AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene21654

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene21654.t1 MTR_4g123470 78.365 208 23 2 2 189 20 225 5.38e-118 333
MS.gene21654.t1 MTR_7g113060 84.615 39 6 0 149 187 1 39 2.80e-17 76.3
MS.gene21654.t1 MTR_7g025150 28.125 192 110 3 7 174 20 207 1.02e-15 72.8
MS.gene21654.t1 MTR_4g085790 27.604 192 111 3 7 174 20 207 8.24e-15 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 38 sgRNAs with CRISPR-Local

Find 61 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATTCCTATCGCTGGATA+TGG 0.237538 5.2:-3109267 MS.gene21654:CDS
AGTTGCGATGTTTCACTCTA+AGG 0.329793 5.2:+3109098 None:intergenic
CCCATACCAATTGTGATGTT+TGG 0.340839 5.2:-3109013 MS.gene21654:CDS
AGGAATTTGCCAAAAGTATC+AGG 0.344083 5.2:+3109118 None:intergenic
TAGGAACTACCTGATACTTT+TGG 0.356273 5.2:-3109127 MS.gene21654:CDS
TCACAGTGCATTGCAAAATC+AGG 0.366017 5.2:-3109793 MS.gene21654:intron
CGATTATTCAACGAATTTAG+TGG 0.373935 5.2:-3109423 MS.gene21654:CDS
TCCAAACATCACAATTGGTA+TGG 0.411232 5.2:+3109012 None:intergenic
ATCTACTTCCACCAAGGTAC+TGG 0.428620 5.2:+3109382 None:intergenic
CCAAACATCACAATTGGTAT+GGG 0.452680 5.2:+3109013 None:intergenic
GAGCAATGGCACTTGCTAGA+TGG 0.455163 5.2:-3109521 MS.gene21654:intron
CTGTTTGACTTCTAGGATGT+TGG 0.457667 5.2:-3109590 MS.gene21654:intron
TTGTGCTGCCAATGGTATTG+AGG 0.463000 5.2:-3108972 MS.gene21654:CDS
ACAGGAATGACGTAGTCATA+TGG 0.475988 5.2:+3109058 None:intergenic
ACACGATGCTACCGCACTCA+TGG 0.499582 5.2:+3109302 None:intergenic
TGTGCTGCCAATGGTATTGA+GGG 0.501205 5.2:-3108971 MS.gene21654:CDS
ATTATTGCTTTCCAGTACCT+TGG 0.503165 5.2:-3109393 MS.gene21654:CDS
GGCCGTTGTTGACAGATGGT+TGG 0.504324 5.2:-3109455 MS.gene21654:intron
TCAATATTTCTACGAGCTAC+CGG 0.507354 5.2:-3109543 MS.gene21654:CDS
CCAATTGTGATGTTTGGAAA+AGG 0.511741 5.2:-3109007 MS.gene21654:CDS
AAATATTGAGCAACGAAGAA+TGG 0.513098 5.2:+3109557 None:intergenic
TCTAGCAAGTGCCATTGCTC+CGG 0.534587 5.2:+3109524 None:intergenic
TTGTGATGTTTGGAAAAGGC+TGG 0.536068 5.2:-3109003 MS.gene21654:CDS
TGGTAAGGTGGATAATCAGC+TGG 0.541144 5.2:+3109327 None:intergenic
TTTCAAGTGCAAGTGTGTCA+TGG 0.544420 5.2:-3108933 MS.gene21654:CDS
ATGCTACCGCACTCATGGAA+TGG 0.547467 5.2:+3109307 None:intergenic
ATTGCTTTCCAGTACCTTGG+TGG 0.549152 5.2:-3109390 MS.gene21654:CDS
TCTGTATATTTGAGTCTCAC+AGG 0.555272 5.2:+3109040 None:intergenic
GTTGATCCATATCCAGCGAT+AGG 0.559408 5.2:+3109261 None:intergenic
GTCTCCGCCCTCAATACCAT+TGG 0.581950 5.2:+3108964 None:intergenic
ACCGCACTCATGGAATGGTA+AGG 0.593653 5.2:+3109312 None:intergenic
TCTACGAGCTACCGGAGCAA+TGG 0.612965 5.2:-3109535 MS.gene21654:CDS
CAAACATCACAATTGGTATG+GGG 0.630299 5.2:+3109014 None:intergenic
GCACTCATGGAATGGTAAGG+TGG 0.647237 5.2:+3109315 None:intergenic
ACCTTACCATTCCATGAGTG+CGG 0.651296 5.2:-3109313 MS.gene21654:CDS
TGGATCAACGAAATCACCGA+AGG 0.668402 5.2:-3109247 MS.gene21654:intron
TTTGAAATCTACTTCCACCA+AGG 0.681040 5.2:+3109376 None:intergenic
GCTGCCAATGGTATTGAGGG+CGG 0.739556 5.2:-3108968 MS.gene21654:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAAATTAAATTCTTTTT+TGG - chr5.2:3109027-3109046 MS.gene21654:CDS 10.0%
!!! TCTAAATTTTTTGTTTTTTT+AGG - chr5.2:3109559-3109578 MS.gene21654:CDS 10.0%
!!! TTATATATGCTATTTTAATA+CGG - chr5.2:3109518-3109537 MS.gene21654:intron 10.0%
!!! AAATTAAATTCTTTTTTGGT+TGG - chr5.2:3109031-3109050 MS.gene21654:CDS 15.0%
!! CATCTTATGTAAATAGAAAA+AGG + chr5.2:3108980-3108999 None:intergenic 20.0%
! AAAAAACAACAAACAACCTT+CGG + chr5.2:3109477-3109496 None:intergenic 25.0%
! AAAAATATGTTATCGTATCC+AGG - chr5.2:3109798-3109817 MS.gene21654:CDS 25.0%
! CAAACAGTGTATCAAAAAAA+GGG + chr5.2:3109102-3109121 None:intergenic 25.0%
! TAGAAAAAGGTTAAATCTAG+TGG + chr5.2:3108967-3108986 None:intergenic 25.0%
! TCAAACAGTGTATCAAAAAA+AGG + chr5.2:3109103-3109122 None:intergenic 25.0%
! TGTTAAACAAATCAGTTAGT+CGG - chr5.2:3109229-3109248 MS.gene21654:intron 25.0%
!! TCATGCACATTAAAAGTATA+CGG + chr5.2:3109011-3109030 None:intergenic 25.0%
!! TTTTCATGCTATTCAATTAG+AGG - chr5.2:3109494-3109513 MS.gene21654:intron 25.0%
AAATATTGAGCAACGAAGAA+TGG + chr5.2:3109151-3109170 None:intergenic 30.0%
AAATCTAGTGGTAAAATTCG+AGG + chr5.2:3108955-3108974 None:intergenic 30.0%
AATCTAGTGGTAAAATTCGA+GGG + chr5.2:3108954-3108973 None:intergenic 30.0%
CGATTATTCAACGAATTTAG+TGG - chr5.2:3109282-3109301 MS.gene21654:CDS 30.0%
ATTATTGCTTTCCAGTACCT+TGG - chr5.2:3109312-3109331 MS.gene21654:CDS 35.0%
CAAACATCACAATTGGTATG+GGG + chr5.2:3109694-3109713 None:intergenic 35.0%
CCAAACATCACAATTGGTAT+GGG + chr5.2:3109695-3109714 None:intergenic 35.0%
CCAATTGTGATGTTTGGAAA+AGG - chr5.2:3109698-3109717 MS.gene21654:intron 35.0%
TCCAAACATCACAATTGGTA+TGG + chr5.2:3109696-3109715 None:intergenic 35.0%
TCTGTATATTTGAGTCTCAC+AGG + chr5.2:3109668-3109687 None:intergenic 35.0%
! CCTTTTCCAAACATCACAAT+TGG + chr5.2:3109701-3109720 None:intergenic 35.0%
! TAGGAACTACCTGATACTTT+TGG - chr5.2:3109578-3109597 MS.gene21654:CDS 35.0%
! TCAATATTTCTACGAGCTAC+CGG - chr5.2:3109162-3109181 MS.gene21654:intron 35.0%
! TGATACACTGTTTGACTTCT+AGG - chr5.2:3109108-3109127 MS.gene21654:CDS 35.0%
! TTTGAAATCTACTTCCACCA+AGG + chr5.2:3109332-3109351 None:intergenic 35.0%
!! AGGAATTTGCCAAAAGTATC+AGG + chr5.2:3109590-3109609 None:intergenic 35.0%
!!! ACTTTTGAAATTCCTATCGC+TGG - chr5.2:3109432-3109451 MS.gene21654:CDS 35.0%
ACAGGAATGACGTAGTCATA+TGG + chr5.2:3109650-3109669 None:intergenic 40.0%
AGTTGCGATGTTTCACTCTA+AGG + chr5.2:3109610-3109629 None:intergenic 40.0%
CCCATACCAATTGTGATGTT+TGG - chr5.2:3109692-3109711 MS.gene21654:intron 40.0%
GAAATTCCTATCGCTGGATA+TGG - chr5.2:3109438-3109457 MS.gene21654:CDS 40.0%
TCACAGTGCATTGCAAAATC+AGG - chr5.2:3108912-3108931 MS.gene21654:CDS 40.0%
TTCCAACCATCTGTCAACAA+CGG + chr5.2:3109255-3109274 None:intergenic 40.0%
TTGTGATGTTTGGAAAAGGC+TGG - chr5.2:3109702-3109721 MS.gene21654:intron 40.0%
! TTTCAAGTGCAAGTGTGTCA+TGG - chr5.2:3109772-3109791 MS.gene21654:intron 40.0%
!! CTGTTTGACTTCTAGGATGT+TGG - chr5.2:3109115-3109134 MS.gene21654:CDS 40.0%
AAGGGAAAACAACTGCAAGC+TGG + chr5.2:3109084-3109103 None:intergenic 45.0%
ACCTTACCATTCCATGAGTG+CGG - chr5.2:3109392-3109411 MS.gene21654:CDS 45.0%
ATCTACTTCCACCAAGGTAC+TGG + chr5.2:3109326-3109345 None:intergenic 45.0%
ATTGCTTTCCAGTACCTTGG+TGG - chr5.2:3109315-3109334 MS.gene21654:CDS 45.0%
GTTGATCCATATCCAGCGAT+AGG + chr5.2:3109447-3109466 None:intergenic 45.0%
TGGATCAACGAAATCACCGA+AGG - chr5.2:3109458-3109477 MS.gene21654:intron 45.0%
TGGTAAGGTGGATAATCAGC+TGG + chr5.2:3109381-3109400 None:intergenic 45.0%
TTGTGCTGCCAATGGTATTG+AGG - chr5.2:3109733-3109752 MS.gene21654:intron 45.0%
! ACGAGTTTTTGTGCTGCCAA+TGG - chr5.2:3109725-3109744 MS.gene21654:intron 45.0%
! TGTGCTGCCAATGGTATTGA+GGG - chr5.2:3109734-3109753 MS.gene21654:intron 45.0%
ACCGCACTCATGGAATGGTA+AGG + chr5.2:3109396-3109415 None:intergenic 50.0%
ATGCTACCGCACTCATGGAA+TGG + chr5.2:3109401-3109420 None:intergenic 50.0%
GCACTCATGGAATGGTAAGG+TGG + chr5.2:3109393-3109412 None:intergenic 50.0%
! GAGCAATGGCACTTGCTAGA+TGG - chr5.2:3109184-3109203 MS.gene21654:intron 50.0%
! TCTAGCAAGTGCCATTGCTC+CGG + chr5.2:3109184-3109203 None:intergenic 50.0%
! TGGCACTTGCTAGATGGTGA+TGG - chr5.2:3109190-3109209 MS.gene21654:intron 50.0%
ACACGATGCTACCGCACTCA+TGG + chr5.2:3109406-3109425 None:intergenic 55.0%
AGTCGGCCGTTGTTGACAGA+TGG - chr5.2:3109246-3109265 MS.gene21654:intron 55.0%
GGCCGTTGTTGACAGATGGT+TGG - chr5.2:3109250-3109269 MS.gene21654:CDS 55.0%
GTCTCCGCCCTCAATACCAT+TGG + chr5.2:3109744-3109763 None:intergenic 55.0%
TCTACGAGCTACCGGAGCAA+TGG - chr5.2:3109170-3109189 MS.gene21654:intron 55.0%
! GCTGCCAATGGTATTGAGGG+CGG - chr5.2:3109737-3109756 MS.gene21654:intron 55.0%


Chromosome Type Strat End Strand Name
chr5.2 gene 3108901 3109826 3108901 ID=MS.gene21654
chr5.2 mRNA 3108901 3109826 3108901 ID=MS.gene21654.t1;Parent=MS.gene21654
chr5.2 exon 3109794 3109826 3109794 ID=MS.gene21654.t1.exon1;Parent=MS.gene21654.t1
chr5.2 CDS 3109794 3109826 3109794 ID=cds.MS.gene21654.t1;Parent=MS.gene21654.t1
chr5.2 exon 3109522 3109597 3109522 ID=MS.gene21654.t1.exon2;Parent=MS.gene21654.t1
chr5.2 CDS 3109522 3109597 3109522 ID=cds.MS.gene21654.t1;Parent=MS.gene21654.t1
chr5.2 exon 3109248 3109462 3109248 ID=MS.gene21654.t1.exon3;Parent=MS.gene21654.t1
chr5.2 CDS 3109248 3109462 3109248 ID=cds.MS.gene21654.t1;Parent=MS.gene21654.t1
chr5.2 exon 3108901 3109146 3108901 ID=MS.gene21654.t1.exon4;Parent=MS.gene21654.t1
chr5.2 CDS 3108901 3109146 3108901 ID=cds.MS.gene21654.t1;Parent=MS.gene21654.t1
Gene Sequence

>MS.gene21654

ATGTTCGTTCTTCACAGTGCATTGCAAAATCAGGTTTGTTGTCGAATTTACCCTCGAATTTTACCACTAGATTTAACCTTTTTCTATTTACATAAGATGAACAGAGTCCGTATACTTTTAATGTGCATGAAAATTAAATTCTTTTTTGGTTGGATTTAATCTTTTTTGTTGTTGTTGAATCCAGCTTGCAGTTGTTTTCCCTTTTTTTGATACACTGTTTGACTTCTAGGATGTTGGAGAACTACAACCATTCTTCGTTGCTCAATATTTCTACGAGCTACCGGAGCAATGGCACTTGCTAGATGGTGATGGAATACTCACAACGTCATGTTAAACAAATCAGTTAGTCGGCCGTTGTTGACAGATGGTTGGAATGCATTGCGATTATTCAACGAATTTAGTGGAAGTAAGATTATTGCTTTCCAGTACCTTGGTGGAAGTAGATTTCAAATCTTTGTTTTTGCTCATAACATTACTCCAGCTGATTATCCACCTTACCATTCCATGAGTGCGGTAGCATCGTGTTATTGTACTTTTGAAATTCCTATCGCTGGATATGGATCAACGAAATCACCGAAGGTTGTTTGTTGTTTTTTTCATGCTATTCAATTAGAGGTTTATATATGCTATTTTAATACGGTATATTTTTGTATGTTATTCTAAATTTTTTGTTTTTTTAGGAACTACCTGATACTTTTGGCAAATTCCTTAGAGTGAAACATCGCAACTACGTCATGTTGTGCGCTCCATATGACTACGTCATTCCTGTGAGACTCAAATATACAGACGACCCCATACCAATTGTGATGTTTGGAAAAGGCTGGACGAGTTTTTGTGCTGCCAATGGTATTGAGGGCGGAGACGTGTTAATTTTCAAGTGCAAGTGTGTCATGGACAAAAAATATGTTATCGTATCCAGGCGTTGA
Protein sequence

>MS.gene21654.t1

MFVLHSALQNQDVGELQPFFVAQYFYELPEQWHLLDDGWNALRLFNEFSGSKIIAFQYLGGSRFQIFVFAHNITPADYPPYHSMSAVASCYCTFEIPIAGYGSTKSPKELPDTFGKFLRVKHRNYVMLCAPYDYVIPVRLKYTDDPIPIVMFGKGWTSFCAANGIEGGDVLIFKCKCVMDKKYVIVSRR