AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1391120


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 tig0021410:-26745 Msa1391120:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 tig0021410:+26858 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 tig0021410:-26943 Msa1391120:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 tig0021410:+26806 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 tig0021410:-26601 Msa1391120:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 tig0021410:-26633 Msa1391120:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 tig0021410:-26906 Msa1391120:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 tig0021410:-26600 Msa1391120:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 tig0021410:+26933 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 tig0021410:-26560 Msa1391120:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 tig0021410:+26924 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 tig0021410:-26990 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 tig0021410:+26561 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 tig0021410:+26644 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 tig0021410:-26555 Msa1391120:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 tig0021410:-26632 Msa1391120:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 tig0021410:-26744 Msa1391120:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 tig0021410:+26982 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 tig0021410:+26549 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 tig0021410:+26750 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 tig0021410:+26567 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 tig0021410:+26489 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 tig0021410:-26796 Msa1391120:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 tig0021410:+26749 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 tig0021410:+26859 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 tig0021410:+26543 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 tig0021410:+26620 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 tig0021410:+26515 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 tig0021410:+26934 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 tig0021410:+26495 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 tig0021410:-26523 Msa1391120:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 tig0021410:+26514 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 tig0021410:+26544 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 tig0021410:-26559 Msa1391120:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 tig0021410:+26781 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 tig0021410:+26682 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 tig0021410:+26896 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 tig0021410:+26547 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 tig0021410:+26600 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 tig0021410:+26708 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 tig0021410:+26548 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 tig0021410:+26813 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 tig0021410:+26621 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 tig0021410:+26983 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 tig0021410:+26814 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 tig0021410:-26629 Msa1391120:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 tig0021410:-26599 Msa1391120:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 tig0021410:-26682 Msa1391120:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 tig0021410:-26780 Msa1391120:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 tig0021410:+26954 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 tig0021410:-26706 Msa1391120:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 tig0021410:+26616 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 tig0021410:+26488 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 tig0021410:+26458 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 tig0021410:+26709 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 tig0021410:+26591 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 tig0021410:+26872 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 tig0021410:+26507 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 tig0021410:+26619 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 tig0021410:+26510 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 tig0021410:+26851 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 tig0021410:+26721 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 tig0021410:+26951 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 tig0021410:+26799 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 tig0021410:+26649 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 tig0021410:+26907 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 tig0021410:+26461 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 tig0021410:-26829 Msa1391120:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 tig0021410:+26603 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 tig0021410:-26722 Msa1391120:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 tig0021410:+26860 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 tig0021410:+26691 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 tig0021410:+26796 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 tig0021410:+26665 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 tig0021410:+26668 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 tig0021410:-26913 Msa1391120:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 tig0021410:+26751 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + tig0021410:26593-26612 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + tig0021410:26518-26537 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + tig0021410:26592-26611 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + tig0021410:26594-26613 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + tig0021410:26601-26620 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - tig0021410:26620-26639 Msa1391120:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + tig0021410:26963-26982 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + tig0021410:26964-26983 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + tig0021410:26519-26538 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + tig0021410:26580-26599 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - tig0021410:26597-26616 Msa1391120:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + tig0021410:26618-26637 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + tig0021410:26685-26704 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + tig0021410:26784-26803 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + tig0021410:26787-26806 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + tig0021410:26803-26822 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + tig0021410:26501-26520 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - tig0021410:26506-26525 Msa1391120:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + tig0021410:26528-26547 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - tig0021410:26536-26555 Msa1391120:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + tig0021410:26686-26705 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + tig0021410:26743-26762 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - tig0021410:26743-26762 Msa1391120:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + tig0021410:26808-26827 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - tig0021410:26848-26867 Msa1391120:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + tig0021410:26861-26880 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + tig0021410:26885-26904 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + tig0021410:26638-26657 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + tig0021410:26639-26658 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - tig0021410:26638-26657 Msa1391120:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + tig0021410:26646-26665 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + tig0021410:26716-26735 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + tig0021410:26744-26763 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + tig0021410:26761-26780 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + tig0021410:26849-26868 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - tig0021410:26849-26868 Msa1391120:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - tig0021410:26850-26869 Msa1391120:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - tig0021410:26890-26909 Msa1391120:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + tig0021410:26903-26922 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + tig0021410:26904-26923 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + tig0021410:26908-26927 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + tig0021410:26909-26928 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + tig0021410:26942-26961 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + tig0021410:26945-26964 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + tig0021410:26957-26976 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + tig0021410:26498-26517 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + tig0021410:26556-26575 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + tig0021410:26671-26690 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - tig0021410:26669-26688 Msa1391120:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + tig0021410:26715-26734 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - tig0021410:26727-26746 Msa1391120:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + tig0021410:26731-26750 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + tig0021410:26770-26789 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - tig0021410:26767-26786 Msa1391120:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + tig0021410:26832-26851 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + tig0021410:26833-26852 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + tig0021410:26836-26855 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + tig0021410:26852-26871 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + tig0021410:26891-26910 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - tig0021410:26889-26908 Msa1391120:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + tig0021410:26905-26924 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + tig0021410:26937-26956 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + tig0021410:26938-26957 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + tig0021410:26545-26564 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - tig0021410:26543-26562 Msa1391120:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + tig0021410:26701-26720 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + tig0021410:26702-26721 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + tig0021410:26703-26722 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - tig0021410:26704-26723 Msa1391120:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - tig0021410:26705-26724 Msa1391120:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + tig0021410:26712-26731 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - tig0021410:26816-26835 Msa1391120:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - tig0021410:26817-26836 Msa1391120:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + tig0021410:26831-26850 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - tig0021410:26894-26913 Msa1391120:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - tig0021410:26926-26945 Msa1391120:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + tig0021410:26653-26672 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + tig0021410:26656-26675 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - tig0021410:26653-26672 Msa1391120:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - tig0021410:26697-26716 Msa1391120:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - tig0021410:26820-26839 Msa1391120:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0021410 gene 26468 27003 26468 ID=Msa1391120;Name=Msa1391120
tig0021410 mRNA 26468 27003 26468 ID=Msa1391120-mRNA-1;Parent=Msa1391120;Name=Msa1391120-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0|0|3|0|173
tig0021410 exon 26866 27003 26866 ID=Msa1391120-mRNA-1:exon:12582;Parent=Msa1391120-mRNA-1
tig0021410 exon 26757 26852 26757 ID=Msa1391120-mRNA-1:exon:12581;Parent=Msa1391120-mRNA-1
tig0021410 exon 26468 26752 26468 ID=Msa1391120-mRNA-1:exon:12580;Parent=Msa1391120-mRNA-1
tig0021410 CDS 26866 27003 26866 ID=Msa1391120-mRNA-1:cds;Parent=Msa1391120-mRNA-1
tig0021410 CDS 26757 26852 26757 ID=Msa1391120-mRNA-1:cds;Parent=Msa1391120-mRNA-1
tig0021410 CDS 26468 26752 26468 ID=Msa1391120-mRNA-1:cds;Parent=Msa1391120-mRNA-1
Gene Sequence

>Msa1391120

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1391120

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS