AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene31968

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31968.t1 MTR_4g088750 90.291 103 6 1 1 99 405 507 1.83e-60 192
MS.gene31968.t1 MTR_4g088755 80.556 108 15 2 1 102 244 351 1.58e-55 176
MS.gene31968.t1 MTR_4g088745 80.556 108 15 2 1 102 249 356 1.75e-55 176
MS.gene31968.t1 MTR_2g013900 81.818 88 16 0 12 99 381 468 2.62e-46 154
MS.gene31968.t1 MTR_4g105770 50.000 50 25 0 9 58 273 322 3.51e-12 61.2
MS.gene31968.t1 MTR_4g132860 42.424 66 34 1 1 62 283 348 9.08e-12 60.1
MS.gene31968.t1 MTR_3g078000 52.000 50 24 0 9 58 272 321 5.75e-11 57.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene31968.t1 AT5G58950 52.941 102 37 1 9 99 424 525 6.33e-29 108
MS.gene31968.t1 AT3G46930 43.750 96 45 1 12 98 384 479 2.00e-20 84.7
MS.gene31968.t1 AT3G46930 53.623 69 32 0 12 80 419 487 9.07e-19 80.1
MS.gene31968.t1 AT1G62400 43.939 66 33 1 1 62 289 354 4.20e-11 58.2

Find 18 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CAGAATATACATGTAAATTT+TGG 0.177770 4.3:+24425220 None:intergenic
CGGACAAAAGGCCTGATTTC+TGG 0.216275 4.3:-24425402 MS.gene31968:CDS
TGATTTCTGGCAGGTTGTTA+AGG 0.378321 4.3:-24425389 MS.gene31968:CDS
GGGCAGTTTGAAGGAATAAT+AGG 0.380516 4.3:+24425469 None:intergenic
GCAATGTTGGTCCTTGAATC+CGG 0.438166 4.3:-24425422 MS.gene31968:CDS
TTAACAACCTGCCAGAAATC+AGG 0.450427 4.3:+24425391 None:intergenic
CTGGCAGGTTGTTAAGGTGT+TGG 0.457283 4.3:-24425383 MS.gene31968:CDS
TCAATTAAAGCTCGCATAGC+TGG 0.473777 4.3:+24425445 None:intergenic
ATAGCTGGTGGGCAGTTTGA+AGG 0.484794 4.3:+24425460 None:intergenic
GGTCCTTGAATCCGGACAAA+AGG 0.490192 4.3:-24425414 MS.gene31968:CDS
GAGCTTTAATTGAGCAATGT+TGG 0.506203 4.3:-24425435 MS.gene31968:CDS
GAATCTTCGCTTGCTCGTGA+TGG 0.512691 4.3:-24425352 MS.gene31968:CDS
GATGTGGTATTCAGAATTCA+AGG 0.515489 4.3:-24425492 MS.gene31968:intron
CAAAAGGCCTGATTTCTGGC+AGG 0.545944 4.3:-24425398 MS.gene31968:CDS
ATTAAAGCTCGCATAGCTGG+TGG 0.550688 4.3:+24425448 None:intergenic
TTAAAGCTCGCATAGCTGGT+GGG 0.626908 4.3:+24425449 None:intergenic
AGTCATGCACATCATAGTAG+TGG 0.636550 4.3:-24425256 MS.gene31968:CDS
ACCCTGCTACAAAACCCTTG+TGG 0.681062 4.3:-24425322 MS.gene31968:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAGAAAAAAATAATATAGA+TGG + chr4.3:24425485-24425504 None:intergenic 10.0%
!! CAAAATAAGATGCATAATTT+GGG + chr4.3:24425440-24425459 None:intergenic 20.0%
!! TCAAAATAAGATGCATAATT+TGG + chr4.3:24425441-24425460 None:intergenic 20.0%
!!! ATACATGTAAATTTTGGTTT+AGG + chr4.3:24425824-24425843 None:intergenic 20.0%
!!! ATCTTATTTTGATAAAAGGA+GGG - chr4.3:24425408-24425427 MS.gene31968:CDS 20.0%
!!! CAGAATATACATGTAAATTT+TGG + chr4.3:24425830-24425849 None:intergenic 20.0%
! AAAAAAAGACTTACTTGCTT+CGG + chr4.3:24425240-24425259 None:intergenic 25.0%
! TTGCATAAGTAAACATAAAC+TGG + chr4.3:24425522-24425541 None:intergenic 25.0%
!!! ACGCATCTTATTTTGATAAA+AGG - chr4.3:24425404-24425423 MS.gene31968:CDS 25.0%
!!! CATCTTATTTTGATAAAAGG+AGG - chr4.3:24425407-24425426 MS.gene31968:CDS 25.0%
ATAAAAAAGGGCTTCTTCAT+TGG - chr4.3:24425756-24425775 MS.gene31968:intron 30.0%
CGTGTCAAAAAATTAAGAAG+GGG + chr4.3:24425387-24425406 None:intergenic 30.0%
GCGTGTCAAAAAATTAAGAA+GGG + chr4.3:24425388-24425407 None:intergenic 30.0%
TGCGTGTCAAAAAATTAAGA+AGG + chr4.3:24425389-24425408 None:intergenic 30.0%
! AAGATGCATAATTTGGGTTT+AGG + chr4.3:24425434-24425453 None:intergenic 30.0%
! AAGGGGTAAGATTGTATTTT+TGG + chr4.3:24425370-24425389 None:intergenic 30.0%
!! CAATTTTAATACTCGTGATG+TGG - chr4.3:24425539-24425558 MS.gene31968:intron 30.0%
GATGTGGTATTCAGAATTCA+AGG - chr4.3:24425555-24425574 MS.gene31968:intron 35.0%
GTGGCCAAGATCATAAAAAA+GGG - chr4.3:24425744-24425763 MS.gene31968:intron 35.0%
TGTGGCCAAGATCATAAAAA+AGG - chr4.3:24425743-24425762 MS.gene31968:intron 35.0%
! GAGCTTTAATTGAGCAATGT+TGG - chr4.3:24425612-24425631 MS.gene31968:intron 35.0%
! TTTTATGATCTTGGCCACAA+GGG + chr4.3:24425742-24425761 None:intergenic 35.0%
! TTTTTATGATCTTGGCCACA+AGG + chr4.3:24425743-24425762 None:intergenic 35.0%
!!! GAAGCCCTTTTTTATGATCT+TGG + chr4.3:24425751-24425770 None:intergenic 35.0%
!!! GTAAATTTTGGTTTAGGCAC+AGG + chr4.3:24425818-24425837 None:intergenic 35.0%
AGTCATGCACATCATAGTAG+TGG - chr4.3:24425791-24425810 MS.gene31968:intron 40.0%
GGGCAGTTTGAAGGAATAAT+AGG + chr4.3:24425581-24425600 None:intergenic 40.0%
TCAATTAAAGCTCGCATAGC+TGG + chr4.3:24425605-24425624 None:intergenic 40.0%
TTAACAACCTGCCAGAAATC+AGG + chr4.3:24425659-24425678 None:intergenic 40.0%
!! TGATTTCTGGCAGGTTGTTA+AGG - chr4.3:24425658-24425677 MS.gene31968:intron 40.0%
ATTAAAGCTCGCATAGCTGG+TGG + chr4.3:24425602-24425621 None:intergenic 45.0%
GCAATGTTGGTCCTTGAATC+CGG - chr4.3:24425625-24425644 MS.gene31968:intron 45.0%
TTAAAGCTCGCATAGCTGGT+GGG + chr4.3:24425601-24425620 None:intergenic 45.0%
! CAGAAATCAGGCCTTTTGTC+CGG + chr4.3:24425647-24425666 None:intergenic 45.0%
ACCCTGCTACAAAACCCTTG+TGG - chr4.3:24425725-24425744 MS.gene31968:intron 50.0%
CGGACAAAAGGCCTGATTTC+TGG - chr4.3:24425645-24425664 MS.gene31968:intron 50.0%
CTGGCAGGTTGTTAAGGTGT+TGG - chr4.3:24425664-24425683 MS.gene31968:intron 50.0%
GAATCTTCGCTTGCTCGTGA+TGG - chr4.3:24425695-24425714 MS.gene31968:intron 50.0%
GGTCCTTGAATCCGGACAAA+AGG - chr4.3:24425633-24425652 MS.gene31968:intron 50.0%
! AGGCCTTTTGTCCGGATTCA+AGG + chr4.3:24425639-24425658 None:intergenic 50.0%
! ATAGCTGGTGGGCAGTTTGA+AGG + chr4.3:24425590-24425609 None:intergenic 50.0%
!! CAAAAGGCCTGATTTCTGGC+AGG - chr4.3:24425649-24425668 MS.gene31968:intron 50.0%
!! GCCACAAGGGTTTTGTAGCA+GGG + chr4.3:24425729-24425748 None:intergenic 50.0%
!! GGCCACAAGGGTTTTGTAGC+AGG + chr4.3:24425730-24425749 None:intergenic 55.0%


Chromosome Type Strat End Strand Name
chr4.3 gene 24425219 24425850 24425219 ID=MS.gene31968
chr4.3 mRNA 24425219 24425850 24425219 ID=MS.gene31968.t1;Parent=MS.gene31968
chr4.3 exon 24425824 24425850 24425824 ID=MS.gene31968.t1.exon1;Parent=MS.gene31968.t1
chr4.3 CDS 24425824 24425850 24425824 ID=cds.MS.gene31968.t1;Parent=MS.gene31968.t1
chr4.3 exon 24425219 24425500 24425219 ID=MS.gene31968.t1.exon2;Parent=MS.gene31968.t1
chr4.3 CDS 24425219 24425500 24425219 ID=cds.MS.gene31968.t1;Parent=MS.gene31968.t1
Gene Sequence

>MS.gene31968

ATGACAATGTTACAAGCACCGAAGCAAGTAAGTCTTTTTTTCAAATTCAAATTTGAAAAGATTTAAATTGAATATTGAATGAGAGTAAAATTTAGATGATAATACAAATATATATTATATATTATCTAATTATAAAACTTAATGTCTACCAAAAATACAATCTTACCCCTTCTTAATTTTTTGACACGCATCTTATTTTGATAAAAGGAGGGCCTAAACCCAAATTATGCATCTTATTTTGAATAAAAGTTGAAGTTTTTCAGCCATCTATATTATTTTTTTCTTTTGAAATTAAAATGACCAGTTTATGTTTACTTATGCAATTTTAATACTCGTGATGTGGTATTCAGAATTCAAGGCCTATTATTCCTTCAAACTGCCCACCAGCTATGCGAGCTTTAATTGAGCAATGTTGGTCCTTGAATCCGGACAAAAGGCCTGATTTCTGGCAGGTTGTTAAGGTGTTGGAACAATTTGAATCTTCGCTTGCTCGTGATGGAACATTGACCCTGCTACAAAACCCTTGTGGCCAAGATCATAAAAAAGGGCTTCTTCATTGGATTCAAAAGCTTAGTCATGCACATCATAGTAGTGGTCCTGTGCCTAAACCAAAATTTACATGTATATTCTGA
Protein sequence

>MS.gene31968.t1

MTMLQAPKQNSRPIIPSNCPPAMRALIEQCWSLNPDKRPDFWQVVKVLEQFESSLARDGTLTLLQNPCGQDHKKGLLHWIQKLSHAHHSSGPVPKPKFTCIF