AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene94417

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene94417.t1 MTR_7g405850 80.263 76 6 2 38 113 28 94 2.16e-34 117
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 44 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTCCATCACCATTTAATTT+TGG 0.165025 7.1:-86602354 None:intergenic
TTAAACTCTCCAAAATTAAA+TGG 0.244854 7.1:+86602345 MS.gene94417:CDS
AGTGAAATATCATGATTTAA+AGG 0.299376 7.1:+86602235 MS.gene94417:CDS
CAACAACTCAGGAGAATTAA+TGG 0.337925 7.1:+86602131 MS.gene94417:intron
GAAGGATTCCTTTCCATCCT+AGG 0.377685 7.1:-86601625 None:intergenic
AAATACCTTCGATTGATAGA+AGG 0.404032 7.1:-86601643 None:intergenic
TATTTCACTGTATTTAGCTC+TGG 0.423345 7.1:-86602221 None:intergenic
CCAATGGTCCATCATCAACT+TGG 0.427516 7.1:-86602174 None:intergenic
TTTAAAGGAAGCTGATTTGA+AGG 0.442829 7.1:+86602250 MS.gene94417:CDS
TGTTGCAAACGATGTTGAAA+AGG 0.485389 7.1:+86602319 MS.gene94417:CDS
TTGCTATTGTCGTTGCTCCT+AGG 0.496558 7.1:+86601608 MS.gene94417:CDS
TCTCCAAAATTAAATGGTGA+TGG 0.515919 7.1:+86602351 MS.gene94417:CDS
TCTCACGCCCAAGTTGATGA+TGG 0.528994 7.1:+86602166 MS.gene94417:CDS
GCTGATGATGATGGTGGGAG+TGG 0.551251 7.1:+86601580 MS.gene94417:CDS
CCAAGTTGATGATGGACCAT+TGG 0.554041 7.1:+86602174 MS.gene94417:CDS
TATTAATCTTATCAATCCAA+TGG 0.563475 7.1:-86602190 None:intergenic
TATTGTCGTTGCTCCTAGGA+TGG 0.566845 7.1:+86601612 MS.gene94417:CDS
CAATGGTCCATCATCAACTT+GGG 0.577723 7.1:-86602173 None:intergenic
AAAGTTGTTGCTGATGATGA+TGG 0.578443 7.1:+86601571 MS.gene94417:CDS
TCGTTGCTCCTAGGATGGAA+AGG 0.616152 7.1:+86601617 MS.gene94417:CDS
GGAATCCTTCTATCAATCGA+AGG 0.618500 7.1:+86601638 MS.gene94417:CDS
GTTGTTGCTGATGATGATGG+TGG 0.645735 7.1:+86601574 MS.gene94417:CDS
TTGTTGCTGATGATGATGGT+GGG 0.649651 7.1:+86601575 MS.gene94417:CDS
TTGGGCGTGAGAATCAAATG+AGG 0.687571 7.1:-86602155 None:intergenic
ATGGTTGTTGATCTTGAACG+TGG 0.764959 7.1:+86601547 MS.gene94417:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGTTTTTTTAATTTTGTTC+AGG + chr7.1:86601811-86601830 MS.gene94417:intron 15.0%
!!! TTTAAGTTTTCTTTTATTTC+AGG + chr7.1:86601731-86601750 MS.gene94417:intron 15.0%
!! AGTGAAATATCATGATTTAA+AGG + chr7.1:86602235-86602254 MS.gene94417:CDS 20.0%
!! TATTAATCTTATCAATCCAA+TGG - chr7.1:86602193-86602212 None:intergenic 20.0%
!! TTAAACTCTCCAAAATTAAA+TGG + chr7.1:86602345-86602364 MS.gene94417:CDS 20.0%
!!! AAGGTATTAACTATTGTTAT+GGG + chr7.1:86602001-86602020 MS.gene94417:intron 20.0%
! AAATATCAATCAGCCAATTA+AGG - chr7.1:86601946-86601965 None:intergenic 25.0%
! AGTTTCTTTAATCCATTGAA+TGG + chr7.1:86601839-86601858 MS.gene94417:intron 25.0%
!!! GAAGGTATTAACTATTGTTA+TGG + chr7.1:86602000-86602019 MS.gene94417:intron 25.0%
AAATACCTTCGATTGATAGA+AGG - chr7.1:86601646-86601665 None:intergenic 30.0%
ACTGCCTATTGAACAAATAA+TGG - chr7.1:86601891-86601910 None:intergenic 30.0%
AGATTAATGCAACCATTCAA+TGG - chr7.1:86601854-86601873 None:intergenic 30.0%
CTGCCTATTGAACAAATAAT+GGG - chr7.1:86601890-86601909 None:intergenic 30.0%
TTGCCCATTATTTGTTCAAT+AGG + chr7.1:86601884-86601903 MS.gene94417:intron 30.0%
! ATTTTCGATCGATCTATGAA+TGG + chr7.1:86601962-86601981 MS.gene94417:intron 30.0%
! TATTTCACTGTATTTAGCTC+TGG - chr7.1:86602224-86602243 None:intergenic 30.0%
!! TTTAAAGGAAGCTGATTTGA+AGG + chr7.1:86602250-86602269 MS.gene94417:CDS 30.0%
ATGAATGGAGTCTTAGCATA+CGG + chr7.1:86601977-86601996 MS.gene94417:intron 35.0%
ATGATACGCTAAGCCTTAAT+TGG + chr7.1:86601930-86601949 MS.gene94417:intron 35.0%
CAACAACTCAGGAGAATTAA+TGG + chr7.1:86602131-86602150 MS.gene94417:intron 35.0%
TATCATACTTGCAACAACTC+AGG + chr7.1:86602120-86602139 MS.gene94417:intron 35.0%
TGTTGCAAACGATGTTGAAA+AGG + chr7.1:86602319-86602338 MS.gene94417:CDS 35.0%
! AAAGTTGTTGCTGATGATGA+TGG + chr7.1:86601571-86601590 MS.gene94417:CDS 35.0%
!!! CAATCGAAGGTATTTTACCT+AGG + chr7.1:86601651-86601670 MS.gene94417:intron 35.0%
ATGGTTGTTGATCTTGAACG+TGG + chr7.1:86601547-86601566 MS.gene94417:CDS 40.0%
CAATGGTCCATCATCAACTT+GGG - chr7.1:86602176-86602195 None:intergenic 40.0%
GGAATCCTTCTATCAATCGA+AGG + chr7.1:86601638-86601657 MS.gene94417:CDS 40.0%
TGAATGGAGTCTTAGCATAC+GGG + chr7.1:86601978-86601997 MS.gene94417:intron 40.0%
TTGTTCAATAGGCAGTAACG+TGG + chr7.1:86601895-86601914 MS.gene94417:intron 40.0%
!! TTGTTGCTGATGATGATGGT+GGG + chr7.1:86601575-86601594 MS.gene94417:CDS 40.0%
CCAATGGTCCATCATCAACT+TGG - chr7.1:86602177-86602196 None:intergenic 45.0%
GAAGGATTCCTTTCCATCCT+AGG - chr7.1:86601628-86601647 None:intergenic 45.0%
TATTGTCGTTGCTCCTAGGA+TGG + chr7.1:86601612-86601631 MS.gene94417:CDS 45.0%
TCAATCACGATTTGCGTCCT+AGG - chr7.1:86601671-86601690 None:intergenic 45.0%
TTGGGCGTGAGAATCAAATG+AGG - chr7.1:86602158-86602177 None:intergenic 45.0%
! TTGCTATTGTCGTTGCTCCT+AGG + chr7.1:86601608-86601627 MS.gene94417:CDS 45.0%
!! CCAAGTTGATGATGGACCAT+TGG + chr7.1:86602174-86602193 MS.gene94417:CDS 45.0%
!! GTTGTTGCTGATGATGATGG+TGG + chr7.1:86601574-86601593 MS.gene94417:CDS 45.0%
TCGTTGCTCCTAGGATGGAA+AGG + chr7.1:86601617-86601636 MS.gene94417:CDS 50.0%
TGGAGTCTTAGCATACGGGA+AGG + chr7.1:86601982-86602001 MS.gene94417:intron 50.0%
!! TCTCACGCCCAAGTTGATGA+TGG + chr7.1:86602166-86602185 MS.gene94417:CDS 50.0%
AATAGGCAGTAACGTGGCGC+TGG + chr7.1:86601901-86601920 MS.gene94417:intron 55.0%
ATAGGCAGTAACGTGGCGCT+GGG + chr7.1:86601902-86601921 MS.gene94417:intron 55.0%
!! GCTGATGATGATGGTGGGAG+TGG + chr7.1:86601580-86601599 MS.gene94417:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.1 gene 86601547 86602370 86601547 ID=MS.gene94417
chr7.1 mRNA 86601547 86602370 86601547 ID=MS.gene94417.t1;Parent=MS.gene94417
chr7.1 exon 86601547 86601659 86601547 ID=MS.gene94417.t1.exon1;Parent=MS.gene94417.t1
chr7.1 CDS 86601547 86601659 86601547 ID=cds.MS.gene94417.t1;Parent=MS.gene94417.t1
chr7.1 exon 86602142 86602370 86602142 ID=MS.gene94417.t1.exon2;Parent=MS.gene94417.t1
chr7.1 CDS 86602142 86602370 86602142 ID=cds.MS.gene94417.t1;Parent=MS.gene94417.t1
Gene Sequence

>MS.gene94417

ATGGTTGTTGATCTTGAACGTGGTAAAGTTGTTGCTGATGATGATGGTGGGAGTGGACACATTGCTATTGTCGTTGCTCCTAGGATGGAAAGGAATCCTTCTATCAATCGAAGGTATTTTACCTAGGACGCAAATCGTGATTGAAATGAGTTTGTTCTATTAATTTGTTTTTGTTTTAAGTTGATTTAAGTTTTCTTTTATTTCAGGAATGATTTAGCTTATTAAGATTATGATAACTATTTAAGTGAATGTTGTTGATGAGTTAAGTTTTTTTAATTTTGTTCAGGAGTTAAGTTTCTTTAATCCATTGAATGGTTGCATTAATCTGATACTCTAATTGCCCATTATTTGTTCAATAGGCAGTAACGTGGCGCTGGGATATCATGATACGCTAAGCCTTAATTGGCTGATTGATATTTTCGATCGATCTATGAATGGAGTCTTAGCATACGGGAAGGTATTAACTATTGTTATGGGTTTATAGTTTAAATGACTAAATATTTACACTACTTTTAGTTAATTTAAATGTTATTTTGCATATTGAAGAAAACATTGATAAAATTATATATCTTCTATCATACTTGCAACAACTCAGGAGAATTAATGGTCCTCATTTGATTCTCACGCCCAAGTTGATGATGGACCATTGGATTGATAAGATTAATAGAATTGTTCCAGAGCTAAATACAGTGAAATATCATGATTTAAAGGAAGCTGATTTGAAGGAAGCTAGCTTATCACATTTACATATATGTATAGCTAGTTTCGAAGATGTTGCAAACGATGTTGAAAAGGAATTTAAACTCTCCAAAATTAAATGGTGA
Protein sequence

>MS.gene94417.t1

MVVDLERGKVVADDDGGSGHIAIVVAPRMERNPSINRRRINGPHLILTPKLMMDHWIDKINRIVPELNTVKYHDLKEADLKEASLSHLHICIASFEDVANDVEKEFKLSKIKW