AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene83935

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83935.t1 MTR_5g039180 98.925 93 1 0 1 93 1 93 9.70e-61 180
MS.gene83935.t1 MTR_7g010120 72.826 92 24 1 1 92 1 91 1.01e-40 129
MS.gene83935.t1 MTR_6g011670 69.737 76 23 0 17 92 15 90 4.66e-34 112
MS.gene83935.t1 MTR_3g438070 74.026 77 18 1 17 93 17 91 4.82e-34 112
MS.gene83935.t1 MTR_7g059260 45.946 74 40 0 8 81 3 76 1.26e-11 55.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene83935.t1 AT1G26945 83.784 74 12 0 19 92 19 92 3.13e-39 125
MS.gene83935.t1 AT3G28857 64.894 94 30 2 1 93 1 92 3.72e-36 118
MS.gene83935.t1 AT3G47710 69.149 94 25 3 1 93 1 91 3.48e-35 115
MS.gene83935.t1 AT5G15160 73.333 75 19 1 19 92 18 92 3.25e-32 108
MS.gene83935.t1 AT1G74500 72.727 77 18 2 17 92 17 91 2.96e-31 105
MS.gene83935.t1 AT5G39860 65.385 78 26 1 17 93 15 92 1.73e-30 103

Find 16 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACCGATTGTCACAACTTT+TGG 0.275530 5.4:-29064590 MS.gene83935:CDS
GAGCGGCTAGCGCGAAGTTC+GGG 0.276939 5.4:+29065107 None:intergenic
GTGCTCAAGCAGCTATTATT+AGG 0.330670 5.4:-29064549 MS.gene83935:CDS
GGAGCGGCTAGCGCGAAGTT+CGG 0.362273 5.4:+29065106 None:intergenic
CTTATAGGTTTCAGCTACTA+AGG 0.382941 5.4:-29064671 MS.gene83935:intron
AGAGGAACCACCGGATTGTC+TGG 0.389390 5.4:+29065184 None:intergenic
GGGGATAAGTTGTTGTAACT+TGG 0.418381 5.4:+29065127 None:intergenic
AATAGCTGCTTGAGCACTGT+TGG 0.496664 5.4:+29064555 None:intergenic
AAGCCAAAAGTTGTGACAAT+CGG 0.524888 5.4:+29064587 None:intergenic
AGATCTCGTTCCAGACAATC+CGG 0.532260 5.4:-29065194 MS.gene83935:CDS
AAATAAATACCTTGTTGGAG+CGG 0.605762 5.4:+29065090 None:intergenic
TCGCGCTAGCCGCTCCAACA+AGG 0.613710 5.4:-29065099 MS.gene83935:intron
AGTGATCTCAGAGGAACCAC+CGG 0.628272 5.4:+29065175 None:intergenic
AGCGGCTAGCGCGAAGTTCG+GGG 0.650397 5.4:+29065108 None:intergenic
TCTCGTTCCAGACAATCCGG+TGG 0.728257 5.4:-29065191 MS.gene83935:CDS
TTGAGCATCAGTGATCTCAG+AGG 0.728981 5.4:+29065166 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTATTTTTTATGGTCTTAT+AGG - chr5.4:29065054-29065073 MS.gene83935:intron 15.0%
!! TAGAAAAATAAATACCTTGT+TGG + chr5.4:29064658-29064677 None:intergenic 20.0%
AAATAAATACCTTGTTGGAG+CGG + chr5.4:29064653-29064672 None:intergenic 30.0%
ACAATACAATACACAAGTTG+TGG + chr5.4:29064915-29064934 None:intergenic 30.0%
CATAAAAAACTTGCATAGAG+AGG - chr5.4:29065114-29065133 MS.gene83935:CDS 30.0%
AAGCCAAAAGTTGTGACAAT+CGG + chr5.4:29065156-29065175 None:intergenic 35.0%
CTTATAGGTTTCAGCTACTA+AGG - chr5.4:29065069-29065088 MS.gene83935:intron 35.0%
GATACAATGCACATATTGTG+TGG - chr5.4:29064832-29064851 MS.gene83935:intron 35.0%
! ATTTGTGAGAGTGTGTATGA+AGG + chr5.4:29064777-29064796 None:intergenic 35.0%
!! TGTGTGGACATTGTTAGTTT+TGG - chr5.4:29064848-29064867 MS.gene83935:intron 35.0%
CAAGTTGTGGCAAAGAATTG+AGG + chr5.4:29064902-29064921 None:intergenic 40.0%
GGGGATAAGTTGTTGTAACT+TGG + chr5.4:29064616-29064635 None:intergenic 40.0%
GTGCATGTGAATGATGACTT+GGG + chr5.4:29064801-29064820 None:intergenic 40.0%
GTGCTCAAGCAGCTATTATT+AGG - chr5.4:29065191-29065210 MS.gene83935:CDS 40.0%
TGTGCATGTGAATGATGACT+TGG + chr5.4:29064802-29064821 None:intergenic 40.0%
! TGACCGATTGTCACAACTTT+TGG - chr5.4:29065150-29065169 MS.gene83935:CDS 40.0%
AGATCTCGTTCCAGACAATC+CGG - chr5.4:29064546-29064565 MS.gene83935:CDS 45.0%
AGCTAGTTGCAACATGCAAG+TGG - chr5.4:29064976-29064995 MS.gene83935:intron 45.0%
GCTAGTTGCAACATGCAAGT+GGG - chr5.4:29064977-29064996 MS.gene83935:intron 45.0%
TTGAGCATCAGTGATCTCAG+AGG + chr5.4:29064577-29064596 None:intergenic 45.0%
! AATAGCTGCTTGAGCACTGT+TGG + chr5.4:29065188-29065207 None:intergenic 45.0%
!!! GTAATATTTTTTATTTTTTA+TGG - chr5.4:29065045-29065064 MS.gene83935:intron 5.0%
AGTGATCTCAGAGGAACCAC+CGG + chr5.4:29064568-29064587 None:intergenic 50.0%
AGTTGCAACATGCAAGTGGG+TGG - chr5.4:29064980-29064999 MS.gene83935:intron 50.0%
AGAGGAACCACCGGATTGTC+TGG + chr5.4:29064559-29064578 None:intergenic 55.0%
TCTCGTTCCAGACAATCCGG+TGG - chr5.4:29064549-29064568 MS.gene83935:CDS 55.0%
AGCGGCTAGCGCGAAGTTCG+GGG + chr5.4:29064635-29064654 None:intergenic 65.0%
GAGCGGCTAGCGCGAAGTTC+GGG + chr5.4:29064636-29064655 None:intergenic 65.0%
GGAGCGGCTAGCGCGAAGTT+CGG + chr5.4:29064637-29064656 None:intergenic 65.0%
TCGCGCTAGCCGCTCCAACA+AGG - chr5.4:29064641-29064660 MS.gene83935:CDS 65.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 29064534 29065228 29064534 ID=MS.gene83935
chr5.4 mRNA 29064534 29065228 29064534 ID=MS.gene83935.t1;Parent=MS.gene83935
chr5.4 exon 29065100 29065228 29065100 ID=MS.gene83935.t1.exon1;Parent=MS.gene83935.t1
chr5.4 CDS 29065100 29065228 29065100 ID=cds.MS.gene83935.t1;Parent=MS.gene83935.t1
chr5.4 exon 29064534 29064686 29064534 ID=MS.gene83935.t1.exon2;Parent=MS.gene83935.t1
chr5.4 CDS 29064534 29064686 29064534 ID=cds.MS.gene83935.t1;Parent=MS.gene83935.t1
Gene Sequence

>MS.gene83935

ATGTCTAGCAGAAGATCTCGTTCCAGACAATCCGGTGGTTCCTCTGAGATCACTGATGCTCAAATCACTGATCTCATTTCCAAGTTACAACAACTTATCCCCGAACTTCGCGCTAGCCGCTCCAACAAGGTATTTATTTTTCTAAATATCGTTGTCTTCATTCTTTAAACTGTCTGCAATTGTACGCAGATGATACTTAATTTATAAAAAATAAAATTATATTTTACTTATAAAACTTTTCCTTCATACACACTCTCACAAATTCCCAAGTCATCATTCACATGCACAATATAAGAATGATACAATGCACATATTGTGTGGACATTGTTAGTTTTGGTAGATAAACAATGTTTATTATGACTCTTCCTCAATTCTTTGCCACAACTTGTGTATTGTATTGTATTGTACTCATTTACTAATCATGCATTAATTACTAGCTTGTAGCTAGTTGCAACATGCAAGTGGGTGGTGTATAAAACTAAAAAAGAAACTCTTTAAAATTTATTAATTTGTAATATTTTTTATTTTTTATGGTCTTATAGGTTTCAGCTACTAAGGTATTGCAAGAGACTTGCAACTACATAAAAAACTTGCATAGAGAGGTTGATGATTTAAGTGACCGATTGTCACAACTTTTGGCTTCTACAGATTCCAACAGTGCTCAAGCAGCTATTATTAGGAGCTTACTTATGTAA
Protein sequence

>MS.gene83935.t1

MSSRRSRSRQSGGSSEITDAQITDLISKLQQLIPELRASRSNKVSATKVLQETCNYIKNLHREVDDLSDRLSQLLASTDSNSAQAAIIRSLLM