AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene007446

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007446.t1 MTR_7g100905 100.000 73 0 0 1 73 1 73 9.50e-47 143
MS.gene007446.t1 MTR_7g100905 100.000 66 0 0 8 73 3 68 3.29e-41 129
MS.gene007446.t1 MTR_7g100880 85.897 78 6 1 1 73 7 84 2.78e-18 71.6
MS.gene007446.t1 MTR_7g100890 90.411 73 6 1 1 73 426 497 2.80e-16 71.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene007446.t1 AT2G37120 76.190 63 15 0 11 73 14 76 5.32e-15 63.2
MS.gene007446.t1 AT3G53370 80.000 60 12 0 14 73 17 76 1.71e-12 57.0

Find 16 sgRNAs with CRISPR-Local

Find 80 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTGATTGTTCTCCTGGTTAT+TGG 0.231388 7.3:+12047501 MS.gene007446:CDS
CCCAGGCTTGATTGTTCTCC+TGG 0.358351 7.3:+12047494 MS.gene007446:CDS
TGGGGAAATGTTTAGAATGC+TGG 0.422488 7.3:+12047456 MS.gene007446:intron
GTTTAGAATGCTGGATCTCA+AGG 0.468079 7.3:+12047465 MS.gene007446:intron
ACCAGGAGAACAATCAAGCC+TGG 0.470447 7.3:-12047495 None:intergenic
ATTGTTCTCCTGGTTATTGG+TGG 0.489076 7.3:+12047504 MS.gene007446:CDS
TTGCTGTTGACATTTCTCAT+TGG 0.497549 7.3:+12047528 MS.gene007446:CDS
AAGCAAGGAGTCTCTGCACC+TGG 0.518649 7.3:+12047642 MS.gene007446:CDS
GTACAGTGCCTCTACTCTCC+AGG 0.535553 7.3:-12047660 None:intergenic
TTGTTCTCCTGGTTATTGGT+GGG 0.546594 7.3:+12047505 MS.gene007446:CDS
GCTTTACGTTTATGCACAGA+AGG 0.577488 7.3:+12047560 MS.gene007446:CDS
ACAGCAACCCACCAATAACC+AGG 0.598951 7.3:-12047512 None:intergenic
CCAGGAGAACAATCAAGCCT+GGG 0.608678 7.3:-12047494 None:intergenic
GGATCTCAAGGGTTCAACCC+AGG 0.613072 7.3:+12047477 MS.gene007446:CDS
TTTAGAATGCTGGATCTCAA+GGG 0.619147 7.3:+12047466 MS.gene007446:intron
TCTCTGCACCTGGAGAGTAG+AGG 0.653251 7.3:+12047652 MS.gene007446:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TTTTTTTTTTATTCACATTT+AGG + chr7.3:12046607-12046626 MS.gene007446:intron 10.0%
!! AAAATAAATAATGAAGAATG+TGG - chr7.3:12046413-12046432 None:intergenic 15.0%
!! AAATAAATAATGAAGAATGT+GGG - chr7.3:12046412-12046431 None:intergenic 15.0%
!! CAATAAAAAAATATTTCCAA+AGG - chr7.3:12047386-12047405 None:intergenic 15.0%
!! GATCTATTCATAATTAAATT+AGG + chr7.3:12046583-12046602 MS.gene007446:intron 15.0%
!! TTATTTGAGAATAACAATAA+GGG - chr7.3:12046977-12046996 None:intergenic 15.0%
!! AGATTCTACTTTGAATATAA+TGG + chr7.3:12047200-12047219 MS.gene007446:intron 20.0%
!! CTTATTTGAGAATAACAATA+AGG - chr7.3:12046978-12046997 None:intergenic 20.0%
!! GATTCTACTTTGAATATAAT+GGG + chr7.3:12047201-12047220 MS.gene007446:intron 20.0%
!! TTTCAGATCTTAAAAATTCA+TGG + chr7.3:12046432-12046451 MS.gene007446:intron 20.0%
!!! CAAAAAAAAGCACTTAAATA+AGG - chr7.3:12047429-12047448 None:intergenic 20.0%
!!! TTTTATTCACATTTAGGTTA+AGG + chr7.3:12046613-12046632 MS.gene007446:intron 20.0%
! AAAATGCATATGATAAAACC+TGG - chr7.3:12046933-12046952 None:intergenic 25.0%
! CATATTACTATTTGCATACA+TGG + chr7.3:12047318-12047337 MS.gene007446:intron 25.0%
! CTCAAAAAAGAAGATGAAAA+AGG + chr7.3:12047611-12047630 MS.gene007446:CDS 25.0%
! GGTTACAAATAACATCAATA+TGG - chr7.3:12046956-12046975 None:intergenic 25.0%
!! TTTACATGTCAATTTTCCTT+TGG + chr7.3:12047367-12047386 MS.gene007446:intron 25.0%
!!! GGAATTGATTTGAAGAAAAT+CGG - chr7.3:12046391-12046410 None:intergenic 25.0%
!!! TGCTTTATTAGACACTTTTA+AGG + chr7.3:12046686-12046705 MS.gene007446:intron 25.0%
!!! TTAATTTGAGAGTGTTTTTG+TGG - chr7.3:12047139-12047158 None:intergenic 25.0%
AAAAGAAGATGAAAAAGGAG+AGG + chr7.3:12047616-12047635 MS.gene007446:CDS 30.0%
AACCATTCAACACAAATTGA+TGG - chr7.3:12046908-12046927 None:intergenic 30.0%
ATTCTCAAATAAGTCTGTGT+AGG + chr7.3:12046985-12047004 MS.gene007446:intron 30.0%
ATTGCAGAGCAAATAAAGAA+TGG - chr7.3:12047297-12047316 None:intergenic 30.0%
TATGAATAGATCCACAAGTA+AGG - chr7.3:12046575-12046594 None:intergenic 30.0%
! TTTTTGTGGAGACATACAAA+AGG - chr7.3:12047125-12047144 None:intergenic 30.0%
!!! AATTTTTTACCTCCATCACT+GGG + chr7.3:12046532-12046551 MS.gene007446:intron 30.0%
!!! TAATTTTTTACCTCCATCAC+TGG + chr7.3:12046531-12046550 MS.gene007446:intron 30.0%
!!! TGCTTTTTTTTGTTGCTCTT+GGG + chr7.3:12047437-12047456 MS.gene007446:intron 30.0%
!!! TTCATCTTCTTTTTTGAGAC+TGG - chr7.3:12047609-12047628 None:intergenic 30.0%
AGAAAATCGGATCTAAGAAG+AGG - chr7.3:12046378-12046397 None:intergenic 35.0%
AGGGCATAGAATATGAGAAA+GGG - chr7.3:12046474-12046493 None:intergenic 35.0%
AGTTATATACGCCTTACTTG+TGG + chr7.3:12046561-12046580 MS.gene007446:intron 35.0%
ATAACTGAAAAACCCAGTGA+TGG - chr7.3:12046547-12046566 None:intergenic 35.0%
ATTGTATTGTACACGCGTTA+AGG + chr7.3:12047025-12047044 MS.gene007446:intron 35.0%
GGAACTGTGAATCATAAATC+AGG - chr7.3:12047104-12047123 None:intergenic 35.0%
TGCCATCAATTTGTGTTGAA+TGG + chr7.3:12046903-12046922 MS.gene007446:intron 35.0%
TTGATTGTTCTCCTGGTTAT+TGG + chr7.3:12047501-12047520 MS.gene007446:CDS 35.0%
! AAGGGCATAGAATATGAGAA+AGG - chr7.3:12046475-12046494 None:intergenic 35.0%
! AAGTAGAATCTCTGATTTGC+AGG - chr7.3:12047191-12047210 None:intergenic 35.0%
! CCTTTGTTTCAAAGAATCTC+TGG + chr7.3:12047239-12047258 MS.gene007446:intron 35.0%
! GATCATGATGATGATGATGA+TGG + chr7.3:12046799-12046818 MS.gene007446:intron 35.0%
! TCAACACAAATTGATGGCAT+TGG - chr7.3:12046902-12046921 None:intergenic 35.0%
! TGAAAGTATGAACGAGCAAA+GGG - chr7.3:12046493-12046512 None:intergenic 35.0%
! TTGAAAGTATGAACGAGCAA+AGG - chr7.3:12046494-12046513 None:intergenic 35.0%
! TTGCTGTTGACATTTCTCAT+TGG + chr7.3:12047528-12047547 MS.gene007446:CDS 35.0%
! TTTAGAATGCTGGATCTCAA+GGG + chr7.3:12047466-12047485 MS.gene007446:intron 35.0%
! TTTGAAACAAAGGAGAGAAG+TGG - chr7.3:12047232-12047251 None:intergenic 35.0%
! TTTGTGTTGAATGGTTTTCC+AGG + chr7.3:12046912-12046931 MS.gene007446:intron 35.0%
!! CCAGAGATTCTTTGAAACAA+AGG - chr7.3:12047242-12047261 None:intergenic 35.0%
!!! GCTTTTTTTTGTTGCTCTTG+GGG + chr7.3:12047438-12047457 MS.gene007446:intron 35.0%
!!! GTGCTTTTTTTTGTTGCTCT+TGG + chr7.3:12047436-12047455 MS.gene007446:intron 35.0%
AGAAGAGGAGAGAAGAATAC+CGG - chr7.3:12046363-12046382 None:intergenic 40.0%
ATTGTTCTCCTGGTTATTGG+TGG + chr7.3:12047504-12047523 MS.gene007446:CDS 40.0%
CATACATGGATGATTGTGAG+TGG + chr7.3:12047332-12047351 MS.gene007446:intron 40.0%
GCTTTACGTTTATGCACAGA+AGG + chr7.3:12047560-12047579 MS.gene007446:CDS 40.0%
GGGCATAGAATATGAGAAAG+GGG - chr7.3:12046473-12046492 None:intergenic 40.0%
TTGTTCTCCTGGTTATTGGT+GGG + chr7.3:12047505-12047524 MS.gene007446:CDS 40.0%
! ATGATGGTGATACTGCAGAA+TGG + chr7.3:12046815-12046834 MS.gene007446:intron 40.0%
! GTTTAGAATGCTGGATCTCA+AGG + chr7.3:12047465-12047484 MS.gene007446:intron 40.0%
! TGGGGAAATGTTTAGAATGC+TGG + chr7.3:12047456-12047475 MS.gene007446:intron 40.0%
!!! ACTGGCTTCTTTTTTCTAGG+AGG - chr7.3:12047591-12047610 None:intergenic 40.0%
!!! CTGGCTTCTTTTTTCTAGGA+GGG - chr7.3:12047590-12047609 None:intergenic 40.0%
!!! GAGACTGGCTTCTTTTTTCT+AGG - chr7.3:12047594-12047613 None:intergenic 40.0%
AAAAAGGAGAGGCTGAAGCA+AGG + chr7.3:12047627-12047646 MS.gene007446:CDS 45.0%
AAGAGGAGAGAAGAATACCG+GGG - chr7.3:12046361-12046380 None:intergenic 45.0%
ACATGGATGATTGTGAGTGG+TGG + chr7.3:12047335-12047354 MS.gene007446:intron 45.0%
ACTGAAAAACCCAGTGATGG+AGG - chr7.3:12046544-12046563 None:intergenic 45.0%
GAAGAGGAGAGAAGAATACC+GGG - chr7.3:12046362-12046381 None:intergenic 45.0%
! ATATGAGAAAGGGGCATGCA+AGG - chr7.3:12046464-12046483 None:intergenic 45.0%
! TATGAGAAAGGGGCATGCAA+GGG - chr7.3:12046463-12046482 None:intergenic 45.0%
ACAGCAACCCACCAATAACC+AGG - chr7.3:12047515-12047534 None:intergenic 50.0%
ACCAGGAGAACAATCAAGCC+TGG - chr7.3:12047498-12047517 None:intergenic 50.0%
AGAGGAGAGAAGAATACCGG+GGG - chr7.3:12046360-12046379 None:intergenic 50.0%
CCAGGAGAACAATCAAGCCT+GGG - chr7.3:12047497-12047516 None:intergenic 50.0%
GAATACCGGGGGGACTTTAT+CGG - chr7.3:12046349-12046368 None:intergenic 50.0%
AAGCAAGGAGTCTCTGCACC+TGG + chr7.3:12047642-12047661 MS.gene007446:CDS 55.0%
CCCAGGCTTGATTGTTCTCC+TGG + chr7.3:12047494-12047513 MS.gene007446:CDS 55.0%
GAGGAGAGAAGAATACCGGG+GGG - chr7.3:12046359-12046378 None:intergenic 55.0%
GGATCTCAAGGGTTCAACCC+AGG + chr7.3:12047477-12047496 MS.gene007446:CDS 55.0%


Chromosome Type Strat End Strand Name
chr7.3 gene 12046342 12047671 12046342 ID=MS.gene007446
chr7.3 mRNA 12046342 12047671 12046342 ID=MS.gene007446.t1;Parent=MS.gene007446
chr7.3 exon 12046342 12046362 12046342 ID=MS.gene007446.t1.exon1;Parent=MS.gene007446.t1
chr7.3 CDS 12046342 12046362 12046342 ID=cds.MS.gene007446.t1;Parent=MS.gene007446.t1
chr7.3 exon 12047471 12047671 12047471 ID=MS.gene007446.t1.exon2;Parent=MS.gene007446.t1
chr7.3 CDS 12047471 12047671 12047471 ID=cds.MS.gene007446.t1;Parent=MS.gene007446.t1
Gene Sequence

>MS.gene007446

ATGGCCGATAAAGTCCCCCCGGTATTCTTCTCTCCTCTTCTTAGATCCGATTTTCTTCAAATCAATTCCCACATTCTTCATTATTTATTTTTTCAGATCTTAAAAATTCATGGATCAACCCTTGCATGCCCCTTTCTCATATTCTATGCCCTTTGCTCGTTCATACTTTCAATCATCATCAAATTTGCTTAATTTTTTACCTCCATCACTGGGTTTTTCAGTTATATACGCCTTACTTGTGGATCTATTCATAATTAAATTAGGATTTTTTTTTTATTCACATTTAGGTTAAGGTTAATTTCACATTTAGATTTAACAATTTAATGATACTTATCTATTTGTTTTGCTTTATTAGACACTTTTAAGGTTTTTTGTTACATTGCTGTCTCTGTAAAAATATAACTTTTATTTAATGCATTGCTGTTTAGTGTTGATCTAATCTATGATTTAGATTTTAGATCATGATGATGATGATGATGGTGATACTGCAGAATGGAATATTAATACTGAAAGTTTGTATTTTTTGATTCATAAAATTCATTTTTGAGCTAAGTTTACCAATGCCATCAATTTGTGTTGAATGGTTTTCCAGGTTTTATCATATGCATTTTCCATATTGATGTTATTTGTAACCCTTATTGTTATTCTCAAATAAGTCTGTGTAGGAAAAAATTGTACACAAGATTGTATTGTACACGCGTTAAGGATCAAAGATATGAATACACAGAAGATGCTCTAGAAATTAAATAGTGAAAGAATCCTGATTTATGATTCACAGTTCCTTTTGTATGTCTCCACAAAAACACTCTCAAATTAAGAAAACAAGTTTTGTGAATTGTCGATCATCCTGCAAATCAGAGATTCTACTTTGAATATAATGGGAAAAACCACTTCTCTCCTTTGTTTCAAAGAATCTCTGGTTGATTAAGAAGATTGCACTTGCACATTGTAGCCATTCTTTATTTGCTCTGCAATTCATATTACTATTTGCATACATGGATGATTGTGAGTGGTGGTTAATTACATTTACATGTCAATTTTCCTTTGGAAATATTTTTTTATTGCTTTTTGCTCTGTTATATGACCTTATTTAAGTGCTTTTTTTTGTTGCTCTTGGGGAAATGTTTAGAATGCTGGATCTCAAGGGTTCAACCCAGGCTTGATTGTTCTCCTGGTTATTGGTGGGTTGCTGTTGACATTTCTCATTGGAAATTATGCGCTTTACGTTTATGCACAGAAGGCTCTCCCTCCTAGAAAAAAGAAGCCAGTCTCAAAAAAGAAGATGAAAAAGGAGAGGCTGAAGCAAGGAGTCTCTGCACCTGGAGAGTAG
Protein sequence

>MS.gene007446.t1

MADKVPPNAGSQGFNPGLIVLLVIGGLLLTFLIGNYALYVYAQKALPPRKKKPVSKKKMKKERLKQGVSAPGE