AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene40529

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene40529.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene40529.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene40529.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.gene40529.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene40529.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene40529.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene40529.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 20 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 5.2:+399460 MS.gene40529:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.318093 5.2:+399471 MS.gene40529:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 5.2:+398765 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 5.2:-398797 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 5.2:-399470 None:intergenic
AGAACCAGGACCATAGGTCT+TGG 0.460388 5.2:-398798 None:intergenic
GAAATTCTCATGGATTGATC+AGG 0.469054 5.2:+399404 MS.gene40529:CDS
CACCCCAAGACCTATGGTCC+TGG 0.491604 5.2:+398794 MS.gene40529:CDS
AGTACGGACTCATGTGTTGC+AGG 0.493102 5.2:+399428 MS.gene40529:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 5.2:+398788 MS.gene40529:CDS
GCATACCATGTGCGAGAACC+AGG 0.516036 5.2:-398812 None:intergenic
CGTGTCTGTGGAAATTCTCA+TGG 0.552496 5.2:+399394 MS.gene40529:CDS
ATGGTCCTGGTTCTCGCACA+TGG 0.572066 5.2:+398807 MS.gene40529:CDS
CATGGATTGATCAGGAAGTA+CGG 0.575110 5.2:+399412 MS.gene40529:CDS
TGTGCGAGAACCAGGACCAT+AGG 0.585453 5.2:-398804 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 5.2:-399459 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 5.2:-398796 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.621677 5.2:+399453 MS.gene40529:CDS
CATGAGAATTTCCACAGACA+CGG 0.627873 5.2:-399393 None:intergenic
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 5.2:-398777 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACGTTAAAAACAAAGAAT+GGG - chr5.2:399192-399211 None:intergenic 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5.2:399154-399173 None:intergenic 20.0%
!! TGATTTACTGAAACAAATTT+CGG + chr5.2:398985-399004 MS.gene40529:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5.2:399119-399138 MS.gene40529:intron 20.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5.2:399193-399212 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr5.2:398968-398987 None:intergenic 25.0%
! TGATAAATGACAGTAATCTA+TGG - chr5.2:398943-398962 None:intergenic 25.0%
!! CCTACTTTGAAAATAAAATG+GGG + chr5.2:399120-399139 MS.gene40529:intron 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5.2:399118-399137 MS.gene40529:intron 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5.2:399197-399216 MS.gene40529:intron 25.0%
ATTCCAGAAAAGTAATGCAT+TGG - chr5.2:399064-399083 None:intergenic 30.0%
CACACCAACTTATTGTTAAT+TGG + chr5.2:398961-398980 MS.gene40529:intron 30.0%
!! AAACCAATGCATTACTTTTC+TGG + chr5.2:399058-399077 MS.gene40529:intron 30.0%
!!! ATCACTTTACCCTCTTTTTT+CGG + chr5.2:399568-399587 MS.gene40529:intron 30.0%
!!! CCCCATTTTATTTTCAAAGT+AGG - chr5.2:399123-399142 None:intergenic 30.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5.2:399473-399492 None:intergenic 35.0%
GAACACAGTACTCAGAAATA+CGG - chr5.2:398903-398922 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5.2:399030-399049 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr5.2:399025-399044 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5.2:399046-399065 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5.2:399471-399490 MS.gene40529:CDS 35.0%
! GAAATTCTCATGGATTGATC+AGG + chr5.2:399404-399423 MS.gene40529:CDS 35.0%
ACGGATCGAAGAATCTTACA+AGG - chr5.2:398884-398903 None:intergenic 40.0%
ACTGCAACACCGAAAAAAGA+GGG - chr5.2:399580-399599 None:intergenic 40.0%
CATGAGAATTTCCACAGACA+CGG - chr5.2:399396-399415 None:intergenic 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr5.2:398883-398902 None:intergenic 40.0%
TACTGCAACACCGAAAAAAG+AGG - chr5.2:399581-399600 None:intergenic 40.0%
TCGAAGAATCTTACAAGGGT+TGG - chr5.2:398879-398898 None:intergenic 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5.2:399412-399431 MS.gene40529:CDS 40.0%
ACAGACACGGCTACAAAACA+AGG - chr5.2:399383-399402 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5.2:399462-399481 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5.2:399460-399479 MS.gene40529:CDS 45.0%
CGTGTCTGTGGAAATTCTCA+TGG + chr5.2:399394-399413 MS.gene40529:CDS 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5.2:399382-399401 MS.gene40529:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG - chr5.2:398799-398818 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr5.2:398788-398807 MS.gene40529:CDS 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5.2:398801-398820 None:intergenic 50.0%
AGTACGGACTCATGTGTTGC+AGG + chr5.2:399428-399447 MS.gene40529:CDS 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5.2:398800-398819 None:intergenic 50.0%
GCATACCATGTGCGAGAACC+AGG - chr5.2:398815-398834 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5.2:398780-398799 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5.2:399453-399472 MS.gene40529:CDS 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5.2:398807-398826 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5.2:398807-398826 MS.gene40529:CDS 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr5.2:398794-398813 MS.gene40529:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 398767 399607 398767 ID=MS.gene40529
chr5.2 mRNA 398767 399607 398767 ID=MS.gene40529.t1;Parent=MS.gene40529
chr5.2 exon 398767 398828 398767 ID=MS.gene40529.t1.exon1;Parent=MS.gene40529.t1
chr5.2 CDS 398767 398828 398767 ID=cds.MS.gene40529.t1;Parent=MS.gene40529.t1
chr5.2 exon 399393 399492 399393 ID=MS.gene40529.t1.exon2;Parent=MS.gene40529.t1
chr5.2 CDS 399393 399492 399393 ID=cds.MS.gene40529.t1;Parent=MS.gene40529.t1
chr5.2 exon 399599 399607 399599 ID=MS.gene40529.t1.exon3;Parent=MS.gene40529.t1
chr5.2 CDS 399599 399607 399599 ID=cds.MS.gene40529.t1;Parent=MS.gene40529.t1
Gene Sequence

>MS.gene40529

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCTCGCACATGGTATGCTATCTATCTATCTCTTTCATTTTATTTTATTTTATATTAAACCAACCCTTGTAAGATTCTTCGATCCGTATTTCTGAGTACTGTGTTCATGTTATAGATGTGATTCCATAGATTACTGTCATTTATCACACCAACTTATTGTTAATTGGATGATTTACTGAAACAAATTTCGGAATTAAACTTGTCTCCGATCCTAATTCATTCAGATCCAACTCAACTCTTGAAACCAATGCATTACTTTTCTGGAATTATTTACTTCTATTCAACTTCTTTTCATTCATGTGTCCTACTTTGAAAATAAAATGGGGTTCTCATACCTTAATTTTCACATCATTTTACATAATAATAATCTCACCCATTCTTTGTTTTTAACGTTTGTACTTGGTGTTTAAAGCTTAAACAATGCAATCTTTGTTGTAAACATCAGTGTTAGTATGTCATAACTACTGTCTTAAGATGAGTTATTGTCACATTTCAACTATTCTTTCTTAACTACATTACATGTACATACTCGATATTGCTCGATTGTAAATGTATGTTTTCTACCTTGTTTTGTAGCCGTGTCTGTGGAAATTCTCATGGATTGATCAGGAAGTACGGACTCATGTGTTGCAGGCAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTGAATATTTTCATCTACTTTTCTATTTGTTAGTGTAGATTTTCTAAATATCTGCTTGTTTTAGCACGAGTTCTCATCACTTTACCCTCTTTTTTCGGTGTTGCAGTATCGCTGA
Protein sequence

>MS.gene40529.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR