AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene92361

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene92361.t1 MTR_5g005130 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene92361.t1 MTR_3g115330 100.000 56 0 0 1 56 1 56 9.62e-38 119
MS.gene92361.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.gene92361.t1 AT4G33865 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene92361.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene92361.t1 AT3G43980 92.857 56 4 0 1 56 1 56 6.55e-34 109
MS.gene92361.t1 AT3G44010 92.857 56 4 0 1 56 1 56 6.55e-34 109

Find 19 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACAGCAATGCCAAGGAAAT+TGG 0.216340 5.1:+273717 MS.gene92361:CDS
CAAGGAAATTGGCTTCATTA+AGG 0.318093 5.1:+273728 MS.gene92361:CDS
TCATGGGTCACTCCAACGTT+TGG 0.416385 5.1:+272992 None:intergenic
GAACCAGGACCATAGGTCTT+GGG 0.430692 5.1:-273024 None:intergenic
CTTAATGAAGCCAATTTCCT+TGG 0.435363 5.1:-273727 None:intergenic
AGAACCAGGACCATAGGTCT+TGG 0.460388 5.1:-273025 None:intergenic
GAAACTCTCATGGATTGATC+AGG 0.487816 5.1:+273661 MS.gene92361:CDS
CACCCCAAGACCTATGGTCC+TGG 0.491604 5.1:+273021 MS.gene92361:CDS
AACTCTCACCCCAAGACCTA+TGG 0.505813 5.1:+273015 MS.gene92361:CDS
GCATACCATGTGCGAGAACC+AGG 0.516036 5.1:-273039 None:intergenic
CGTGTCTGTGGAAACTCTCA+TGG 0.528677 5.1:+273651 MS.gene92361:CDS
ATGGTCCTGGTTCTCGCACA+TGG 0.572066 5.1:+273034 MS.gene92361:CDS
CATGGATTGATCAGGAAGTA+CGG 0.572937 5.1:+273669 MS.gene92361:CDS
TGTGCGAGAACCAGGACCAT+AGG 0.585453 5.1:-273031 None:intergenic
CAATTTCCTTGGCATTGCTG+TGG 0.593734 5.1:-273716 None:intergenic
AACCAGGACCATAGGTCTTG+GGG 0.607026 5.1:-273023 None:intergenic
GTGCTTCCACAGCAATGCCA+AGG 0.623139 5.1:+273710 MS.gene92361:CDS
CATGAGAGTTTCCACAGACA+CGG 0.630579 5.1:-273650 None:intergenic
GGGGTGAGAGTTCCAAACGT+TGG 0.647246 5.1:-273004 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAACGTTAAAAACAAAGAAT+GGG - chr5.1:273445-273464 None:intergenic 20.0%
!! GTAAAATGATGTGAAAATTA+AGG - chr5.1:273407-273426 None:intergenic 20.0%
!! TGATTTACTGAAACAAATTT+CGG + chr5.1:273212-273231 MS.gene92361:intron 20.0%
!!! TCCTACTTTGAAAATAAAAT+GGG + chr5.1:273372-273391 MS.gene92361:intron 20.0%
! CAAACGTTAAAAACAAAGAA+TGG - chr5.1:273446-273465 None:intergenic 25.0%
! TCATCCAATTAACAATAAGT+TGG - chr5.1:273195-273214 None:intergenic 25.0%
! TGATAAATGACAGTAATCTA+TGG - chr5.1:273170-273189 None:intergenic 25.0%
!! GTCCTACTTTGAAAATAAAA+TGG + chr5.1:273371-273390 MS.gene92361:intron 25.0%
!!! TCCCATTTTATTTTCAAAGT+AGG - chr5.1:273376-273395 None:intergenic 25.0%
!!! TTGTTTTTAACGTTTGTACT+TGG + chr5.1:273450-273469 MS.gene92361:intron 25.0%
CACACCAACTTATTGTTAAT+TGG + chr5.1:273188-273207 MS.gene92361:intron 30.0%
! CATTAAGGTGAATATTTTGC+TGG + chr5.1:273743-273762 MS.gene92361:intron 30.0%
AAGCACATCGAAAAATGCAT+TGG - chr5.1:273291-273310 None:intergenic 35.0%
CTTAATGAAGCCAATTTCCT+TGG - chr5.1:273730-273749 None:intergenic 35.0%
GAACACAGTACTCAGAAATA+CGG - chr5.1:273130-273149 None:intergenic 35.0%
GAGTTGGATCTGAATGAATT+AGG - chr5.1:273257-273276 None:intergenic 35.0%
GGATCTGAATGAATTAGGAT+CGG - chr5.1:273252-273271 None:intergenic 35.0%
! ATTGGTTTCAAGAGTTGAGT+TGG - chr5.1:273273-273292 None:intergenic 35.0%
! CAAGGAAATTGGCTTCATTA+AGG + chr5.1:273728-273747 MS.gene92361:CDS 35.0%
ACGGATCGAAGAATCTTACA+AGG - chr5.1:273111-273130 None:intergenic 40.0%
CATCACTTTCCACTTCTTTC+CGG + chr5.1:273806-273825 MS.gene92361:intron 40.0%
CGGATCGAAGAATCTTACAA+GGG - chr5.1:273110-273129 None:intergenic 40.0%
TCGAAGAATCTTACAAGGGT+TGG - chr5.1:273106-273125 None:intergenic 40.0%
! CATGGATTGATCAGGAAGTA+CGG + chr5.1:273669-273688 MS.gene92361:CDS 40.0%
! GAAACTCTCATGGATTGATC+AGG + chr5.1:273661-273680 MS.gene92361:CDS 40.0%
! TCGATGTGCTTGTACTTTTC+TGG + chr5.1:273300-273319 MS.gene92361:intron 40.0%
ACAGACACGGCTACAAAACA+AGG - chr5.1:273640-273659 None:intergenic 45.0%
CAATTTCCTTGGCATTGCTG+TGG - chr5.1:273719-273738 None:intergenic 45.0%
CACAGCAATGCCAAGGAAAT+TGG + chr5.1:273717-273736 MS.gene92361:CDS 45.0%
CATGAGAGTTTCCACAGACA+CGG - chr5.1:273653-273672 None:intergenic 45.0%
!! TTGTTTTGTAGCCGTGTCTG+TGG + chr5.1:273639-273658 MS.gene92361:intron 45.0%
AACCAGGACCATAGGTCTTG+GGG - chr5.1:273026-273045 None:intergenic 50.0%
AACTCTCACCCCAAGACCTA+TGG + chr5.1:273015-273034 MS.gene92361:CDS 50.0%
ACTGCAACACCGGAAAGAAG+TGG - chr5.1:273818-273837 None:intergenic 50.0%
AGAACCAGGACCATAGGTCT+TGG - chr5.1:273028-273047 None:intergenic 50.0%
CGTGTCTGTGGAAACTCTCA+TGG + chr5.1:273651-273670 MS.gene92361:CDS 50.0%
GAACCAGGACCATAGGTCTT+GGG - chr5.1:273027-273046 None:intergenic 50.0%
GCATACCATGTGCGAGAACC+AGG - chr5.1:273042-273061 None:intergenic 55.0%
GGGGTGAGAGTTCCAAACGT+TGG - chr5.1:273007-273026 None:intergenic 55.0%
GTGCTTCCACAGCAATGCCA+AGG + chr5.1:273710-273729 MS.gene92361:CDS 55.0%
TGTGCGAGAACCAGGACCAT+AGG - chr5.1:273034-273053 None:intergenic 55.0%
! ATGGTCCTGGTTCTCGCACA+TGG + chr5.1:273034-273053 MS.gene92361:CDS 55.0%
CACCCCAAGACCTATGGTCC+TGG + chr5.1:273021-273040 MS.gene92361:CDS 60.0%


Chromosome Type Strat End Strand Name
chr5.1 gene 272994 273845 272994 ID=MS.gene92361
chr5.1 mRNA 272994 273845 272994 ID=MS.gene92361.t1;Parent=MS.gene92361
chr5.1 exon 272994 273055 272994 ID=MS.gene92361.t1.exon1;Parent=MS.gene92361.t1
chr5.1 CDS 272994 273055 272994 ID=cds.MS.gene92361.t1;Parent=MS.gene92361.t1
chr5.1 exon 273650 273749 273650 ID=MS.gene92361.t1.exon2;Parent=MS.gene92361.t1
chr5.1 CDS 273650 273749 273650 ID=cds.MS.gene92361.t1;Parent=MS.gene92361.t1
chr5.1 exon 273837 273845 273837 ID=MS.gene92361.t1.exon3;Parent=MS.gene92361.t1
chr5.1 CDS 273837 273845 273837 ID=cds.MS.gene92361.t1;Parent=MS.gene92361.t1
Gene Sequence

>MS.gene92361

ATGGGTCACTCCAACGTTTGGAACTCTCACCCCAAGACCTATGGTCCTGGTTCTCGCACATGGTATGCTATCTATCTATCTCTTTCATTTTATTTTATTTTATATTAAACCAACCCTTGTAAGATTCTTCGATCCGTATTTCTGAGTACTGTGTTCATGTTATAGATGTGATTCCATAGATTACTGTCATTTATCACACCAACTTATTGTTAATTGGATGATTTACTGAAACAAATTTCGGAATTAAACTTGTCTCCGATCCTAATTCATTCAGATCCAACTCAACTCTTGAAACCAATGCATTTTTCGATGTGCTTGTACTTTTCTGGAATTATTATTTACTTCTATTCAACTTCTTTTCATTCATTCTGACATGTGTCCTACTTTGAAAATAAAATGGGATTCTCATACCTTAATTTTCACATCATTTTACATAATAATAATCTCACCCATTCTTTGTTTTTAACGTTTGTACTTGGTGTTTAAAGCTTAAACAATGCAATCTTTGTTGTAAACATCAGTGTTAGTATGTCATAACTACTGTCTTAAGATGAGTTATTGTCACACACATTTCAACTATTCTTTCTTAGCTACATTACATGTACATACTTGATATTGCTCGATTGTAAATGTATGTTTTCTACCTTGTTTTGTAGCCGTGTCTGTGGAAACTCTCATGGATTGATCAGGAAGTACGGACTCATGTGTTGCAGACAGTGCTTCCACAGCAATGCCAAGGAAATTGGCTTCATTAAGGTGAATATTTTGCTGGTCTAGATTTCTAAATATCTGCTTGTTTTAGCACGAGTTCTCATCACTTTCCACTTCTTTCCGGTGTTGCAGTATCGCTGA
Protein sequence

>MS.gene92361.t1

MGHSNVWNSHPKTYGPGSRTCRVCGNSHGLIRKYGLMCCRQCFHSNAKEIGFIKYR