364 None:intergenic
ACGGTAGATACGGTTGTTAG+GGG 0.651272 3_1:+86278663 None:intergenic
TGTGTTGTGTTCAAACTGCA+AGG 0.652118 3_1:-86278498 Msa0383380:CDS
CATCACGATAAAGTGTGTGA+AGG 0.657024 3_1:-86278782 Msa0383380:CDS
AACCTTGCAATGGAAAAGGA+TGG 0.676800 3_1:-86278729 Msa0383380:CDS
ACGCATGCATGTGATTGTGA+GGG 0.709226 3_1:+86278365 None:intergenic
CTTTGCACGAAGGACATCGA+CGG 0.718197 3_1:+86278644 None:intergenic
TGTAACTGGAAATTGAAGGG+AGG 0.723775 3_1:+86278860 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATATATATATAATTGTTGC+AGG - chr3_1:86278668-86278687 Msa0383380:CDS 15.0%
!! TATTATTTAAGAAAAAAAGG+TGG - chr3_1:86278865-86278884 Msa0383380:CDS 15.0%
!! TATATATATATAATTGTTGC+AGG - chr3_1:86278668-86278687 Msa0383380:CDS 15.0%
!! TATTATTTAAGAAAAAAAGG+TGG - chr3_1:86278865-86278884 Msa0383380:CDS 15.0%
!! GAGATGATGAATTAATTAAT+AGG + chr3_1:86278762-86278781 None:intergenic 20.0%
!! GAGATGATGAATTAATTAAT+AGG + chr3_1:86278762-86278781 None:intergenic 20.0%
! ATGATATTAGCAATAACGTA+CGG + chr3_1:86278578-86278597 None:intergenic 25.0%
! TATATATAATTGTTGCAGGT+TGG - chr3_1:86278672-86278691 Msa0383380:CDS 25.0%
! TCATTTCCTTCATTCAATTA+AGG - chr3_1:86278785-86278804 Msa0383380:CDS 25.0%
! ATGATATTAGCAATAACGTA+CGG + chr3_1:86278578-86278597 None:intergenic 25.0%
! TATATATAATTGTTGCAGGT+TGG - chr3_1:86278672-86278691 Msa0383380:CDS 25.0%
! TCATTTCCTTCATTCAATTA+AGG - chr3_1:86278785-86278804 Msa0383380:CDS 25.0%
! AAAGCACCTTAATTGAATGA+AGG + chr3_1:86278794-86278813 None:intergenic 30.0%
GTATTCTACTCTACATACAT+TGG + chr3_1:86278895-86278914 None:intergenic 30.0%
! AAAGCACCTTAATTGAATGA+AGG + chr3_1:86278794-86278813 None:intergenic 30.0%
GTATTCTACTCTACATACAT+TGG + chr3_1:86278895-86278914 None:intergenic 30.0%
GTCTGTAACTGGAAATTGAA+GGG + chr3_1:86278342-86278361 None:intergenic 35.0%
TGTCTGTAACTGGAAATTGA+AGG + chr3_1:86278343-86278362 None:intergenic 35.0%
GTATTGTTCCTTATAGCAGT+AGG - chr3_1:86278377-86278396 Msa0383380:three_prime_UTR 35.0%
ATATGATGCCTACTGCTATA+AGG + chr3_1:86278388-86278407 None:intergenic 35.0%
!! TTGGTATGTGAGTTTTGTGA+AGG - chr3_1:86278490-86278509 Msa0383380:CDS 35.0%
!!! GGGCTTTGACATTAGTTTTT+TGG + chr3_1:86278516-86278535 None:intergenic 35.0%
ATAGGAGAATCGTTGAAATC+AGG + chr3_1:86278744-86278763 None:intergenic 35.0%
TCAAGTGAGCAGTTAAATGA+AGG + chr3_1:86278921-86278940 None:intergenic 35.0%
GTCTGTAACTGGAAATTGAA+GGG + chr3_1:86278342-86278361 None:intergenic 35.0%
TGTCTGTAACTGGAAATTGA+AGG + chr3_1:86278343-86278362 None:intergenic 35.0%
GTATTGTTCCTTATAGCAGT+AGG - chr3_1:86278377-86278396 Msa0383380:three_prime_UTR 35.0%
ATATGATGCCTACTGCTATA+AGG + chr3_1:86278388-86278407 None:intergenic 35.0%
!! TTGGTATGTGAGTTTTGTGA+AGG - chr3_1:86278490-86278509 Msa0383380:CDS 35.0%
!!! GGGCTTTGACATTAGTTTTT+TGG + chr3_1:86278516-86278535 None:intergenic 35.0%
ATAGGAGAATCGTTGAAATC+AGG + chr3_1:86278744-86278763 None:intergenic 35.0%
TCAAGTGAGCAGTTAAATGA+AGG + chr3_1:86278921-86278940 None:intergenic 35.0%
GTAACTGGAAATTGAAGGGA+GGG + chr3_1:86278338-86278357 None:intergenic 40.0%
TGTAACTGGAAATTGAAGGG+AGG + chr3_1:86278339-86278358 None:intergenic 40.0%
CATCACGATAAAGTGTGTGA+AGG - chr3_1:86278414-86278433 Msa0383380:three_prime_UTR 40.0%
ATCATGTGTGAACCTTGCAA+TGG - chr3_1:86278457-86278476 Msa0383380:CDS 40.0%
TGTGAACCTTGCAATGGAAA+AGG - chr3_1:86278463-86278482 Msa0383380:CDS 40.0%
AACCTTGCAATGGAAAAGGA+TGG - chr3_1:86278467-86278486 Msa0383380:CDS 40.0%
! AACCATCCTTTTCCATTGCA+AGG + chr3_1:86278472-86278491 None:intergenic 40.0%
TTGCAATGGAAAAGGATGGT+TGG - chr3_1:86278471-86278490 Msa0383380:CDS 40.0%
TGTGTTGTGTTCAAACTGCA+AGG - chr3_1:86278698-86278717 Msa0383380:CDS 40.0%
GTAACTGGAAATTGAAGGGA+GGG + chr3_1:86278338-86278357 None:intergenic 40.0%
TGTAACTGGAAATTGAAGGG+AGG + chr3_1:86278339-86278358 None:intergenic 40.0%
CATCACGATAAAGTGTGTGA+AGG - chr3_1:86278414-86278433 Msa0383380:three_prime_UTR 40.0%
ATCATGTGTGAACCTTGCAA+TGG - chr3_1:86278457-86278476 Msa0383380:CDS 40.0%
TGTGAACCTTGCAATGGAAA+AGG - chr3_1:86278463-86278482 Msa0383380:CDS 40.0%
AACCTTGCAATGGAAAAGGA+TGG - chr3_1:86278467-86278486 Msa0383380:CDS 40.0%
! AACCATCCTTTTCCATTGCA+AGG + chr3_1:86278472-86278491 None:intergenic 40.0%
TTGCAATGGAAAAGGATGGT+TGG - chr3_1:86278471-86278490 Msa0383380:CDS 40.0%
TGTGTTGTGTTCAAACTGCA+AGG - chr3_1:86278698-86278717 Msa0383380:CDS 40.0%
GGAGGAGAGAAGAGGATTAA+TGG - chr3_1:86278285-86278304 Msa0383380:three_prime_UTR 45.0%
GAAGGGAGGGTGAGAATAAA+CGG + chr3_1:86278325-86278344 None:intergenic 45.0%
CACGATAAAGTGTGTGAAGG+TGG - chr3_1:86278417-86278436 Msa0383380:three_prime_UTR 45.0%
ACGGTAGATACGGTTGTTAG+GGG + chr3_1:86278536-86278555 None:intergenic 45.0%
GACGGTAGATACGGTTGTTA+GGG + chr3_1:86278537-86278556 None:intergenic 45.0%
AAGGACATCGACGGTAGATA+CGG + chr3_1:86278546-86278565 None:intergenic 45.0%
ACGCATGCATGTGATTGTGA+GGG + chr3_1:86278834-86278853 None:intergenic 45.0%
TACGCATGCATGTGATTGTG+AGG + chr3_1:86278835-86278854 None:intergenic 45.0%
GGAGGAGAGAAGAGGATTAA+TGG - chr3_1:86278285-86278304 Msa0383380:three_prime_UTR 45.0%
GAAGGGAGGGTGAGAATAAA+CGG + chr3_1:86278325-86278344 None:intergenic 45.0%
CACGATAAAGTGTGTGAAGG+TGG - chr3_1:86278417-86278436 Msa0383380:three_prime_UTR 45.0%
ACGGTAGATACGGTTGTTAG+GGG + chr3_1:86278536-86278555 None:intergenic 45.0%
GACGGTAGATACGGTTGTTA+GGG + chr3_1:86278537-86278556 None:intergenic 45.0%
AAGGACATCGACGGTAGATA+CGG + chr3_1:86278546-86278565 None:intergenic 45.0%
ACGCATGCATGTGATTGTGA+GGG + chr3_1:86278834-86278853 None:intergenic 45.0%
TACGCATGCATGTGATTGTG+AGG + chr3_1:86278835-86278854 None:intergenic 45.0%
!! TATTATTATTTAAGAAAAAA+AGG - chr3_1:86278862-86278881 Msa0383380:CDS 5.0%
!! TATTATTATTTAAGAAAAAA+AGG - chr3_1:86278862-86278881 Msa0383380:CDS 5.0%
TTCACTCAACCGATCCATCG+TGG - chr3_1:86278263-86278282 Msa0383380:three_prime_UTR 50.0%
TCACTCAACCGATCCATCGT+GGG - chr3_1:86278264-86278283 Msa0383380:three_prime_UTR 50.0%
CCTACGACTGTGTCTGTAAC+TGG + chr3_1:86278353-86278372 None:intergenic 50.0%
CCAGTTACAGACACAGTCGT+AGG - chr3_1:86278350-86278369 Msa0383380:three_prime_UTR 50.0%
TACAGACACAGTCGTAGGCT+TGG - chr3_1:86278355-86278374 Msa0383380:three_prime_UTR 50.0%
CGACGGTAGATACGGTTGTT+AGG + chr3_1:86278538-86278557 None:intergenic 50.0%
CTTTGCACGAAGGACATCGA+CGG + chr3_1:86278555-86278574 None:intergenic 50.0%
TAACGTACGGCTTTGCACGA+AGG + chr3_1:86278565-86278584 None:intergenic 50.0%
TTCACTCAACCGATCCATCG+TGG - chr3_1:86278263-86278282 Msa0383380:three_prime_UTR 50.0%
TCACTCAACCGATCCATCGT+GGG - chr3_1:86278264-86278283 Msa0383380:three_prime_UTR 50.0%
CCTACGACTGTGTCTGTAAC+TGG + chr3_1:86278353-86278372 None:intergenic 50.0%
CCAGTTACAGACACAGTCGT+AGG - chr3_1:86278350-86278369 Msa0383380:three_prime_UTR 50.0%
TACAGACACAGTCGTAGGCT+TGG - chr3_1:86278355-86278374 Msa0383380:three_prime_UTR 50.0%
CGACGGTAGATACGGTTGTT+AGG + chr3_1:86278538-86278557 None:intergenic 50.0%
CTTTGCACGAAGGACATCGA+CGG + chr3_1:86278555-86278574 None:intergenic 50.0%
TAACGTACGGCTTTGCACGA+AGG + chr3_1:86278565-86278584 None:intergenic 50.0%
TCTCTCCTCCCACGATGGAT+CGG + chr3_1:86278275-86278294 None:intergenic 55.0%
TCTCTCCTCCCACGATGGAT+CGG + chr3_1:86278275-86278294 None:intergenic 55.0%
CTCAACCGATCCATCGTGGG+AGG - chr3_1:86278267-86278286 Msa0383380:three_prime_UTR 60.0%
CCTCTTCTCTCCTCCCACGA+TGG + chr3_1:86278280-86278299 None:intergenic 60.0%
CCATCGTGGGAGGAGAGAAG+AGG - chr3_1:86278277-86278296 Msa0383380:three_prime_UTR 60.0%
CTCAACCGATCCATCGTGGG+AGG - chr3_1:86278267-86278286 Msa0383380:three_prime_UTR 60.0%
CCTCTTCTCTCCTCCCACGA+TGG + chr3_1:86278280-86278299 None:intergenic 60.0%
CCATCGTGGGAGGAGAGAAG+AGG - chr3_1:86278277-86278296 Msa0383380:three_prime_UTR 60.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 86278235 86278983 86278235 ID=Msa0383380;Name=Msa0383380
chr3_1 mRNA 86278235 86278983 86278235 ID=Msa0383380-mRNA-1;Parent=Msa0383380;Name=Msa0383380-mRNA-1;_AED=0.01;_eAED=0.01;_QI=6|1|1|1|1|1|2|213|138
chr3_1 exon 86278235 86278528 86278235 ID=Msa0383380-mRNA-1:exon:22757;Parent=Msa0383380-mRNA-1
chr3_1 exon 86278642 86278983 86278642 ID=Msa0383380-mRNA-1:exon:22756;Parent=Msa0383380-mRNA-1
chr3_1 five_prime_UTR 86278978 86278983 86278978 ID=Msa0383380-mRNA-1:five_prime_utr;Parent=Msa0383380-mRNA-1
chr3_1 CDS 86278642 86278977 86278642 ID=Msa0383380-mRNA-1:cds;Parent=Msa0383380-mRNA-1
chr3_1 CDS 86278448 86278528 86278448 ID=Msa0383380-mRNA-1:cds;Parent=Msa0383380-mRNA-1
chr3_1 three_prime_UTR 86278235 86278447 86278235 ID=Msa0383380-mRNA-1:three_prime_utr;Parent=Msa0383380-mRNA-1
Gene Sequence

>Msa0383380

ATGAGGAAGAATCACGATAAAGTTCACTCAACCGATCCATCGTGGGAGGAGAGAAGAGGATTAATGGCTGTTGCAGTAACACCGTTTATTCTCACCCTCCCTTCAATTTCCAGTTACAGACACAGTCGTAGGCTTGGTATTGTTCCTTATAGCAGTAGGCATCATATTCGCAGCATCACGATAAAGTGTGTGAAGGTGGATACAGATACAATAAATATCATGTGTGAACCTTGCAATGGAAAAGGATGGTTGGTATGTGAGTTTTGTGAAGGCCAAAAAACTAATGTCAAAGCCCCTAACAACCGTATCTACCGTCGATGTCCTTCGTGCAAAGCCGTTGGATATGTGTTGTGTTCAAACTGCAAGGTCTTCAAATGTGTCACTTTTCCTGATTTCAACGATTCTCCTATTAATTAA

Protein sequence

>Msa0383380

MRKNHDKVHSTDPSWEERRGLMAVAVTPFILTLPSISSYRHSRRLGIVPYSSRHHIRSITIKCVKVDTDTINIMCEPCNGKGWLVCEFCEGQKTNVKAPNNRIYRRCPSCKAVGYVLCSNCKVFKCVTFPDFNDSPIN*