AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene046945

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene046945.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene046945.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene046945.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.gene046945.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene046945.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene046945.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene046945.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 19 sgRNAs with CRISPR-Local

Find 47 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 5.4:+386425 MS.gene046945:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.318093 5.4:+386436 MS.gene046945:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 5.4:+385686 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 5.4:-385718 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 5.4:-386435 None:intergenic
AGAACCAGGACCATAGGTCT+TGG 0.460388 5.4:-385719 None:intergenic
GAAACTCTCATGGATTGATC+AGG 0.487816 5.4:+386369 MS.gene046945:CDS
CCATACCATGTGCGAGAACC+AGG 0.488541 5.4:-385733 None:intergenic
CACCCCAAGACCTATGGTCC+TGG 0.491604 5.4:+385715 MS.gene046945:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 5.4:+385709 MS.gene046945:CDS
CGTGTCTGTGGAAACTCTCA+TGG 0.528677 5.4:+386359 MS.gene046945:CDS
ATGGTCCTGGTTCTCGCACA+TGG 0.572066 5.4:+385728 MS.gene046945:CDS
CATGGATTGATCAGGAAGTA+CGG 0.572937 5.4:+386377 MS.gene046945:CDS
TGTGCGAGAACCAGGACCAT+AGG 0.585453 5.4:-385725 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 5.4:-386424 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 5.4:-385717 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.623139 5.4:+386418 MS.gene046945:CDS
CATGAGAGTTTCCACAGACA+CGG 0.630579 5.4:-386358 None:intergenic
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 5.4:-385698 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTATTTTGAATTTTTTTT+AGG + chr5.4:385869-385888 MS.gene046945:intron 10.0%
!! AAACGTTAAAAACAAAGAAT+GGG - chr5.4:386155-386174 None:intergenic 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5.4:386117-386136 None:intergenic 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5.4:386082-386101 MS.gene046945:intron 20.0%
! AAACTCGAATCAAATATTGT+AGG - chr5.4:385853-385872 None:intergenic 25.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5.4:386156-386175 None:intergenic 25.0%
! CAACTTACTGAAACAAATTT+CGG + chr5.4:385922-385941 MS.gene046945:intron 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5.4:386081-386100 MS.gene046945:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr5.4:386086-386105 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5.4:386160-386179 MS.gene046945:intron 25.0%
TCGAATCAAATATTGTAGGA+GGG - chr5.4:385849-385868 None:intergenic 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr5.4:386451-386470 MS.gene046945:intron 30.0%
! CGAAATTTGTTTCAGTAAGT+TGG - chr5.4:385924-385943 None:intergenic 30.0%
AAGCACATCGAAAAATGCAT+TGG - chr5.4:386001-386020 None:intergenic 35.0%
ACGAATCGAAGAATCTTACA+AGG - chr5.4:385800-385819 None:intergenic 35.0%
CGAATCGAAGAATCTTACAA+GGG - chr5.4:385799-385818 None:intergenic 35.0%
CTCGAATCAAATATTGTAGG+AGG - chr5.4:385850-385869 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5.4:386438-386457 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5.4:385967-385986 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr5.4:385962-385981 None:intergenic 35.0%
TGGTGAATGACAGTAATCTA+TGG - chr5.4:385899-385918 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5.4:385983-386002 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5.4:386436-386455 MS.gene046945:CDS 35.0%
!! TTTGTTTCAGTAAGTTGGTG+TGG - chr5.4:385919-385938 None:intergenic 35.0%
CATCACTTTCCACTTCTTTC+CGG + chr5.4:386513-386532 MS.gene046945:intron 40.0%
TCGAAGAATCTTACAAGGGT+AGG - chr5.4:385795-385814 None:intergenic 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5.4:386377-386396 MS.gene046945:CDS 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr5.4:386369-386388 MS.gene046945:CDS 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr5.4:386010-386029 MS.gene046945:intron 40.0%
ACAGACACGGCTACAAAACA+AGG - chr5.4:386348-386367 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5.4:386427-386446 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5.4:386425-386444 MS.gene046945:CDS 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr5.4:386361-386380 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5.4:386347-386366 MS.gene046945:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG - chr5.4:385720-385739 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr5.4:385709-385728 MS.gene046945:CDS 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr5.4:386525-386544 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5.4:385722-385741 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr5.4:386359-386378 MS.gene046945:CDS 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5.4:385721-385740 None:intergenic 50.0%
CCATACCATGTGCGAGAACC+AGG - chr5.4:385736-385755 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5.4:385701-385720 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5.4:386418-386437 MS.gene046945:CDS 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5.4:385728-385747 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5.4:385728-385747 MS.gene046945:CDS 55.0%
! CCTGGTTCTCGCACATGGTA+TGG + chr5.4:385733-385752 MS.gene046945:intron 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr5.4:385715-385734 MS.gene046945:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 385688 386552 385688 ID=MS.gene046945
chr5.4 mRNA 385688 386552 385688 ID=MS.gene046945.t1;Parent=MS.gene046945
chr5.4 exon 385688 385749 385688 ID=MS.gene046945.t1.exon1;Parent=MS.gene046945.t1
chr5.4 CDS 385688 385749 385688 ID=cds.MS.gene046945.t1;Parent=MS.gene046945.t1
chr5.4 exon 386358 386457 386358 ID=MS.gene046945.t1.exon2;Parent=MS.gene046945.t1
chr5.4 CDS 386358 386457 386358 ID=cds.MS.gene046945.t1;Parent=MS.gene046945.t1
chr5.4 exon 386544 386552 386544 ID=MS.gene046945.t1.exon3;Parent=MS.gene046945.t1
chr5.4 CDS 386544 386552 386544 ID=cds.MS.gene046945.t1;Parent=MS.gene046945.t1
Gene Sequence

>MS.gene046945

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCTCGCACATGGTATGGTATCTATCTATCTCTTTCATTTTATTTTATTTAAAACCTACCCTTGTAAGATTCTTCGATTCGTATTTCTGATTACTGTGTTCATGTAAGCCCTCCTACAATATTTGATTCGAGTTTATTTTGAATTTTTTTTAGGATTTCCATAGATTACTGTCATTCACCACACCAACTTACTGAAACAAATTTCGGAATTAAACTTGTCTCCGATCCTAATTCATTCAGATCCAACTCAACTCTTGAAACCAATGCATTTTTCGATGTGCTTGTACTTTTCTGGAATTATTATTTACTTCTATTCAACTTCTTTTCATTCATTCTGACATGTGTCCTACTTTGAAAATAAAATGGGATTCTCATACCTTAATTTTCACATCATTTTACATAATAATAATCTCACCCATTCTTTGTTTTTAACGTTTGTACTTGGTTTAAAGCTTAAACAATGCAATCTTTGTTGTAAACATCAGTGTTAGTATGTCATAACTACTGTCTTAAGATGAGTTATTGTCACACACATTTCAACTATTCTTTCTTAGCTACATTACATGTACATACTTGATATTGCTCGATTGTAAATGTATGTTTTCTACCTTGTTTTGTAGCCGTGTCTGTGGAAACTCTCATGGATTGATCAGGAAGTACGGACTCATGTGTTGCAGACAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTGAATATTTTGCTGGTCTAGATTTCTAAATATCTGCTTTTTTAGCACGAGTTCTCATCACTTTCCACTTCTTTCCGGTGTTGCAGTATCGCTGA
Protein sequence

>MS.gene046945.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR