AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0405540


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 77 sgRNAs with CRISPR-Local

Find 81 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGCTGCCTCCCGTAGGAGTC+TGG 0.214220 3_2:-40292701 Msa0405540:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 3_2:+40292814 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 3_2:-40292899 Msa0405540:CDS
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 3_2:-40292557 Msa0405540:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 3_2:-40292589 Msa0405540:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 3_2:-40292556 Msa0405540:CDS
CAATGCCGTGTGGAGGTAAA+AGG 0.348698 3_2:+40292762 None:intergenic
CAAGCGTTATCCGGAATGAT+TGG 0.365557 3_2:+40292889 None:intergenic
CTCTGTCTTACCGTGGCTGC+TGG 0.390939 3_2:-40292862 Msa0405540:CDS
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 3_2:-40292516 Msa0405540:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 3_2:+40292880 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 3_2:-40292946 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 3_2:+40292517 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 3_2:+40292600 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 3_2:-40292511 Msa0405540:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 3_2:-40292588 Msa0405540:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 3_2:-40292700 Msa0405540:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 3_2:+40292938 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 3_2:+40292505 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 3_2:+40292706 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 3_2:+40292523 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 3_2:+40292445 None:intergenic
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 3_2:+40292705 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 3_2:+40292815 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 3_2:+40292499 None:intergenic
CCACACGGCATTGCTCCGTC+AGG 0.499380 3_2:-40292752 Msa0405540:CDS
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 3_2:+40292576 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 3_2:+40292471 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 3_2:+40292890 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 3_2:+40292451 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 3_2:-40292479 Msa0405540:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 3_2:+40292470 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 3_2:+40292500 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 3_2:-40292515 Msa0405540:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 3_2:+40292737 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 3_2:+40292638 None:intergenic
TAACTCTGTGCCAGCAGCCA+CGG 0.546303 3_2:+40292852 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 3_2:+40292503 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 3_2:+40292556 None:intergenic
GTGTGGAGGTAAAAGGCCTA+CGG 0.556074 3_2:+40292769 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 3_2:+40292664 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 3_2:+40292504 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 3_2:+40292577 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 3_2:+40292939 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 3_2:-40292585 Msa0405540:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 3_2:-40292555 Msa0405540:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 3_2:-40292638 Msa0405540:CDS
TGTGGAGGTAAAAGGCCTAC+GGG 0.584049 3_2:+40292770 None:intergenic
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 3_2:-40292736 Msa0405540:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 3_2:+40292910 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 3_2:-40292662 Msa0405540:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 3_2:+40292572 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 3_2:+40292444 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 3_2:+40292414 None:intergenic
GACGGAGCAATGCCGTGTGG+AGG 0.608359 3_2:+40292755 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 3_2:+40292665 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 3_2:+40292547 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 3_2:+40292828 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 3_2:+40292463 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 3_2:+40292575 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 3_2:+40292466 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 3_2:+40292807 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 3_2:+40292677 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 3_2:+40292907 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 3_2:+40292605 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 3_2:+40292417 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 3_2:-40292785 Msa0405540:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 3_2:+40292559 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 3_2:-40292678 Msa0405540:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 3_2:+40292816 None:intergenic
CAGCAGCCACGGTAAGACAG+AGG 0.684983 3_2:+40292863 None:intergenic
TTGCATCCTCTGTCTTACCG+TGG 0.687884 3_2:-40292869 Msa0405540:CDS
CCTGACGGAGCAATGCCGTG+TGG 0.695031 3_2:+40292752 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 3_2:+40292647 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 3_2:+40292621 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 3_2:+40292624 None:intergenic
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 3_2:+40292707 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr3_2:40292549-40292568 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr3_2:40292474-40292493 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr3_2:40292548-40292567 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr3_2:40292550-40292569 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr3_2:40292557-40292576 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr3_2:40292576-40292595 Msa0405540:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr3_2:40292919-40292938 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr3_2:40292920-40292939 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr3_2:40292475-40292494 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr3_2:40292536-40292555 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr3_2:40292553-40292572 Msa0405540:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr3_2:40292574-40292593 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr3_2:40292641-40292660 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr3_2:40292740-40292759 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr3_2:40292743-40292762 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr3_2:40292759-40292778 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr3_2:40292457-40292476 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr3_2:40292462-40292481 Msa0405540:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr3_2:40292484-40292503 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+TGG - chr3_2:40292492-40292511 Msa0405540:CDS 50.0%
TGTGGAGGTAAAAGGCCTAC+GGG + chr3_2:40292594-40292613 None:intergenic 50.0%
GTGTGGAGGTAAAAGGCCTA+CGG + chr3_2:40292595-40292614 None:intergenic 50.0%
! GTAGGCCTTTTACCTCCACA+CGG - chr3_2:40292594-40292613 Msa0405540:CDS 50.0%
CAATGCCGTGTGGAGGTAAA+AGG + chr3_2:40292602-40292621 None:intergenic 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr3_2:40292642-40292661 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr3_2:40292699-40292718 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr3_2:40292699-40292718 Msa0405540:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr3_2:40292764-40292783 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr3_2:40292804-40292823 Msa0405540:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr3_2:40292817-40292836 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr3_2:40292841-40292860 None:intergenic 50.0%
TAACTCTGTGCCAGCAGCCA+CGG + chr3_2:40292512-40292531 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr3_2:40292672-40292691 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr3_2:40292700-40292719 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr3_2:40292717-40292736 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr3_2:40292805-40292824 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr3_2:40292805-40292824 Msa0405540:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr3_2:40292806-40292825 Msa0405540:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr3_2:40292846-40292865 Msa0405540:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr3_2:40292859-40292878 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr3_2:40292860-40292879 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr3_2:40292864-40292883 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr3_2:40292865-40292884 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr3_2:40292898-40292917 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr3_2:40292901-40292920 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr3_2:40292913-40292932 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr3_2:40292454-40292473 None:intergenic 60.0%
CAGCAGCCACGGTAAGACAG+AGG + chr3_2:40292501-40292520 None:intergenic 60.0%
CTCTGTCTTACCGTGGCTGC+TGG - chr3_2:40292499-40292518 Msa0405540:CDS 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr3_2:40292627-40292646 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr3_2:40292625-40292644 Msa0405540:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr3_2:40292671-40292690 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr3_2:40292683-40292702 Msa0405540:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr3_2:40292687-40292706 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr3_2:40292726-40292745 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr3_2:40292723-40292742 Msa0405540:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr3_2:40292788-40292807 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr3_2:40292789-40292808 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr3_2:40292792-40292811 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr3_2:40292808-40292827 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr3_2:40292847-40292866 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr3_2:40292845-40292864 Msa0405540:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr3_2:40292861-40292880 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr3_2:40292893-40292912 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr3_2:40292894-40292913 None:intergenic 60.0%
GACGGAGCAATGCCGTGTGG+AGG + chr3_2:40292609-40292628 None:intergenic 65.0%
CCTGACGGAGCAATGCCGTG+TGG + chr3_2:40292612-40292631 None:intergenic 65.0%
CCACACGGCATTGCTCCGTC+AGG - chr3_2:40292609-40292628 Msa0405540:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr3_2:40292657-40292676 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr3_2:40292658-40292677 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr3_2:40292659-40292678 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr3_2:40292660-40292679 Msa0405540:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr3_2:40292661-40292680 Msa0405540:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr3_2:40292668-40292687 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr3_2:40292772-40292791 Msa0405540:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr3_2:40292773-40292792 Msa0405540:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr3_2:40292787-40292806 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr3_2:40292850-40292869 Msa0405540:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr3_2:40292882-40292901 Msa0405540:CDS 65.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr3_2:40292653-40292672 Msa0405540:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr3_2:40292776-40292795 Msa0405540:CDS 75.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 40292424 40292959 40292424 ID=Msa0405540;Name=Msa0405540
chr3_2 mRNA 40292424 40292959 40292424 ID=Msa0405540-mRNA-1;Parent=Msa0405540;Name=Msa0405540-mRNA-1;_AED=0.20;_eAED=0.23;_QI=0|0|0|1|0|0|3|0|173
chr3_2 exon 40292822 40292959 40292822 ID=Msa0405540-mRNA-1:exon:7835;Parent=Msa0405540-mRNA-1
chr3_2 exon 40292713 40292808 40292713 ID=Msa0405540-mRNA-1:exon:7834;Parent=Msa0405540-mRNA-1
chr3_2 exon 40292424 40292708 40292424 ID=Msa0405540-mRNA-1:exon:7833;Parent=Msa0405540-mRNA-1
chr3_2 CDS 40292822 40292959 40292822 ID=Msa0405540-mRNA-1:cds;Parent=Msa0405540-mRNA-1
chr3_2 CDS 40292713 40292808 40292713 ID=Msa0405540-mRNA-1:cds;Parent=Msa0405540-mRNA-1
chr3_2 CDS 40292424 40292708 40292424 ID=Msa0405540-mRNA-1:cds;Parent=Msa0405540-mRNA-1
Gene Sequence

>Msa0405540

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGTGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACACGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa0405540

LGFDGELKKPPTDALRPIIPDNACILCLTVAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS