AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene61387

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene61387.t1 MTR_6g086760 87.778 90 11 0 1 90 1 90 2.93e-51 155
MS.gene61387.t1 MTR_6g086765 88.000 50 6 0 25 74 42 91 1.16e-21 85.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTAGATGTACCTTCTTCATT+TGG 0.332645 6.3:-80210284 None:intergenic
GCGTCATTCTCCTGCTGGTT+TGG 0.360082 6.3:-80210320 None:intergenic
CTTAAGCGTCATTCTCCTGC+TGG 0.404962 6.3:-80210325 None:intergenic
AAATGAAGAAGGTACATCTA+AGG 0.414920 6.3:+80210286 MS.gene61387:CDS
GGAGGGAAGCGGTGGATGCC+AGG 0.415483 6.3:-80209773 None:intergenic
AAGCGGTGGATGCCAGGTGG+AGG 0.484160 6.3:-80209767 None:intergenic
TCGTCAATCACACTGCAAAC+AGG 0.488932 6.3:-80209794 None:intergenic
AGCTGAAGTTCCAAACCAGC+AGG 0.526615 6.3:+80210310 MS.gene61387:CDS
AGACCGCAAATGCCTCCACC+TGG 0.565108 6.3:+80209755 None:intergenic
CACTGCAAACAGGAGGGAAG+CGG 0.570902 6.3:-80209784 None:intergenic
CGAACTTTCTGCAGAACCCA+AGG 0.585785 6.3:+80209814 MS.gene61387:CDS
GCTGAAGTTCCAAATGAAGA+AGG 0.589203 6.3:+80210275 MS.gene61387:CDS
TGCAAACAGGAGGGAAGCGG+TGG 0.590963 6.3:-80209781 None:intergenic
GGGAAGCGGTGGATGCCAGG+TGG 0.618199 6.3:-80209770 None:intergenic
TCAATCACACTGCAAACAGG+AGG 0.629072 6.3:-80209791 None:intergenic
CAATCACACTGCAAACAGGA+GGG 0.665161 6.3:-80209790 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATGTTAACTAAGTTTATG+GGG + chr6.3:80209851-80209870 MS.gene61387:intron 20.0%
!! ATATGAGCAATAATATTGTT+AGG - chr6.3:80209975-80209994 None:intergenic 20.0%
!! GAAATGTTAACTAAGTTTAT+GGG + chr6.3:80209850-80209869 MS.gene61387:intron 20.0%
!! TGAAATGTTAACTAAGTTTA+TGG + chr6.3:80209849-80209868 MS.gene61387:intron 20.0%
!! TTATTAAAGAACTCGATATA+TGG - chr6.3:80209919-80209938 None:intergenic 20.0%
!!! AGAAAGAAGCTGATTTTAAA+AGG + chr6.3:80210180-80210199 MS.gene61387:CDS 25.0%
!!! GAAAGAAGCTGATTTTAAAA+GGG + chr6.3:80210181-80210200 MS.gene61387:CDS 25.0%
TAAATTTAAAGAACTTGCCG+CGG - chr6.3:80210042-80210061 None:intergenic 30.0%
TTAGATGTACCTTCTTCATT+TGG - chr6.3:80210287-80210306 None:intergenic 30.0%
TTCATGAAAAAACTTGCCTT+GGG - chr6.3:80209833-80209852 None:intergenic 30.0%
TTTCATGAAAAAACTTGCCT+TGG - chr6.3:80209834-80209853 None:intergenic 30.0%
! AAATGAAGAAGGTACATCTA+AGG + chr6.3:80210286-80210305 MS.gene61387:CDS 30.0%
AAATTTAAAGAACTTGCCGC+GGG - chr6.3:80210041-80210060 None:intergenic 35.0%
AGATGAAAAAGCTGCATCTA+AGG + chr6.3:80210250-80210269 MS.gene61387:CDS 35.0%
!! CTGCTTTTCAATTTCATCGA+GGG - chr6.3:80210162-80210181 None:intergenic 35.0%
!! TCTGCTTTTCAATTTCATCG+AGG - chr6.3:80210163-80210182 None:intergenic 35.0%
GCTGAAGTTCCAAATGAAGA+AGG + chr6.3:80210275-80210294 MS.gene61387:CDS 40.0%
TGTTAGGCTTCAATTTCTGC+TGG - chr6.3:80209959-80209978 None:intergenic 40.0%
TTAACCGATAAACCAGCAGT+TGG + chr6.3:80210112-80210131 MS.gene61387:intron 40.0%
!! AACTCCAACTGCTGGTTTAT+CGG - chr6.3:80210119-80210138 None:intergenic 40.0%
CAATCACACTGCAAACAGGA+GGG - chr6.3:80209793-80209812 None:intergenic 45.0%
CATACAACAACTCCAACTGC+TGG - chr6.3:80210127-80210146 None:intergenic 45.0%
TCAATCACACTGCAAACAGG+AGG - chr6.3:80209794-80209813 None:intergenic 45.0%
TCGTCAATCACACTGCAAAC+AGG - chr6.3:80209797-80209816 None:intergenic 45.0%
TGTGTCTGATTTACAACCCG+CGG + chr6.3:80210022-80210041 MS.gene61387:intron 45.0%
AGCTGAAGTTCCAAACCAGC+AGG + chr6.3:80210310-80210329 MS.gene61387:CDS 50.0%
CGAACTTTCTGCAGAACCCA+AGG + chr6.3:80209814-80209833 MS.gene61387:CDS 50.0%
TGGAGTTGTTGTATGCAGCG+CGG + chr6.3:80210132-80210151 MS.gene61387:intron 50.0%
CACTGCAAACAGGAGGGAAG+CGG - chr6.3:80209787-80209806 None:intergenic 55.0%
! GCGTCATTCTCCTGCTGGTT+TGG - chr6.3:80210323-80210342 None:intergenic 55.0%
TGCAAACAGGAGGGAAGCGG+TGG - chr6.3:80209784-80209803 None:intergenic 60.0%
AAGCGGTGGATGCCAGGTGG+AGG - chr6.3:80209770-80209789 None:intergenic 65.0%
GGAGGGAAGCGGTGGATGCC+AGG - chr6.3:80209776-80209795 None:intergenic 70.0%
GGGAAGCGGTGGATGCCAGG+TGG - chr6.3:80209773-80209792 None:intergenic 70.0%


Chromosome Type Strat End Strand Name
chr6.3 gene 80209764 80210346 80209764 ID=MS.gene61387
chr6.3 mRNA 80209764 80210346 80209764 ID=MS.gene61387.t1;Parent=MS.gene61387
chr6.3 exon 80209764 80209839 80209764 ID=MS.gene61387.t1.exon1;Parent=MS.gene61387.t1
chr6.3 CDS 80209764 80209839 80209764 ID=cds.MS.gene61387.t1;Parent=MS.gene61387.t1
chr6.3 exon 80210150 80210346 80210150 ID=MS.gene61387.t1.exon2;Parent=MS.gene61387.t1
chr6.3 CDS 80210150 80210346 80210150 ID=cds.MS.gene61387.t1;Parent=MS.gene61387.t1
Gene Sequence

>MS.gene61387

ATGCCTCCACCTGGCATCCACCGCTTCCCTCCTGTTTGCAGTGTGATTGACGAACTTTCTGCAGAACCCAAGGCAAGTTTTTTCATGAAATGTTAACTAAGTTTATGGGGCTGAAGCAATACTTCTTATAAAAACAATCTTATTTTCTTTGTCCATATATCGAGTTCTTTAATAATATTTATCTCTATATCACCAGCAGAAATTGAAGCCTAACAATATTATTGCTCATATTGAAAAGCTCGTGAGAACTGCGAAGACTGTGTCTGATTTACAACCCGCGGCAAGTTCTTTAAATTTAAGTTTCATACTTTTAGTTTCTTTGTTTATATTTGAGTTCTTTAATATTAATTAACCGATAAACCAGCAGTTGGAGTTGTTGTATGCAGCGCGGACTGCCCTCGATGAAATTGAAAAGCAGAAAGAAGCTGATTTTAAAAGGGCTGCAGTTGAAATTAAGAAACTGAGAGTTCAAATTCAAAAGAAGATAGATGAAAAAGCTGCATCTAAGGCAGCTGAAGTTCCAAATGAAGAAGGTACATCTAAGGCAGCTGAAGTTCCAAACCAGCAGGAGAATGACGCTTAA
Protein sequence

>MS.gene61387.t1

MPPPGIHRFPPVCSVIDELSAEPKATRTALDEIEKQKEADFKRAAVEIKKLRVQIQKKIDEKAASKAAEVPNEEGTSKAAEVPNQQENDA