AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086750


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 7_2:-87545908 Msa1086750:intron
GAAGAAACAATGACGGTATC+TGG 0.223499 7_2:+87546021 None:intergenic
CGCTTTACGCCCAATCATTC+CGG 0.287091 7_2:-87546106 Msa1086750:CDS
CAATGCCGCGTGGAGGTAAA+AGG 0.308793 7_2:+87545969 None:intergenic
TCCTTTCGCTCCTCAGCTTA+CGG 0.318574 7_2:-87545764 Msa1086750:CDS
ATCAGACGCGAGCCCCTCCT+TGG 0.323688 7_2:-87545796 Msa1086750:CDS
CTCTGTCTTACCGCGGCTGC+TGG 0.335301 7_2:-87546069 Msa1086750:CDS
CCTTTCGCTCCTCAGCTTAC+GGG 0.341229 7_2:-87545763 Msa1086750:CDS
CAAGCGTTATCCGGAATGAT+TGG 0.365557 7_2:+87546096 None:intergenic
CAGCTGTTGTTCCCCTCCCA+AGG 0.401225 7_2:-87545723 Msa1086750:CDS
CAGAGGATGCAAGCGTTATC+CGG 0.442617 7_2:+87546087 None:intergenic
GGTTGAGCCCTGGGATTTGA+CGG 0.443812 7_2:-87546153 None:intergenic
CTTGGGAGGGGAACAACAGC+TGG 0.448224 7_2:+87545724 None:intergenic
CTCGCGTCTGATTAGCTAGT+TGG 0.450357 7_2:+87545807 None:intergenic
GTTGTTCCCCTCCCAAGGGC+AGG 0.453286 7_2:-87545718 Msa1086750:CDS
TCAGACGCGAGCCCCTCCTT+GGG 0.455699 7_2:-87545795 Msa1086750:CDS
GCTGCCTCCCGTAGGAGTCT+GGG 0.465822 7_2:-87545907 Msa1086750:intron
TAAGTTCGCCGTCAAATCCC+AGG 0.467544 7_2:+87546145 None:intergenic
TAAGAACCTGCCCTTGGGAG+GGG 0.474163 7_2:+87545712 None:intergenic
CTCCTACGGGAGGCAGCAGT+GGG 0.476121 7_2:+87545913 None:intergenic
AGGGGAACAACAGCTGGAAA+CGG 0.479232 7_2:+87545730 None:intergenic
TTTACACATGCAAGTCGAAC+GGG 0.480570 7_2:+87545652 None:intergenic
CCACGCGGCATTGCTCCGTC+AGG 0.484232 7_2:-87545959 Msa1086750:CDS
ACTCCTACGGGAGGCAGCAG+TGG 0.491996 7_2:+87545912 None:intergenic
AAGAAACAATGACGGTATCT+GGG 0.492143 7_2:+87546022 None:intergenic
AACGCGTAAGAACCTGCCCT+TGG 0.497667 7_2:+87545706 None:intergenic
AGGAGGAATCCGCCCAAGGA+GGG 0.502243 7_2:+87545783 None:intergenic
TGGTGTTTCCAGTGGCGGAC+GGG 0.506464 7_2:+87545678 None:intergenic
AAGCGTTATCCGGAATGATT+GGG 0.511219 7_2:+87546097 None:intergenic
CATGCAAGTCGAACGGGAAG+TGG 0.511388 7_2:+87545658 None:intergenic
GTTACTCACCCGTCCGCCAC+TGG 0.515654 7_2:-87545686 Msa1086750:CDS
GTGGTGTTTCCAGTGGCGGA+CGG 0.521309 7_2:+87545677 None:intergenic
ACGCGTAAGAACCTGCCCTT+GGG 0.530469 7_2:+87545707 None:intergenic
AGCTGTTGTTCCCCTCCCAA+GGG 0.533909 7_2:-87545722 Msa1086750:CDS
CGCAATGGGCGAAAGCCTGA+CGG 0.536266 7_2:+87545944 None:intergenic
CCAAGGCGGTGATCAGTAGC+TGG 0.540351 7_2:+87545845 None:intergenic
TAACTCTGTGCCAGCAGCCG+CGG 0.544469 7_2:+87546059 None:intergenic
CGTAAGAACCTGCCCTTGGG+AGG 0.550231 7_2:+87545710 None:intergenic
CCCGTAAGCTGAGGAGCGAA+AGG 0.554829 7_2:+87545763 None:intergenic
GAGAGGATGATCAGCCACAC+TGG 0.556699 7_2:+87545871 None:intergenic
GTAAGAACCTGCCCTTGGGA+GGG 0.557080 7_2:+87545711 None:intergenic
GCGTGGAGGTAAAAGGCCTA+CGG 0.560249 7_2:+87545976 None:intergenic
GGAGGAATCCGCCCAAGGAG+GGG 0.562553 7_2:+87545784 None:intergenic
AAGTTCGCCGTCAAATCCCA+GGG 0.564420 7_2:+87546146 None:intergenic
CGTGGAGGTAAAAGGCCTAC+GGG 0.570032 7_2:+87545977 None:intergenic
GACGCGAGCCCCTCCTTGGG+CGG 0.572606 7_2:-87545792 Msa1086750:CDS
CTTTCGCTCCTCAGCTTACG+GGG 0.577687 7_2:-87545762 Msa1086750:CDS
CCAGCTACTGATCACCGCCT+TGG 0.578071 7_2:-87545845 Msa1086750:CDS
CGTCAGGCTTTCGCCCATTG+CGG 0.587223 7_2:-87545943 Msa1086750:CDS
GGGCGTAAAGCGTCTGTAGG+TGG 0.587281 7_2:+87546117 None:intergenic
AGTGTGGCTGATCATCCTCT+CGG 0.593369 7_2:-87545869 Msa1086750:CDS
CGAAAGGAGGAATCCGCCCA+AGG 0.596152 7_2:+87545779 None:intergenic
CTTTACACATGCAAGTCGAA+CGG 0.597034 7_2:+87545651 None:intergenic
TCCTGGCTCAGGATGAACGC+TGG 0.603603 7_2:+87545621 None:intergenic
AGAGGATGATCAGCCACACT+GGG 0.612353 7_2:+87545872 None:intergenic
TGCTAATACCCCGTAAGCTG+AGG 0.615470 7_2:+87545754 None:intergenic
GGTATCTGGGGAATAAGCAT+CGG 0.620214 7_2:+87546035 None:intergenic
ACGGGAAGTGGTGTTTCCAG+TGG 0.620953 7_2:+87545670 None:intergenic
AAGGAGGAATCCGCCCAAGG+AGG 0.622334 7_2:+87545782 None:intergenic
GGAAGTGGTGTTTCCAGTGG+CGG 0.627120 7_2:+87545673 None:intergenic
TCCTGGAGAAGAAACAATGA+CGG 0.628601 7_2:+87546014 None:intergenic
GCCACACTGGGACTGAGACA+AGG 0.629204 7_2:+87545884 None:intergenic
ATTGGGCGTAAAGCGTCTGT+AGG 0.632255 7_2:+87546114 None:intergenic
GACGGAGCAATGCCGCGTGG+AGG 0.640730 7_2:+87545962 None:intergenic
GTCTGATTAGCTAGTTGGTG+AGG 0.641304 7_2:+87545812 None:intergenic
CAGCAGCCGCGGTAAGACAG+AGG 0.650015 7_2:+87546070 None:intergenic
TGGCTCAGGATGAACGCTGG+CGG 0.650788 7_2:+87545624 None:intergenic
AAAAGAAGTTCATGACCCGT+AGG 0.653857 7_2:-87545992 Msa1086750:CDS
GTAAGCTGAGGAGCGAAAGG+AGG 0.654589 7_2:+87545766 None:intergenic
GCCTTGTCTCAGTCCCAGTG+TGG 0.654955 7_2:-87545885 Msa1086750:CDS
AGAAACAATGACGGTATCTG+GGG 0.658343 7_2:+87546023 None:intergenic
TGATCAGTAGCTGGTCCGAG+AGG 0.705254 7_2:+87545854 None:intergenic
CCTGACGGAGCAATGCCGCG+TGG 0.711882 7_2:+87545959 None:intergenic
GGTGAGGTAATAGCTTACCA+AGG 0.724474 7_2:+87545828 None:intergenic
GAGGTAATAGCTTACCAAGG+CGG 0.748896 7_2:+87545831 None:intergenic
TTGCATCCTCTGTCTTACCG+CGG 0.760348 7_2:-87546076 Msa1086750:CDS
TCCTACGGGAGGCAGCAGTG+GGG 0.779333 7_2:+87545914 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
AAGAAACAATGACGGTATCT+GGG + chr7_2:87545756-87545775 None:intergenic 35.0%
AAGCGTTATCCGGAATGATT+GGG + chr7_2:87545681-87545700 None:intergenic 40.0%
AGAAACAATGACGGTATCTG+GGG + chr7_2:87545755-87545774 None:intergenic 40.0%
GAAGAAACAATGACGGTATC+TGG + chr7_2:87545757-87545776 None:intergenic 40.0%
TCCTGGAGAAGAAACAATGA+CGG + chr7_2:87545764-87545783 None:intergenic 40.0%
AAAAGAAGTTCATGACCCGT+AGG - chr7_2:87545783-87545802 Msa1086750:CDS 40.0%
TTTACACATGCAAGTCGAAC+GGG + chr7_2:87546126-87546145 None:intergenic 40.0%
CTTTACACATGCAAGTCGAA+CGG + chr7_2:87546127-87546146 None:intergenic 40.0%
CAAGCGTTATCCGGAATGAT+TGG + chr7_2:87545682-87545701 None:intergenic 45.0%
GGTATCTGGGGAATAAGCAT+CGG + chr7_2:87545743-87545762 None:intergenic 45.0%
! ACCGTCATTGTTTCTTCTCC+AGG - chr7_2:87545760-87545779 Msa1086750:CDS 45.0%
! GGGTCATGAACTTCTTTTCC+TGG + chr7_2:87545781-87545800 None:intergenic 45.0%
! AGTGGGGAATTTTCCGCAAT+GGG + chr7_2:87545848-87545867 None:intergenic 45.0%
GAGGTAATAGCTTACCAAGG+CGG + chr7_2:87545947-87545966 None:intergenic 45.0%
GGTGAGGTAATAGCTTACCA+AGG + chr7_2:87545950-87545969 None:intergenic 45.0%
! GTCTGATTAGCTAGTTGGTG+AGG + chr7_2:87545966-87545985 None:intergenic 45.0%
! ATTGGGCGTAAAGCGTCTGT+AGG + chr7_2:87545664-87545683 None:intergenic 50.0%
CGCTTTACGCCCAATCATTC+CGG - chr7_2:87545669-87545688 Msa1086750:CDS 50.0%
CAGAGGATGCAAGCGTTATC+CGG + chr7_2:87545691-87545710 None:intergenic 50.0%
TTGCATCCTCTGTCTTACCG+CGG - chr7_2:87545699-87545718 Msa1086750:CDS 50.0%
! CAGTGGGGAATTTTCCGCAA+TGG + chr7_2:87545849-87545868 None:intergenic 50.0%
AGAGGATGATCAGCCACACT+GGG + chr7_2:87545906-87545925 None:intergenic 50.0%
AGTGTGGCTGATCATCCTCT+CGG - chr7_2:87545906-87545925 Msa1086750:intron 50.0%
! CTCGCGTCTGATTAGCTAGT+TGG + chr7_2:87545971-87545990 None:intergenic 50.0%
TCCTTTCGCTCCTCAGCTTA+CGG - chr7_2:87546011-87546030 Msa1086750:intron 50.0%
TGCTAATACCCCGTAAGCTG+AGG + chr7_2:87546024-87546043 None:intergenic 50.0%
AGGGGAACAACAGCTGGAAA+CGG + chr7_2:87546048-87546067 None:intergenic 50.0%
CGTGGAGGTAAAAGGCCTAC+GGG + chr7_2:87545801-87545820 None:intergenic 55.0%
GCGTGGAGGTAAAAGGCCTA+CGG + chr7_2:87545802-87545821 None:intergenic 55.0%
! GTAGGCCTTTTACCTCCACG+CGG - chr7_2:87545801-87545820 Msa1086750:CDS 55.0%
CAATGCCGCGTGGAGGTAAA+AGG + chr7_2:87545809-87545828 None:intergenic 55.0%
AGACAAGGCCCAGACTCCTA+CGG + chr7_2:87545879-87545898 None:intergenic 55.0%
GAGAGGATGATCAGCCACAC+TGG + chr7_2:87545907-87545926 None:intergenic 55.0%
TGATCAGTAGCTGGTCCGAG+AGG + chr7_2:87545924-87545943 None:intergenic 55.0%
GTAAGCTGAGGAGCGAAAGG+AGG + chr7_2:87546012-87546031 None:intergenic 55.0%
CCTTTCGCTCCTCAGCTTAC+GGG - chr7_2:87546012-87546031 Msa1086750:intron 55.0%
CTTTCGCTCCTCAGCTTACG+GGG - chr7_2:87546013-87546032 Msa1086750:intron 55.0%
AGCTGTTGTTCCCCTCCCAA+GGG - chr7_2:87546053-87546072 Msa1086750:CDS 55.0%
TAAGAACCTGCCCTTGGGAG+GGG + chr7_2:87546066-87546085 None:intergenic 55.0%
GTAAGAACCTGCCCTTGGGA+GGG + chr7_2:87546067-87546086 None:intergenic 55.0%
ACGCGTAAGAACCTGCCCTT+GGG + chr7_2:87546071-87546090 None:intergenic 55.0%
AACGCGTAAGAACCTGCCCT+TGG + chr7_2:87546072-87546091 None:intergenic 55.0%
GGAAGTGGTGTTTCCAGTGG+CGG + chr7_2:87546105-87546124 None:intergenic 55.0%
ACGGGAAGTGGTGTTTCCAG+TGG + chr7_2:87546108-87546127 None:intergenic 55.0%
CATGCAAGTCGAACGGGAAG+TGG + chr7_2:87546120-87546139 None:intergenic 55.0%
! GGGCGTAAAGCGTCTGTAGG+TGG + chr7_2:87545661-87545680 None:intergenic 60.0%
TAACTCTGTGCCAGCAGCCG+CGG + chr7_2:87545719-87545738 None:intergenic 60.0%
CGCAATGGGCGAAAGCCTGA+CGG + chr7_2:87545834-87545853 None:intergenic 60.0%
CGTCAGGCTTTCGCCCATTG+CGG - chr7_2:87545832-87545851 Msa1086750:CDS 60.0%
GACAAGGCCCAGACTCCTAC+GGG + chr7_2:87545878-87545897 None:intergenic 60.0%
GCCTTGTCTCAGTCCCAGTG+TGG - chr7_2:87545890-87545909 Msa1086750:CDS 60.0%
GCCACACTGGGACTGAGACA+AGG + chr7_2:87545894-87545913 None:intergenic 60.0%
CCAAGGCGGTGATCAGTAGC+TGG + chr7_2:87545933-87545952 None:intergenic 60.0%
CCAGCTACTGATCACCGCCT+TGG - chr7_2:87545930-87545949 Msa1086750:CDS 60.0%
AGGAGGAATCCGCCCAAGGA+GGG + chr7_2:87545995-87546014 None:intergenic 60.0%
AAGGAGGAATCCGCCCAAGG+AGG + chr7_2:87545996-87546015 None:intergenic 60.0%
CGAAAGGAGGAATCCGCCCA+AGG + chr7_2:87545999-87546018 None:intergenic 60.0%
CCCGTAAGCTGAGGAGCGAA+AGG + chr7_2:87546015-87546034 None:intergenic 60.0%
CTTGGGAGGGGAACAACAGC+TGG + chr7_2:87546054-87546073 None:intergenic 60.0%
CAGCTGTTGTTCCCCTCCCA+AGG - chr7_2:87546052-87546071 Msa1086750:CDS 60.0%
CGTAAGAACCTGCCCTTGGG+AGG + chr7_2:87546068-87546087 None:intergenic 60.0%
!! TGGTGTTTCCAGTGGCGGAC+GGG + chr7_2:87546100-87546119 None:intergenic 60.0%
! GTGGTGTTTCCAGTGGCGGA+CGG + chr7_2:87546101-87546120 None:intergenic 60.0%
CAGCAGCCGCGGTAAGACAG+AGG + chr7_2:87545708-87545727 None:intergenic 65.0%
CTCTGTCTTACCGCGGCTGC+TGG - chr7_2:87545706-87545725 Msa1086750:CDS 65.0%
TCCTACGGGAGGCAGCAGTG+GGG + chr7_2:87545864-87545883 None:intergenic 65.0%
CTCCTACGGGAGGCAGCAGT+GGG + chr7_2:87545865-87545884 None:intergenic 65.0%
ACTCCTACGGGAGGCAGCAG+TGG + chr7_2:87545866-87545885 None:intergenic 65.0%
TGCTGCCTCCCGTAGGAGTC+TGG - chr7_2:87545867-87545886 Msa1086750:CDS 65.0%
GCTGCCTCCCGTAGGAGTCT+GGG - chr7_2:87545868-87545887 Msa1086750:CDS 65.0%
AAGGCCCAGACTCCTACGGG+AGG + chr7_2:87545875-87545894 None:intergenic 65.0%
ATCAGACGCGAGCCCCTCCT+TGG - chr7_2:87545979-87545998 Msa1086750:CDS 65.0%
TCAGACGCGAGCCCCTCCTT+GGG - chr7_2:87545980-87545999 Msa1086750:CDS 65.0%
GGAGGAATCCGCCCAAGGAG+GGG + chr7_2:87545994-87546013 None:intergenic 65.0%
GTTGTTCCCCTCCCAAGGGC+AGG - chr7_2:87546057-87546076 Msa1086750:CDS 65.0%
GTTACTCACCCGTCCGCCAC+TGG - chr7_2:87546089-87546108 Msa1086750:CDS 65.0%
GACGGAGCAATGCCGCGTGG+AGG + chr7_2:87545816-87545835 None:intergenic 70.0%
CCTGACGGAGCAATGCCGCG+TGG + chr7_2:87545819-87545838 None:intergenic 70.0%
CCACGCGGCATTGCTCCGTC+AGG - chr7_2:87545816-87545835 Msa1086750:CDS 70.0%
TCCCCACTGCTGCCTCCCGT+AGG - chr7_2:87545860-87545879 Msa1086750:CDS 70.0%
GACGCGAGCCCCTCCTTGGG+CGG - chr7_2:87545983-87546002 Msa1086750:CDS 75.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87545631 87546166 87545631 ID=Msa1086750;Name=Msa1086750
chr7_2 mRNA 87545631 87546166 87545631 ID=Msa1086750-mRNA-1;Parent=Msa1086750;Name=Msa1086750-mRNA-1;_AED=0.42;_eAED=0.44;_QI=0|0|0|1|0.5|0|3|0|173
chr7_2 exon 87546029 87546166 87546029 ID=Msa1086750-mRNA-1:exon:23861;Parent=Msa1086750-mRNA-1
chr7_2 exon 87545920 87546015 87545920 ID=Msa1086750-mRNA-1:exon:23860;Parent=Msa1086750-mRNA-1
chr7_2 exon 87545631 87545915 87545631 ID=Msa1086750-mRNA-1:exon:23859;Parent=Msa1086750-mRNA-1
chr7_2 CDS 87546029 87546166 87546029 ID=Msa1086750-mRNA-1:cds;Parent=Msa1086750-mRNA-1
chr7_2 CDS 87545920 87546015 87545920 ID=Msa1086750-mRNA-1:cds;Parent=Msa1086750-mRNA-1
chr7_2 CDS 87545631 87545915 87545631 ID=Msa1086750-mRNA-1:cds;Parent=Msa1086750-mRNA-1
Gene Sequence

>Msa1086750

CTGGGATTTGACGGCGAACTTAAAAAGCCACCTACAGACGCTTTACGCCCAATCATTCCGGATAACGCTTGCATCCTCTGTCTTACCGCGGCTGCTGGCACAGAGTTAGCCGATGCTTATTCCCCAGATACCGTCATTGAAAAGAAGTTCATGACCCGTAGGCCTTTTACCTCCACGCGGCATTGCTCCGTCAGGCTTTCGCCCATTGCGGAAAATTCCCCACTGCTGCCTCCCGAGTCTGGGCCTTGTCTCAGTCCCAGTGTGGCTGATCATCCTCTCGGACCAGCTACTGATCACCGCCTTGGTAAGCTATTACCTCACCAACTAGCTAATCAGACGCGAGCCCCTCCTTGGGCGGATTCCTCCTTTCGCTCCTCAGCTTACGGGGTATTAGCAGCCGTTTCCAGCTGTTGTTCCCCTCCCAAGGGCAGGTTCTTACGCGTTACTCACCCGTCCGCCACTGGAAACACCACTTCCCGTTCGACTTGCATGTGTAAAGCATGCCGCCAGCGTTCATCC

Protein sequence

>Msa1086750

LGFDGELKKPPTDALRPIIPDNACILCLTAAAGTELADAYSPDTVIEKKFMTRRPFTSTRHCSVRLSPIAENSPLLPPESGPCLSPSVADHPLGPATDHRLGKLLPHQLANQTRAPPWADSSFRSSAYGVLAAVSSCCSPPKGRFLRVTHPSATGNTTSRSTCMCKACRQRSS