AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1367670

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1367670 MtrunA17_Chr5g0448731 83.007 153 14 5 1 143 1 151 2.21e-73 216
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1367670 AT4G35320.1 44.444 126 65 2 13 134 15 139 1.89e-21 84.3

Find 42 sgRNAs with CRISPR-Local

Find 46 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGCAGCAGCATCTCCTAATT+TGG 0.208008 tig0018533:+75860 None:intergenic
AGCATCTCCTAATTTGGTTT+TGG 0.264987 tig0018533:+75866 None:intergenic
GTGTCAACCAAAACCAAATT+AGG 0.315228 tig0018533:-75873 Msa1367670:CDS
TCAAGATCTGTTGCAAAGAT+AGG 0.315447 tig0018533:+75666 None:intergenic
CCCTTTCCACTTCTACTTGT+TGG 0.332543 tig0018533:+75906 None:intergenic
GTTGGAAACATGTTATTTGC+AGG 0.354673 tig0018533:-75596 Msa1367670:CDS
GGTGGACCTGGAGCTGGGCC+TGG 0.359670 tig0018533:-75704 Msa1367670:CDS
TGAGAATGACGACTTGGATC+TGG 0.361698 tig0018533:+75758 None:intergenic
TGGGCGACTCTATCAGAAAT+TGG 0.371725 tig0018533:-75725 Msa1367670:CDS
TTGCTGACTTCCCGTGATAA+GGG 0.402825 tig0018533:-75621 Msa1367670:CDS
GTCATTCTCATTCTCATCCA+TGG 0.415773 tig0018533:-75745 Msa1367670:CDS
GTTGCTGACTTCCCGTGATA+AGG 0.430057 tig0018533:-75622 Msa1367670:CDS
GATGCTGCTGCTGCTGATGC+AGG 0.432107 tig0018533:-75849 Msa1367670:CDS
GAAATTGGTGGACCTGGAGC+TGG 0.438969 tig0018533:-75710 Msa1367670:CDS
GCCGACATGGTTTGAGGAAG+AGG 0.443482 tig0018533:+75522 None:intergenic
TGCGTAGTAATAATCAGAAT+TGG 0.448686 tig0018533:+75545 None:intergenic
CAGTGAGAGAGGAAGTTGAT+AGG 0.455790 tig0018533:+75808 None:intergenic
GCTGCTGCTGCTGATGCAGG+AGG 0.460455 tig0018533:-75846 Msa1367670:CDS
GAGGATCCAGGCCCAGCTCC+AGG 0.463280 tig0018533:+75698 None:intergenic
CTATCAGAAATTGGTGGACC+TGG 0.485539 tig0018533:-75716 Msa1367670:CDS
AGATCTTGAAATGAATGAGC+AGG 0.491670 tig0018533:-75652 Msa1367670:CDS
CCAACAAGTAGAAGTGGAAA+GGG 0.494860 tig0018533:-75906 Msa1367670:CDS
CAAAGATAGGCTTCCTTGAG+AGG 0.500750 tig0018533:+75679 None:intergenic
ATCACGGGAAGTCAGCAACT+TGG 0.507000 tig0018533:+75626 None:intergenic
GAGAATGACGACTTGGATCT+GGG 0.517935 tig0018533:+75759 None:intergenic
AACATGTTATTTGCAGGATG+AGG 0.535337 tig0018533:-75590 Msa1367670:CDS
GTTTCCAACTCCCCTTATCA+CGG 0.535374 tig0018533:+75610 None:intergenic
TCATTCTCATTCTCATCCAT+GGG 0.545509 tig0018533:-75744 Msa1367670:CDS
AAATTGGTGGACCTGGAGCT+GGG 0.557795 tig0018533:-75709 Msa1367670:CDS
GTGTAAGCCGACATGGTTTG+AGG 0.558720 tig0018533:+75516 None:intergenic
AGGCTTCCTTGAGAGGATCC+AGG 0.559333 tig0018533:+75686 None:intergenic
ACCAACAAGTAGAAGTGGAA+AGG 0.562172 tig0018533:-75907 Msa1367670:CDS
TTTCCAACTCCCCTTATCAC+GGG 0.565961 tig0018533:+75611 None:intergenic
TTCTTACCAACAAGTAGAAG+TGG 0.570154 tig0018533:-75912 Msa1367670:CDS
TGTTGTTTCTGCAGTGAGAG+AGG 0.590813 tig0018533:+75797 None:intergenic
TGCTGACTTCCCGTGATAAG+GGG 0.596069 tig0018533:-75620 Msa1367670:CDS
TCATTGTGTGTAAGCCGACA+TGG 0.600825 tig0018533:+75509 None:intergenic
GCGACTCTATCAGAAATTGG+TGG 0.617542 tig0018533:-75722 Msa1367670:CDS
TGAGAATGAGAATGACGACT+TGG 0.638362 tig0018533:+75752 None:intergenic
ATTTCTGATAGAGTCGCCCA+TGG 0.647698 tig0018533:+75728 None:intergenic
ACCTCTTCCTCAAACCATGT+CGG 0.673431 tig0018533:-75523 Msa1367670:CDS
CAACAAGTAGAAGTGGAAAG+GGG 0.687682 tig0018533:-75905 Msa1367670:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
TGCGTAGTAATAATCAGAAT+TGG + tig0018533:75885-75904 None:intergenic 30.0%
TTCTTACCAACAAGTAGAAG+TGG - tig0018533:75515-75534 Msa1367670:CDS 35.0%
!!! ATTTGGTTTTGGTTGACACA+GGG + tig0018533:75553-75572 None:intergenic 35.0%
!!! AATTTGGTTTTGGTTGACAC+AGG + tig0018533:75554-75573 None:intergenic 35.0%
GTGTCAACCAAAACCAAATT+AGG - tig0018533:75554-75573 Msa1367670:CDS 35.0%
!! AGCATCTCCTAATTTGGTTT+TGG + tig0018533:75564-75583 None:intergenic 35.0%
TCATTCTCATTCTCATCCAT+GGG - tig0018533:75683-75702 Msa1367670:CDS 35.0%
TCAAGATCTGTTGCAAAGAT+AGG + tig0018533:75764-75783 None:intergenic 35.0%
AGATCTTGAAATGAATGAGC+AGG - tig0018533:75775-75794 Msa1367670:CDS 35.0%
! GTTGGAAACATGTTATTTGC+AGG - tig0018533:75831-75850 Msa1367670:CDS 35.0%
! AACATGTTATTTGCAGGATG+AGG - tig0018533:75837-75856 Msa1367670:CDS 35.0%
ACCAACAAGTAGAAGTGGAA+AGG - tig0018533:75520-75539 Msa1367670:CDS 40.0%
CCAACAAGTAGAAGTGGAAA+GGG - tig0018533:75521-75540 Msa1367670:CDS 40.0%
CAACAAGTAGAAGTGGAAAG+GGG - tig0018533:75522-75541 Msa1367670:CDS 40.0%
TGAGAATGAGAATGACGACT+TGG + tig0018533:75678-75697 None:intergenic 40.0%
GTCATTCTCATTCTCATCCA+TGG - tig0018533:75682-75701 Msa1367670:CDS 40.0%
CCCTTTCCACTTCTACTTGT+TGG + tig0018533:75524-75543 None:intergenic 45.0%
AGCAGCAGCATCTCCTAATT+TGG + tig0018533:75570-75589 None:intergenic 45.0%
! CAGTGAGAGAGGAAGTTGAT+AGG + tig0018533:75622-75641 None:intergenic 45.0%
!! TGTTGTTTCTGCAGTGAGAG+AGG + tig0018533:75633-75652 None:intergenic 45.0%
! GAGAATGACGACTTGGATCT+GGG + tig0018533:75671-75690 None:intergenic 45.0%
! TGAGAATGACGACTTGGATC+TGG + tig0018533:75672-75691 None:intergenic 45.0%
ATTTCTGATAGAGTCGCCCA+TGG + tig0018533:75702-75721 None:intergenic 45.0%
TGGGCGACTCTATCAGAAAT+TGG - tig0018533:75702-75721 Msa1367670:CDS 45.0%
GCGACTCTATCAGAAATTGG+TGG - tig0018533:75705-75724 Msa1367670:CDS 45.0%
! CTATCAGAAATTGGTGGACC+TGG - tig0018533:75711-75730 Msa1367670:CDS 45.0%
CAAAGATAGGCTTCCTTGAG+AGG + tig0018533:75751-75770 None:intergenic 45.0%
!! TTGCTGACTTCCCGTGATAA+GGG - tig0018533:75806-75825 Msa1367670:CDS 45.0%
TTTCCAACTCCCCTTATCAC+GGG + tig0018533:75819-75838 None:intergenic 45.0%
GTTTCCAACTCCCCTTATCA+CGG + tig0018533:75820-75839 None:intergenic 45.0%
ACCTCTTCCTCAAACCATGT+CGG - tig0018533:75904-75923 Msa1367670:CDS 45.0%
TCATTGTGTGTAAGCCGACA+TGG + tig0018533:75921-75940 None:intergenic 45.0%
! AAATTGGTGGACCTGGAGCT+GGG - tig0018533:75718-75737 Msa1367670:CDS 50.0%
ATCACGGGAAGTCAGCAACT+TGG + tig0018533:75804-75823 None:intergenic 50.0%
!! GTTGCTGACTTCCCGTGATA+AGG - tig0018533:75805-75824 Msa1367670:CDS 50.0%
!! TGCTGACTTCCCGTGATAAG+GGG - tig0018533:75807-75826 Msa1367670:CDS 50.0%
GTGTAAGCCGACATGGTTTG+AGG + tig0018533:75914-75933 None:intergenic 50.0%
! GAAATTGGTGGACCTGGAGC+TGG - tig0018533:75717-75736 Msa1367670:CDS 55.0%
AGGCTTCCTTGAGAGGATCC+AGG + tig0018533:75744-75763 None:intergenic 55.0%
CTTCCCGTGATAAGGGGAGT+TGG - tig0018533:75813-75832 Msa1367670:CDS 55.0%
GCCGACATGGTTTGAGGAAG+AGG + tig0018533:75908-75927 None:intergenic 55.0%
GATGCTGCTGCTGCTGATGC+AGG - tig0018533:75578-75597 Msa1367670:CDS 60.0%
GCTGCTGCTGCTGATGCAGG+AGG - tig0018533:75581-75600 Msa1367670:CDS 65.0%
GCTGGGCCTGGATCCTCTCA+AGG - tig0018533:75735-75754 Msa1367670:CDS 65.0%
GAGGATCCAGGCCCAGCTCC+AGG + tig0018533:75732-75751 None:intergenic 70.0%
GGTGGACCTGGAGCTGGGCC+TGG - tig0018533:75723-75742 Msa1367670:CDS 75.0%
Chromosome Type Strat End Strand Name
tig0018533 gene 75509 75940 75509 ID=Msa1367670;Name=Msa1367670
tig0018533 mRNA 75509 75940 75509 ID=Msa1367670-mRNA-1;Parent=Msa1367670;Name=Msa1367670-mRNA-1;_AED=0.00;_eAED=0.01;_QI=0|-1|0|1|-1|1|1|0|143
tig0018533 exon 75509 75940 75509 ID=Msa1367670-mRNA-1:exon:39;Parent=Msa1367670-mRNA-1
tig0018533 CDS 75509 75940 75509 ID=Msa1367670-mRNA-1:cds;Parent=Msa1367670-mRNA-1
Gene Sequence

>Msa1367670

ATGAGCTTCTTACCAACAAGTAGAAGTGGAAAGGGGTCTCTCCCTGTGTCAACCAAAACCAAATTAGGAGATGCTGCTGCTGCTGATGCAGGAGGCTTTATTCGCAGACGCCTATCAACTTCCTCTCTCACTGCAGAAACAACAGCAGCATCATTTATTCCCAGATCCAAGTCGTCATTCTCATTCTCATCCATGGGCGACTCTATCAGAAATTGGTGGACCTGGAGCTGGGCCTGGATCCTCTCAAGGAAGCCTATCTTTGCAACAGATCTTGAAATGAATGAGCAGGAAACCAAGTTGCTGACTTCCCGTGATAAGGGGAGTTGGAAACATGTTATTTGCAGGATGAGGTCTGAGATCAGAAGAAGAATCACCAATTCTGATTATTACTACGCACCTCTTCCTCAAACCATGTCGGCTTACACACAATGA
Protein sequence

>Msa1367670

MSFLPTSRSGKGSLPVSTKTKLGDAAAADAGGFIRRRLSTSSLTAETTAASFIPRSKSSFSFSSMGDSIRNWWTWSWAWILSRKPIFATDLEMNEQETKLLTSRDKGSWKHVICRMRSEIRRRITNSDYYYAPLPQTMSAYTQ*