AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0626220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0626220 MtrunA17_Chr4g0001971 85.714 28 4 0 1 28 1 28 8.65e-12 56.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 12 sgRNAs with CRISPR-Local

Find 97 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATTTCATTTCTTGCATGTTT+TGG 0.252992 4_3:-5554843 Msa0626220:five_prime_UTR
CTATCAGCAACTAGAGCATT+TGG 0.351728 4_3:-5552497 Msa0626220:intron
AAAATCTGAGGAGGTGAAAC+AGG 0.371893 4_3:+5554759 None:intergenic
TGTAAGGTTGTTGAAAACTT+TGG 0.382351 4_3:-5554943 None:intergenic
TATGGTCATGGATGATGCTT+TGG 0.425253 4_3:-5554793 Msa0626220:CDS
TTTGATTACAGTGCATGGGC+TGG 0.532116 4_3:-5552473 Msa0626220:CDS
TGGAAATCTAGAAAGAGATC+AGG 0.533990 4_3:-5554735 Msa0626220:intron
CTAGATTTCCAGAAAATCTG+AGG 0.541060 4_3:+5554747 None:intergenic
CTTGCAGTTGGTGACAATCT+CGG 0.543009 4_3:-5552440 Msa0626220:CDS
GTCATGGATGATGCTTTGGA+TGG 0.553546 4_3:-5554789 Msa0626220:CDS
CGAGATTGTCACCAACTGCA+AGG 0.583431 4_3:+5552441 None:intergenic
GATTTCCAGAAAATCTGAGG+AGG 0.685426 4_3:+5554750 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTATTAAAAAAAAAATTAT+GGG + chr4_3:5553970-5553989 None:intergenic 0.0%
!! AATTATTAAAAAAAAAATTA+TGG + chr4_3:5553971-5553990 None:intergenic 0.0%
!! TAAATACTACAAATAATATA+TGG + chr4_3:5552829-5552848 None:intergenic 10.0%
!! ATATATTATTTGTAGTATTT+AGG - chr4_3:5552828-5552847 Msa0626220:intron 10.0%
!!! TTTTTGTATGATAAAAATTT+TGG + chr4_3:5553174-5553193 None:intergenic 10.0%
!!! TTATAATTTTGTTCAAAATA+TGG + chr4_3:5553698-5553717 None:intergenic 10.0%
!!! TTTAAATTTTTCAAATAGAT+AGG - chr4_3:5554252-5554271 Msa0626220:intron 10.0%
!! GTGCTAATATATATATATAT+AGG - chr4_3:5552723-5552742 Msa0626220:intron 15.0%
!!! CTTTATTATTTTATCTTGTA+TGG - chr4_3:5552774-5552793 Msa0626220:intron 15.0%
!!! ATACGTTAGTATAATATTTT+TGG - chr4_3:5553147-5553166 Msa0626220:intron 15.0%
!! TTACATGAAAATAATAGTAT+CGG + chr4_3:5553299-5553318 None:intergenic 15.0%
!! TTAAATAGATAAAAACTTAG+CGG + chr4_3:5553531-5553550 None:intergenic 15.0%
!! TATCTATTTAATATGATTGT+TGG - chr4_3:5553540-5553559 Msa0626220:intron 15.0%
!! TTAAACATAAATGTAAAGAA+AGG - chr4_3:5553736-5553755 Msa0626220:intron 15.0%
!! ACTTCTTTAAATCAAAATTT+AGG - chr4_3:5554054-5554073 Msa0626220:intron 15.0%
!!! TTTTAAAGGATATATAACAA+TGG + chr4_3:5554184-5554203 None:intergenic 15.0%
!!! CTTAATTTTTACATTTTGTT+TGG + chr4_3:5554409-5554428 None:intergenic 15.0%
!! ATTAATAAAAAGAAGTTATC+AGG + chr4_3:5554829-5554848 None:intergenic 15.0%
!! TACTACAAATAATATATGGT+GGG + chr4_3:5552825-5552844 None:intergenic 20.0%
!! ATACTACAAATAATATATGG+TGG + chr4_3:5552826-5552845 None:intergenic 20.0%
!! TATTATACTAACGTATTGTT+TGG + chr4_3:5553143-5553162 None:intergenic 20.0%
!! AGCATTTATAATATTACTCT+TGG - chr4_3:5553399-5553418 Msa0626220:intron 20.0%
!! ATAATGAATATTATATGCAC+TGG - chr4_3:5553581-5553600 Msa0626220:intron 20.0%
!! TTGATACATAAATGTAATAG+TGG + chr4_3:5553633-5553652 None:intergenic 20.0%
!!! GTATAACAAATTTTTGGTAT+CGG - chr4_3:5553830-5553849 Msa0626220:intron 20.0%
!! AGTTAAAATGTGCAAAAAAA+AGG + chr4_3:5553945-5553964 None:intergenic 20.0%
!!! TTAATATGAAGTTGAGTTTT+TGG + chr4_3:5554005-5554024 None:intergenic 20.0%
!!! TTTGATTTAAAGAAGTTGTA+GGG + chr4_3:5554050-5554069 None:intergenic 20.0%
!!! TTTTGATTTAAAGAAGTTGT+AGG + chr4_3:5554051-5554070 None:intergenic 20.0%
!!! CAAAATTTAGGTTTCAATTA+TGG - chr4_3:5554066-5554085 Msa0626220:intron 20.0%
!!! TTTTTAGAATCTTTACTCTT+CGG - chr4_3:5554124-5554143 Msa0626220:intron 20.0%
!!! TCTTTTAAAGGATATAACAA+TGG + chr4_3:5554153-5554172 None:intergenic 20.0%
!!! ATGGATCATTTTTCTTTTAA+AGG + chr4_3:5554165-5554184 None:intergenic 20.0%
!!! ATGGATCATTTTTCTTTTAA+AGG + chr4_3:5554165-5554184 None:intergenic 20.0%
!!! ATTTTTGTTACACATAACAA+TGG + chr4_3:5554217-5554236 None:intergenic 20.0%
!! TTGTTATGTGTAACAAAAAT+TGG - chr4_3:5554217-5554236 Msa0626220:intron 20.0%
!!! AATTTTTACATTTTGTTTGG+TGG + chr4_3:5554406-5554425 None:intergenic 20.0%
!! TTCAACTTTAGTAAGATAAT+AGG + chr4_3:5554593-5554612 None:intergenic 20.0%
!! ATTTCATTTCTTGCATGTTT+TGG - chr4_3:5552522-5552541 Msa0626220:intron 25.0%
!!! AGAAAATTTTGAAGCAACTA+TGG - chr4_3:5552554-5552573 Msa0626220:intron 25.0%
! TAAAAGTTGAAGAACAGAAA+AGG + chr4_3:5552658-5552677 None:intergenic 25.0%
!!! GTGTTTAATTGAGCATTTTT+TGG - chr4_3:5552850-5552869 Msa0626220:intron 25.0%
!! ACTTGTATGATTTGAAATTG+AGG - chr4_3:5552945-5552964 Msa0626220:intron 25.0%
!!! TAACATTTTGTTTTGTAAGC+TGG - chr4_3:5552987-5553006 Msa0626220:intron 25.0%
!!! GCTTTATTTGTTATTATGGT+TGG - chr4_3:5553113-5553132 Msa0626220:intron 25.0%
!! ATTGAACAAGTTTTCAATCT+AGG + chr4_3:5553255-5553274 None:intergenic 25.0%
! ATATGAATATAGTTGGTTGT+TGG + chr4_3:5553453-5553472 None:intergenic 25.0%
! GTGATTGATATGAATATAGT+TGG + chr4_3:5553460-5553479 None:intergenic 25.0%
!!! GAGAGAGTATAACAAATTTT+TGG - chr4_3:5553824-5553843 Msa0626220:intron 25.0%
!!! TTTTAGAATCTTTACTCTTC+GGG - chr4_3:5554125-5554144 Msa0626220:intron 25.0%
! GTACGCAAATAAAACAAAAT+AGG - chr4_3:5554512-5554531 Msa0626220:intron 25.0%
! TTAGTAAGATAATAGGAGAT+TGG + chr4_3:5554586-5554605 None:intergenic 25.0%
! ATGGATGATTCGATAAATTT+AGG - chr4_3:5554653-5554672 Msa0626220:intron 25.0%
TAAAACCAAAAAGACTTGCA+AGG - chr4_3:5552470-5552489 Msa0626220:CDS 30.0%
! ATTTTCCTTGCAAGTCTTTT+TGG + chr4_3:5552478-5552497 None:intergenic 30.0%
!! CGCTGCTTTATTTGTTATTA+TGG - chr4_3:5553109-5553128 Msa0626220:intron 30.0%
TTGTATAAAGTAAGCTCAGT+TGG - chr4_3:5554343-5554362 Msa0626220:intron 30.0%
TGTATAAAGTAAGCTCAGTT+GGG - chr4_3:5554344-5554363 Msa0626220:intron 30.0%
TCCACAAATTTAACGATGAT+AGG - chr4_3:5554485-5554504 Msa0626220:intron 30.0%
CCACAAATTTAACGATGATA+GGG - chr4_3:5554486-5554505 Msa0626220:intron 30.0%
CACAAATTTAACGATGATAG+GGG - chr4_3:5554487-5554506 Msa0626220:intron 30.0%
GTTAGAAAACATTGCAGTAA+AGG + chr4_3:5554683-5554702 None:intergenic 30.0%
CTTTATGTAATTGCAAGAAG+AGG + chr4_3:5554783-5554802 None:intergenic 30.0%
!!! TTTTGAAGCAACTATGGTCA+TGG - chr4_3:5552560-5552579 Msa0626220:intron 35.0%
CTAGATTTCCAGAAAATCTG+AGG + chr4_3:5552621-5552640 None:intergenic 35.0%
TGGAAATCTAGAAAGAGATC+AGG - chr4_3:5552630-5552649 Msa0626220:intron 35.0%
TTATTCAGTGTAACCAAGAG+AGG - chr4_3:5553037-5553056 Msa0626220:intron 35.0%
GTACAATAGTGGTTAACAGT+TGG - chr4_3:5553070-5553089 Msa0626220:intron 35.0%
! ATAGTATCGGACTATTGTGT+TGG + chr4_3:5553286-5553305 None:intergenic 35.0%
!!! AGTTGGTTGTTGGTGTTTTT+TGG + chr4_3:5553443-5553462 None:intergenic 35.0%
GATAAAAACTTAGCGGAGAA+AGG + chr4_3:5553524-5553543 None:intergenic 35.0%
TTGTACACACTCTATCTCTA+CGG + chr4_3:5553785-5553804 None:intergenic 35.0%
TGCAAAAAAAAGGAGTCAGT+TGG + chr4_3:5553935-5553954 None:intergenic 35.0%
CCCTATCATCGTTAAATTTG+TGG + chr4_3:5554489-5554508 None:intergenic 35.0%
! CAATAAGAAAGTGTGAACGA+TGG - chr4_3:5554634-5554653 Msa0626220:intron 35.0%
TATTAGACATGTGTTCACGA+AGG + chr4_3:5554710-5554729 None:intergenic 35.0%
!!! TTGGTTTTGATTACAGTGCA+TGG - chr4_3:5554887-5554906 Msa0626220:five_prime_UTR 35.0%
!!! TGGTTTTGATTACAGTGCAT+GGG - chr4_3:5554888-5554907 Msa0626220:five_prime_UTR 35.0%
TATGGTCATGGATGATGCTT+TGG - chr4_3:5552572-5552591 Msa0626220:intron 40.0%
AAAATCTGAGGAGGTGAAAC+AGG + chr4_3:5552609-5552628 None:intergenic 40.0%
! TTTCACCTCCTCAGATTTTC+TGG - chr4_3:5552610-5552629 Msa0626220:intron 40.0%
GATTTCCAGAAAATCTGAGG+AGG + chr4_3:5552618-5552637 None:intergenic 40.0%
! GAGAGAGAAGTGTACAATAG+TGG - chr4_3:5553059-5553078 Msa0626220:intron 40.0%
GAAGTTATCAGGATGTCGTT+GGG + chr4_3:5554818-5554837 None:intergenic 40.0%
AGAAGTTATCAGGATGTCGT+TGG + chr4_3:5554819-5554838 None:intergenic 40.0%
! CTATCAGCAACTAGAGCATT+TGG - chr4_3:5554868-5554887 Msa0626220:five_prime_UTR 40.0%
! GTCATGGATGATGCTTTGGA+TGG - chr4_3:5552576-5552595 Msa0626220:intron 45.0%
TACACTTCTCTCTCCTCTCT+TGG + chr4_3:5553053-5553072 None:intergenic 45.0%
TCTCTACGGTTGCGTCAAAT+TGG + chr4_3:5553771-5553790 None:intergenic 45.0%
AATCACTGCCACACTTACTG+TGG - chr4_3:5554754-5554773 Msa0626220:CDS 45.0%
GCTCTAGTTGCTGATAGAGT+TGG + chr4_3:5554865-5554884 None:intergenic 45.0%
TTTGATTACAGTGCATGGGC+TGG - chr4_3:5554892-5554911 Msa0626220:five_prime_UTR 45.0%
GGTGACAAAAACCTTGCAGT+TGG - chr4_3:5554913-5554932 Msa0626220:five_prime_UTR 45.0%
!! CTTGCAGTTGGTGACAATCT+CGG - chr4_3:5554925-5554944 Msa0626220:five_prime_UTR 45.0%
!! AAAAAAAAAAAAAAAAACTT+TGG - chr4_3:5554312-5554331 Msa0626220:intron 5.0%
CGAGATTGTCACCAACTGCA+AGG + chr4_3:5554927-5554946 None:intergenic 50.0%
AGAGGACGCCACAGTAAGTG+TGG + chr4_3:5554765-5554784 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 5552433 5554954 5552433 ID=Msa0626220;Name=Msa0626220
chr4_3 mRNA 5552433 5554954 5552433 ID=Msa0626220-mRNA-1;Parent=Msa0626220;Name=Msa0626220-mRNA-1;_AED=0.49;_eAED=0.49;_QI=140|0|0.5|1|1|1|2|0|52
chr4_3 exon 5552433 5552512 5552433 ID=Msa0626220-mRNA-1:exon:1553;Parent=Msa0626220-mRNA-1
chr4_3 exon 5554736 5554954 5554736 ID=Msa0626220-mRNA-1:exon:1552;Parent=Msa0626220-mRNA-1
chr4_3 five_prime_UTR 5554815 5554954 5554815 ID=Msa0626220-mRNA-1:five_prime_utr;Parent=Msa0626220-mRNA-1
chr4_3 CDS 5554736 5554814 5554736 ID=Msa0626220-mRNA-1:cds;Parent=Msa0626220-mRNA-1
chr4_3 CDS 5552433 5552512 5552433 ID=Msa0626220-mRNA-1:cds;Parent=Msa0626220-mRNA-1
Gene Sequence

>Msa0626220

ATGGTCATGGATGATGCTTTGGATGGTTTCTCTCCTGTTTCACCTCCTCAGATTTTCTGGAAATCTAGAAAGAGATCAGCAACTAGAGCATTTGGTTTTGATTACAGTGCATGGGCTGGTGACAAAAACCTTGCAGTTGGTGACAATCTCGGTAAGTAA

Protein sequence

>Msa0626220

MVMDDALDGFSPVSPPQIFWKSRKRSATRAFGFDYSAWAGDKNLAVGDNLGK*