AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene024965

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024965.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene024965.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene024965.t1 MTR_1g106755 100.000 56 0 0 1 56 1 56 9.62e-38 119
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene024965.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene024965.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene024965.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene024965.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 19 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 5.3:+482954 MS.gene024965:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.318093 5.3:+482965 MS.gene024965:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 5.3:+482234 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 5.3:-482266 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 5.3:-482964 None:intergenic
AGAACCAGGACCATAGGTCT+TGG 0.460388 5.3:-482267 None:intergenic
GAAACTCTCATGGATTGATC+AGG 0.487816 5.3:+482898 MS.gene024965:CDS
CCATACCATGTGCGAGAACC+AGG 0.488541 5.3:-482281 None:intergenic
CACCCCAAGACCTATGGTCC+TGG 0.491604 5.3:+482263 MS.gene024965:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 5.3:+482257 MS.gene024965:CDS
CGTGTCTGTGGAAACTCTCA+TGG 0.528677 5.3:+482888 MS.gene024965:CDS
ATGGTCCTGGTTCTCGCACA+TGG 0.572066 5.3:+482276 MS.gene024965:CDS
CATGGATTGATCAGGAAGTA+CGG 0.572937 5.3:+482906 MS.gene024965:CDS
TGTGCGAGAACCAGGACCAT+AGG 0.585453 5.3:-482273 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 5.3:-482953 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 5.3:-482265 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.623139 5.3:+482947 MS.gene024965:CDS
CATGAGAGTTTCCACAGACA+CGG 0.630579 5.3:-482887 None:intergenic
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 5.3:-482246 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACGTTAAAAACAAAGAAT+GGG - chr5.3:482682-482701 None:intergenic 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5.3:482644-482663 None:intergenic 20.0%
!! TGATTTACTGAAACAAATTT+CGG + chr5.3:482449-482468 MS.gene024965:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5.3:482609-482628 MS.gene024965:intron 20.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5.3:482683-482702 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr5.3:482432-482451 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5.3:482608-482627 MS.gene024965:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr5.3:482613-482632 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5.3:482687-482706 MS.gene024965:intron 25.0%
AACATCAGTACTCAGAAATA+CGG - chr5.3:482372-482391 None:intergenic 30.0%
CACACCAACTTATTGTTAAT+TGG + chr5.3:482425-482444 MS.gene024965:intron 30.0%
TGATGAATGACAGTAATCTA+TGG - chr5.3:482407-482426 None:intergenic 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr5.3:482980-482999 MS.gene024965:intron 30.0%
AAGCACATCGAAAAATGCAT+TGG - chr5.3:482528-482547 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5.3:482967-482986 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5.3:482494-482513 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr5.3:482489-482508 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5.3:482510-482529 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5.3:482965-482984 MS.gene024965:CDS 35.0%
ACGGATCGAAGAATCTTACA+AGG - chr5.3:482353-482372 None:intergenic 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr5.3:483043-483062 MS.gene024965:intron 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr5.3:482352-482371 None:intergenic 40.0%
TCGAAGAATCTTACAAGGGT+TGG - chr5.3:482348-482367 None:intergenic 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5.3:482906-482925 MS.gene024965:CDS 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr5.3:482898-482917 MS.gene024965:CDS 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr5.3:482537-482556 MS.gene024965:intron 40.0%
ACAGACACGGCTACAAAACA+AGG - chr5.3:482877-482896 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5.3:482956-482975 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5.3:482954-482973 MS.gene024965:CDS 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr5.3:482890-482909 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5.3:482876-482895 MS.gene024965:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG - chr5.3:482268-482287 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr5.3:482257-482276 MS.gene024965:CDS 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr5.3:483055-483074 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5.3:482270-482289 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr5.3:482888-482907 MS.gene024965:CDS 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5.3:482269-482288 None:intergenic 50.0%
CCATACCATGTGCGAGAACC+AGG - chr5.3:482284-482303 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5.3:482249-482268 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5.3:482947-482966 MS.gene024965:CDS 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5.3:482276-482295 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5.3:482276-482295 MS.gene024965:CDS 55.0%
! CCTGGTTCTCGCACATGGTA+TGG + chr5.3:482281-482300 MS.gene024965:intron 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr5.3:482263-482282 MS.gene024965:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 482236 483082 482236 ID=MS.gene024965
chr5.3 mRNA 482236 483082 482236 ID=MS.gene024965.t1;Parent=MS.gene024965
chr5.3 exon 482236 482297 482236 ID=MS.gene024965.t1.exon1;Parent=MS.gene024965.t1
chr5.3 CDS 482236 482297 482236 ID=cds.MS.gene024965.t1;Parent=MS.gene024965.t1
chr5.3 exon 482887 482986 482887 ID=MS.gene024965.t1.exon2;Parent=MS.gene024965.t1
chr5.3 CDS 482887 482986 482887 ID=cds.MS.gene024965.t1;Parent=MS.gene024965.t1
chr5.3 exon 483074 483082 483074 ID=MS.gene024965.t1.exon3;Parent=MS.gene024965.t1
chr5.3 CDS 483074 483082 483074 ID=cds.MS.gene024965.t1;Parent=MS.gene024965.t1
Gene Sequence

>MS.gene024965

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCTCGCACATGGTATGGTATCTATCTATCTCTTTCATTTTATTTTATTTTATATTAAACCAACCCTTGTAAGATTCTTCGATCCGTATTTCTGAGTACTGATGTTATAGATGTGATTCCATAGATTACTGTCATTCATCACACCAACTTATTGTTAATTGGATGATTTACTGAAACAAATTTCGGTTTTAAACTTGTCTCCGATCCTAATTCATTCAGATCCAACTCAACTCTTGAAACCAATGCATTTTTCGATGTGCTTGTACTTTTCTGGAATTATTATTTACTTCTATTCAACTTCTTTTCATTCATTCTGACATGTGTCCTACTTTGAAAATAAAATGGGATTCTCATACCTTAATTTTCACATCATTTTACATAATAATAATCTCACCCATTCTTTGTTTTTAACGTTTGTACTTGGTGTTTAAAGCTTAAACAATGCAATCTTTGTTGTAAACATCAGTGTTAGTATGTCATAACTACTGTCTTAAGATGAGTTATTGTCACACACATTTCAACTATTCTTTCTTAGCTACATTACATGTACATACTTGATATTGCTCGATTGTAAATGTATGTTTTCTACCTTGTTTTGTAGCCGTGTCTGTGGAAACTCTCATGGATTGATCAGGAAGTACGGACTCATGTGTTGCAGACAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTGAATATTTTGCTGGTCTAGATTTCTAAATATCTGCTTGTTTTAGCACGAGTTCTCATCACTTTCCACTTCTTTCCGGTGTTGCAGTATCGCTGA
Protein sequence

>MS.gene024965.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR