AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene051317


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051317.t1 MTR_5g029590 98.485 66 1 0 65 130 189 254 3.23e-35 124
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene051317.t1 AT2G35490 68.182 66 21 0 65 130 209 274 1.37e-20 85.9
MS.gene051317.t1 AT4G04020 54.545 66 30 0 65 130 150 215 2.34e-15 71.2
MS.gene051317.t1 AT4G22240 50.000 66 33 0 65 130 142 207 3.56e-15 70.5

Find 35 sgRNAs with CRISPR-Local

Find 70 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAGCTTCTTAATGGAAAT+TGG 0.139850 5.4:+19914284 MS.gene051317:CDS
ATGATTGTCAAACTGATTTC+AGG 0.207100 5.4:+19915186 MS.gene051317:CDS
GAGGAACCAGAGCTTCTTAA+TGG 0.294675 5.4:+19914277 MS.gene051317:CDS
ACTGAGCTTGGGTTTCGAGC+TGG 0.339922 5.4:+19914181 MS.gene051317:CDS
CTGAGCTTGGGTTTCGAGCT+GGG 0.348135 5.4:+19914182 MS.gene051317:CDS
GAGAATACCTGTATTCTTGC+AGG 0.368434 5.4:-19915389 None:intergenic
CGGTTTATGGGACTGAGCTT+GGG 0.396439 5.4:+19914170 None:intergenic
AGAAGCTCTGGTTCCTCAAC+CGG 0.397078 5.4:-19914271 None:intergenic
ACGGTTTATGGGACTGAGCT+TGG 0.399549 5.4:+19914169 None:intergenic
GTCGGAGTTCGTGGCTCAGC+TGG 0.423316 5.4:+19914225 MS.gene051317:CDS
CAATTTCCATTAAGAAGCTC+TGG 0.437020 5.4:-19914283 None:intergenic
CCCTACCGCTGCTCCGGTTG+AGG 0.446206 5.4:+19914258 MS.gene051317:CDS
CTGAAAGATGATGAGGCAAA+AGG 0.448168 5.4:-19915338 None:intergenic
AGAGCTTCTTAATGGAAATT+GGG 0.453732 5.4:+19914285 MS.gene051317:CDS
TCGAAGCCCTGCAAGAATAC+AGG 0.454672 5.4:+19915382 MS.gene051317:CDS
GTTCACAACAGTGGAGCTAT+AGG 0.458564 5.4:-19915297 None:intergenic
AGCTGAGGTGTCGGAGTTCG+TGG 0.459710 5.4:+19914216 MS.gene051317:CDS
AGCAGCAGGAGCATTACCTT+TGG 0.464327 5.4:+19915241 MS.gene051317:CDS
TTCTAACCCTACCGCTGCTC+CGG 0.478623 5.4:+19914252 MS.gene051317:CDS
GCTTGGGTTTCGAGCTGGGT+CGG 0.485721 5.4:+19914186 MS.gene051317:CDS
TCCTCAACCGGAGCAGCGGT+AGG 0.508926 5.4:-19914259 None:intergenic
AGCATTACCTTTGGTGAAGG+TGG 0.517212 5.4:+19915250 MS.gene051317:CDS
CTGTTGCCTCTTCTAGCAGC+AGG 0.518463 5.4:+19915227 MS.gene051317:CDS
TGAAAGATGATGAGGCAAAA+GGG 0.519153 5.4:-19915337 None:intergenic
AGAATACCTGTATTCTTGCA+GGG 0.561505 5.4:-19915388 None:intergenic
TGGGTCGGAGGTTCGAGCTG+AGG 0.566095 5.4:+19914201 MS.gene051317:CDS
AGGAGCATTACCTTTGGTGA+AGG 0.578672 5.4:+19915247 MS.gene051317:CDS
TGGTTCCTCAACCGGAGCAG+CGG 0.582763 5.4:-19914263 None:intergenic
GGAGGTTCGAGCTGAGGTGT+CGG 0.585365 5.4:+19914207 MS.gene051317:CDS
CCTCAACCGGAGCAGCGGTA+GGG 0.586793 5.4:-19914258 None:intergenic
TGGGTTTCGAGCTGGGTCGG+AGG 0.599924 5.4:+19914189 MS.gene051317:CDS
AGGGCTTCGAACTTCAAATG+AGG 0.604253 5.4:-19915369 None:intergenic
AATGCTCCTGCTGCTAGAAG+AGG 0.620670 5.4:-19915233 None:intergenic
AGATGCACTGAAAGATGATG+AGG 0.643499 5.4:-19915345 None:intergenic
TGTCACAGAGTTCACAACAG+TGG 0.699209 5.4:-19915306 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAACTATTTATATTGTAAA+AGG + chr5.4:19914841-19914860 MS.gene051317:intron 10.0%
!!! TTTTACAAATTTTAATCATA+GGG + chr5.4:19914471-19914490 MS.gene051317:intron 10.0%
!!! CTTTTACAAATTTTAATCAT+AGG + chr5.4:19914470-19914489 MS.gene051317:intron 15.0%
!!! GAAAGTATCTTTTTTATGTT+GGG + chr5.4:19914733-19914752 MS.gene051317:intron 20.0%
!!! TGAAAGTATCTTTTTTATGT+TGG + chr5.4:19914732-19914751 MS.gene051317:intron 20.0%
! AATAAGATGTTAACACAAAC+AGG - chr5.4:19914777-19914796 None:intergenic 25.0%
! ATAAGATGTTAACACAAACA+GGG - chr5.4:19914776-19914795 None:intergenic 25.0%
!! ATGTTTTCAATGCAAAGTAA+AGG - chr5.4:19915064-19915083 None:intergenic 25.0%
!! ATTTTGTATCTTAGAAACGA+AGG + chr5.4:19915089-19915108 MS.gene051317:intron 25.0%
!! CAACTTATTGACAATGTTTT+AGG + chr5.4:19914948-19914967 MS.gene051317:intron 25.0%
ACTTATTTGAGCTTATCTAC+TGG - chr5.4:19915018-19915037 None:intergenic 30.0%
ACTTTGCATTGAAAACATAG+AGG + chr5.4:19915066-19915085 MS.gene051317:intron 30.0%
AGAGCTTCTTAATGGAAATT+GGG + chr5.4:19914285-19914304 MS.gene051317:CDS 30.0%
AGTTTGATTGACATCATAGT+TGG + chr5.4:19914501-19914520 MS.gene051317:intron 30.0%
GTTTGATTGACATCATAGTT+GGG + chr5.4:19914502-19914521 MS.gene051317:intron 30.0%
! ATACGTTTTATGAGACTGTT+TGG - chr5.4:19914994-19915013 None:intergenic 30.0%
! ATGATTGTCAAACTGATTTC+AGG + chr5.4:19915186-19915205 MS.gene051317:CDS 30.0%
! TACGTTTTATGAGACTGTTT+GGG - chr5.4:19914993-19915012 None:intergenic 30.0%
ACGTCACACTGATAATAAGT+TGG + chr5.4:19914582-19914601 MS.gene051317:intron 35.0%
AGAATACCTGTATTCTTGCA+GGG - chr5.4:19915391-19915410 None:intergenic 35.0%
CAAAATAAGCCAATCCAAAC+AGG + chr5.4:19915038-19915057 MS.gene051317:intron 35.0%
CAATTTCCATTAAGAAGCTC+TGG - chr5.4:19914286-19914305 None:intergenic 35.0%
CAGAGCTTCTTAATGGAAAT+TGG + chr5.4:19914284-19914303 MS.gene051317:CDS 35.0%
TATACTATGAAGCACAAGCA+CGG + chr5.4:19914539-19914558 MS.gene051317:intron 35.0%
TGAAAGATGATGAGGCAAAA+GGG - chr5.4:19915340-19915359 None:intergenic 35.0%
! ATTTTATCCACCTTCACCAA+AGG - chr5.4:19915260-19915279 None:intergenic 35.0%
!! GTTGGGAGTATTTAGAACTT+AGG + chr5.4:19914750-19914769 MS.gene051317:intron 35.0%
!!! AAACGAAGGTATTTTTGCCA+CGG + chr5.4:19915103-19915122 MS.gene051317:intron 35.0%
!!! TTTTGAGTTAGTTACATCCG+TGG - chr5.4:19915123-19915142 None:intergenic 35.0%
AAGTAAAGGCCTGTTTGGAT+TGG - chr5.4:19915050-19915069 None:intergenic 40.0%
AGATGCACTGAAAGATGATG+AGG - chr5.4:19915348-19915367 None:intergenic 40.0%
ATGCAAAGTAAAGGCCTGTT+TGG - chr5.4:19915055-19915074 None:intergenic 40.0%
CTGAAAGATGATGAGGCAAA+AGG - chr5.4:19915341-19915360 None:intergenic 40.0%
GAGAATACCTGTATTCTTGC+AGG - chr5.4:19915392-19915411 None:intergenic 40.0%
!! GCTGTTTTCACAAGCTATCT+TGG + chr5.4:19914900-19914919 MS.gene051317:intron 40.0%
AGAGTCTGACACGACACATT+TGG - chr5.4:19914644-19914663 None:intergenic 45.0%
AGCATTACCTTTGGTGAAGG+TGG + chr5.4:19915250-19915269 MS.gene051317:CDS 45.0%
AGGGCTTCGAACTTCAAATG+AGG - chr5.4:19915372-19915391 None:intergenic 45.0%
GAGGAACCAGAGCTTCTTAA+TGG + chr5.4:19914277-19914296 MS.gene051317:CDS 45.0%
GTTCACAACAGTGGAGCTAT+AGG - chr5.4:19915300-19915319 None:intergenic 45.0%
TGTCACAGAGTTCACAACAG+TGG - chr5.4:19915309-19915328 None:intergenic 45.0%
!! AGGAGCATTACCTTTGGTGA+AGG + chr5.4:19915247-19915266 MS.gene051317:CDS 45.0%
AATGCTCCTGCTGCTAGAAG+AGG - chr5.4:19915236-19915255 None:intergenic 50.0%
TCGAAGCCCTGCAAGAATAC+AGG + chr5.4:19915382-19915401 MS.gene051317:CDS 50.0%
TGAAGCACAAGCACGGATAC+CGG + chr5.4:19914546-19914565 MS.gene051317:intron 50.0%
! ACACTCCACATTGAAGGCGT+GGG - chr5.4:19914685-19914704 None:intergenic 50.0%
! AGAAGCTCTGGTTCCTCAAC+CGG - chr5.4:19914274-19914293 None:intergenic 50.0%
! GCACTGACACTCCACATTGA+AGG - chr5.4:19914691-19914710 None:intergenic 50.0%
!! AGCAGCAGGAGCATTACCTT+TGG + chr5.4:19915241-19915260 MS.gene051317:CDS 50.0%
ACAAGCACGGATACCGGACA+GGG + chr5.4:19914552-19914571 MS.gene051317:intron 55.0%
ACTGAGCTTGGGTTTCGAGC+TGG + chr5.4:19914181-19914200 MS.gene051317:CDS 55.0%
CTGAGCTTGGGTTTCGAGCT+GGG + chr5.4:19914182-19914201 MS.gene051317:CDS 55.0%
CTGTTGCCTCTTCTAGCAGC+AGG + chr5.4:19915227-19915246 MS.gene051317:CDS 55.0%
GACACTCCACATTGAAGGCG+TGG - chr5.4:19914686-19914705 None:intergenic 55.0%
TGACGTCTCAATGCCCTGTC+CGG - chr5.4:19914568-19914587 None:intergenic 55.0%
TTCTAACCCTACCGCTGCTC+CGG + chr5.4:19914252-19914271 MS.gene051317:CDS 55.0%
CACAAGCACGGATACCGGAC+AGG + chr5.4:19914551-19914570 MS.gene051317:intron 60.0%
CAGCACCCACGCCTTCAATG+TGG + chr5.4:19914677-19914696 MS.gene051317:intron 60.0%
GCTTGGGTTTCGAGCTGGGT+CGG + chr5.4:19914186-19914205 MS.gene051317:CDS 60.0%
GGAGGTTCGAGCTGAGGTGT+CGG + chr5.4:19914207-19914226 MS.gene051317:CDS 60.0%
TGGTTCCTCAACCGGAGCAG+CGG - chr5.4:19914266-19914285 None:intergenic 60.0%
!! AGCTGAGGTGTCGGAGTTCG+TGG + chr5.4:19914216-19914235 MS.gene051317:CDS 60.0%
CCTCAACCGGAGCAGCGGTA+GGG - chr5.4:19914261-19914280 None:intergenic 65.0%
GTCGGAGTTCGTGGCTCAGC+TGG + chr5.4:19914225-19914244 MS.gene051317:CDS 65.0%
TCCTCAACCGGAGCAGCGGT+AGG - chr5.4:19914262-19914281 None:intergenic 65.0%
TGGGTCGGAGGTTCGAGCTG+AGG + chr5.4:19914201-19914220 MS.gene051317:CDS 65.0%
TGGGTTTCGAGCTGGGTCGG+AGG + chr5.4:19914189-19914208 MS.gene051317:CDS 65.0%
! GCGTGGGTGCTGTCAGACAC+GGG - chr5.4:19914669-19914688 None:intergenic 65.0%
! GGCGTGGGTGCTGTCAGACA+CGG - chr5.4:19914670-19914689 None:intergenic 65.0%
CCCTACCGCTGCTCCGGTTG+AGG + chr5.4:19914258-19914277 MS.gene051317:CDS 70.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 19914176 19915415 19914176 ID=MS.gene051317
chr5.4 mRNA 19914176 19915415 19914176 ID=MS.gene051317.t1;Parent=MS.gene051317
chr5.4 exon 19914176 19914314 19914176 ID=MS.gene051317.t1.exon1;Parent=MS.gene051317.t1
chr5.4 CDS 19914176 19914314 19914176 ID=cds.MS.gene051317.t1;Parent=MS.gene051317.t1
chr5.4 exon 19915156 19915415 19915156 ID=MS.gene051317.t1.exon2;Parent=MS.gene051317.t1
chr5.4 CDS 19915156 19915415 19915156 ID=cds.MS.gene051317.t1;Parent=MS.gene051317.t1
Gene Sequence

>MS.gene051317

ATGGGACTGAGCTTGGGTTTCGAGCTGGGTCGGAGGTTCGAGCTGAGGTGTCGGAGTTCGTGGCTCAGCTGGAAGCTTCTAACCCTACCGCTGCTCCGGTTGAGGAACCAGAGCTTCTTAATGGAAATTGGGTGTTGCTGTAAGTTTGAATCATTTTGCAAGTTTTGAATTTCATTTTGTTTAATATTACTGTTTTAATTATCAAGTGTTTAATGTTAGTATTAGTATTATAATAAGTGTTTAAATTTGATATAGTTATAATTAAATTCAAACATGTGAAACTTTCGAATGAGTCTTTTACAAATTTTAATCATAGGGTAGTGAAAGTTTGATTGACATCATAGTTGGGAATCTCTGTATAAATATACTATGAAGCACAAGCACGGATACCGGACAGGGCATTGAGACGTCACACTGATAATAAGTTGGAAATATGAAATATTTGTGTTTGTATGTAATGTGTAGCCAAATGTGTCGTGTCAGACTCTGACCCGTGTCTGACAGCACCCACGCCTTCAATGTGGAGTGTCAGTGCTACATAGAGCTACATAGACAATGAAAGTATCTTTTTTATGTTGGGAGTATTTAGAACTTAGGCCCTGTTTGTGTTAACATCTTATTTGCAGCTTATAGTACAAGTGTTTATCATGATAAACACTTATGTATAAACTATTTATATTGTAAAAGGTAAAATAAAGTTAAATTGTTTTTGTATAAGCTATAAGCTGTTTTCACAAGCTATCTTGGAGAACTTATAAAAATAAGCTGAAAACAACTTATTGACAATGTTTTAGGTTGTTTTCATATAATTTCTCCCAAACAGTCTCATAAAACGTATGCCAGTAGATAAGCTCAAATAAGTCAAAATAAGCCAATCCAAACAGGCCTTTACTTTGCATTGAAAACATAGAGGATTTTGTATCTTAGAAACGAAGGTATTTTTGCCACGGATGTAACTAACTCAAAATGTGCTGTATTAGTGAGTGTTAATCGAAGTGCTTATTGTTTCTATGATTGTCAAACTGATTTCAGGTACACAGCATCTTCTGAACTGTTGCCTCTTCTAGCAGCAGGAGCATTACCTTTGGTGAAGGTGGATAAAATCTTGCAAACAATTGATACCTATAGCTCCACTGTTGTGAACTCTGTGACATTGTCTAGCCCTTTTGCCTCATCATCTTTCAGTGCATCTGCCTCATTTGAAGTTCGAAGCCCTGCAAGAATACAGGTATTCTCGTGA

Protein sequence

>MS.gene051317.t1

MGLSLGFELGRRFELRCRSSWLSWKLLTLPLLRLRNQSFLMEIGCCLSVNRSAYCFYDCQTDFRYTASSELLPLLAAGALPLVKVDKILQTIDTYSSTVVNSVTLSSPFASSSFSASASFEVRSPARIQVFS