AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0293650


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0293650 MtrunA17_Chr4g0013851 90.299 134 13 0 1 134 1 134 2.61e-79 238
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0293650 AT1G50510.1 65.414 133 37 1 2 134 3 126 1.16e-48 159

Find 26 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGACATCTTCAGCAGCTTTA+CGG 0.284366 2_3:+45097383 Msa0293650:CDS
GCATATGTTGTGAGTGCTTT+TGG 0.306875 2_3:+45098427 Msa0293650:CDS
ACTTGAAAGGTTAGCTACTT+TGG 0.339699 2_3:+45098369 Msa0293650:CDS
TCTAAAATTGCAATAGTTGC+AGG 0.353501 2_3:-45097916 None:intergenic
CTTGAAAGGTTAGCTACTTT+GGG 0.365927 2_3:+45098370 Msa0293650:CDS
GCATACATAAATATGATCTA+TGG 0.375299 2_3:-45098455 None:intergenic
TTATTTGAATAGGTCTAAGT+TGG 0.424654 2_3:+45098341 Msa0293650:intron
AAATTTGCAAACTGCGAAAG+AGG 0.448124 2_3:+45097861 Msa0293650:CDS
AAACAATCTTCGACGACACT+TGG 0.469924 2_3:+45097408 Msa0293650:CDS
GTTTCTGAAGCGTTATCACT+TGG 0.477839 2_3:+45097687 Msa0293650:CDS
ATGTTTGATGTGCAGCATAC+AGG 0.490157 2_3:+45097615 Msa0293650:intron
TAGAATACCATGTGAAATGA+TGG 0.512409 2_3:-45097736 None:intergenic
TATTTGAATAGGTCTAAGTT+GGG 0.519069 2_3:+45098342 Msa0293650:intron
CAAACTGCGAAAGAGGTTGA+AGG 0.526352 2_3:+45097868 Msa0293650:CDS
CAATGTGAAGGTAGCTTCAG+AGG 0.537312 2_3:+45097665 Msa0293650:CDS
TTTCTGAAGCGTTATCACTT+GGG 0.556780 2_3:+45097688 Msa0293650:CDS
CATACAGGAGTTAATGCTGT+TGG 0.561292 2_3:+45097630 Msa0293650:CDS
AGCTCAGAAAACAGCTCGAA+GGG 0.563723 2_3:+45098399 Msa0293650:CDS
TAAGTTGGGAAGAACTTGAA+AGG 0.573929 2_3:+45098356 Msa0293650:CDS
GAAGGTATTGTGAGAGAGAA+CGG 0.587911 2_3:+45097886 Msa0293650:CDS
AGACAATAAATACCTACGAT+AGG 0.609485 2_3:-45097946 None:intergenic
GAGCTCAGAAAACAGCTCGA+AGG 0.611591 2_3:+45098398 Msa0293650:CDS
TTAGATGGCGTGCCTATCGT+AGG 0.613078 2_3:+45097934 Msa0293650:CDS
AGCTTCGTCAATCAATGTGA+AGG 0.629269 2_3:+45097653 Msa0293650:CDS
TTCGTCTGACACAGTCAACA+AGG 0.640187 2_3:+45097432 Msa0293650:CDS
GAATCTACCATCATTTCACA+TGG 0.668989 2_3:+45097729 Msa0293650:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTATTCTATATCTTTTCATA+TGG + chr2_3:45097751-45097770 Msa0293650:intron 20.0%
!! ATAATCCAAAAACTAAGATA+CGG - chr2_3:45097811-45097830 None:intergenic 20.0%
!!! GTATTCTATATCTTTTCATA+TGG + chr2_3:45097751-45097770 Msa0293650:intron 20.0%
!! ATAATCCAAAAACTAAGATA+CGG - chr2_3:45097811-45097830 None:intergenic 20.0%
! TTTGCAACAAATAGTAATGA+TGG - chr2_3:45097483-45097502 None:intergenic 25.0%
! TGAATGTAAGAACTTTCAAA+AGG - chr2_3:45097539-45097558 None:intergenic 25.0%
! TGTTCTCTTCATTACAAATA+TGG + chr2_3:45098134-45098153 Msa0293650:intron 25.0%
! TTCATTACAAATATGGATGT+TGG + chr2_3:45098141-45098160 Msa0293650:intron 25.0%
! AACAAACATTTGCAATCATT+GGG - chr2_3:45098267-45098286 None:intergenic 25.0%
!!! ACTTGCTCTTTTATTTGAAT+AGG + chr2_3:45098331-45098350 Msa0293650:intron 25.0%
! TTATTTGAATAGGTCTAAGT+TGG + chr2_3:45098341-45098360 Msa0293650:intron 25.0%
! TATTTGAATAGGTCTAAGTT+GGG + chr2_3:45098342-45098361 Msa0293650:intron 25.0%
! GCATACATAAATATGATCTA+TGG - chr2_3:45098458-45098477 None:intergenic 25.0%
! TTTGCAACAAATAGTAATGA+TGG - chr2_3:45097483-45097502 None:intergenic 25.0%
! TGAATGTAAGAACTTTCAAA+AGG - chr2_3:45097539-45097558 None:intergenic 25.0%
! TGTTCTCTTCATTACAAATA+TGG + chr2_3:45098134-45098153 Msa0293650:intron 25.0%
! TTCATTACAAATATGGATGT+TGG + chr2_3:45098141-45098160 Msa0293650:intron 25.0%
! AACAAACATTTGCAATCATT+GGG - chr2_3:45098267-45098286 None:intergenic 25.0%
!!! ACTTGCTCTTTTATTTGAAT+AGG + chr2_3:45098331-45098350 Msa0293650:intron 25.0%
! TTATTTGAATAGGTCTAAGT+TGG + chr2_3:45098341-45098360 Msa0293650:intron 25.0%
! TATTTGAATAGGTCTAAGTT+GGG + chr2_3:45098342-45098361 Msa0293650:intron 25.0%
! GCATACATAAATATGATCTA+TGG - chr2_3:45098458-45098477 None:intergenic 25.0%
TAGAATACCATGTGAAATGA+TGG - chr2_3:45097739-45097758 None:intergenic 30.0%
!! GAAATCCGTATCTTAGTTTT+TGG + chr2_3:45097803-45097822 Msa0293650:intron 30.0%
!!! TGGATTATGATCTTGTTTTC+AGG + chr2_3:45097823-45097842 Msa0293650:intron 30.0%
!!! GGATTATGATCTTGTTTTCA+GGG + chr2_3:45097824-45097843 Msa0293650:intron 30.0%
!! GTTTGCAAATTTTGAGGATA+TGG - chr2_3:45097853-45097872 None:intergenic 30.0%
! TCTAAAATTGCAATAGTTGC+AGG - chr2_3:45097919-45097938 None:intergenic 30.0%
! GCAACTATTGCAATTTTAGA+TGG + chr2_3:45097919-45097938 Msa0293650:CDS 30.0%
AGACAATAAATACCTACGAT+AGG - chr2_3:45097949-45097968 None:intergenic 30.0%
AGGTATTTATTGTCTACCTT+CGG + chr2_3:45097954-45097973 Msa0293650:intron 30.0%
ACAAACATTTGCAATCATTG+GGG - chr2_3:45098266-45098285 None:intergenic 30.0%
CAACAAACATTTGCAATCAT+TGG - chr2_3:45098268-45098287 None:intergenic 30.0%
TAGAATACCATGTGAAATGA+TGG - chr2_3:45097739-45097758 None:intergenic 30.0%
!! GAAATCCGTATCTTAGTTTT+TGG + chr2_3:45097803-45097822 Msa0293650:intron 30.0%
!!! TGGATTATGATCTTGTTTTC+AGG + chr2_3:45097823-45097842 Msa0293650:intron 30.0%
!!! GGATTATGATCTTGTTTTCA+GGG + chr2_3:45097824-45097843 Msa0293650:intron 30.0%
!! GTTTGCAAATTTTGAGGATA+TGG - chr2_3:45097853-45097872 None:intergenic 30.0%
! TCTAAAATTGCAATAGTTGC+AGG - chr2_3:45097919-45097938 None:intergenic 30.0%
! GCAACTATTGCAATTTTAGA+TGG + chr2_3:45097919-45097938 Msa0293650:CDS 30.0%
AGACAATAAATACCTACGAT+AGG - chr2_3:45097949-45097968 None:intergenic 30.0%
AGGTATTTATTGTCTACCTT+CGG + chr2_3:45097954-45097973 Msa0293650:intron 30.0%
ACAAACATTTGCAATCATTG+GGG - chr2_3:45098266-45098285 None:intergenic 30.0%
CAACAAACATTTGCAATCAT+TGG - chr2_3:45098268-45098287 None:intergenic 30.0%
!! TTTCTGAAGCGTTATCACTT+GGG + chr2_3:45097688-45097707 Msa0293650:CDS 35.0%
GAATCTACCATCATTTCACA+TGG + chr2_3:45097729-45097748 Msa0293650:CDS 35.0%
! TTCGCAGTTTGCAAATTTTG+AGG - chr2_3:45097859-45097878 None:intergenic 35.0%
AAATTTGCAAACTGCGAAAG+AGG + chr2_3:45097861-45097880 Msa0293650:CDS 35.0%
!!! TCGTACTCGTGTTATTTTTG+TGG + chr2_3:45098073-45098092 Msa0293650:intron 35.0%
! CGTTTATCTTTTAGACGTCA+TGG - chr2_3:45098230-45098249 None:intergenic 35.0%
! TAAGTTGGGAAGAACTTGAA+AGG + chr2_3:45098356-45098375 Msa0293650:CDS 35.0%
! ACTTGAAAGGTTAGCTACTT+TGG + chr2_3:45098369-45098388 Msa0293650:CDS 35.0%
! CTTGAAAGGTTAGCTACTTT+GGG + chr2_3:45098370-45098389 Msa0293650:CDS 35.0%
!! TTTCTGAAGCGTTATCACTT+GGG + chr2_3:45097688-45097707 Msa0293650:CDS 35.0%
GAATCTACCATCATTTCACA+TGG + chr2_3:45097729-45097748 Msa0293650:CDS 35.0%
! TTCGCAGTTTGCAAATTTTG+AGG - chr2_3:45097859-45097878 None:intergenic 35.0%
AAATTTGCAAACTGCGAAAG+AGG + chr2_3:45097861-45097880 Msa0293650:CDS 35.0%
!!! TCGTACTCGTGTTATTTTTG+TGG + chr2_3:45098073-45098092 Msa0293650:intron 35.0%
! CGTTTATCTTTTAGACGTCA+TGG - chr2_3:45098230-45098249 None:intergenic 35.0%
! TAAGTTGGGAAGAACTTGAA+AGG + chr2_3:45098356-45098375 Msa0293650:CDS 35.0%
! ACTTGAAAGGTTAGCTACTT+TGG + chr2_3:45098369-45098388 Msa0293650:CDS 35.0%
! CTTGAAAGGTTAGCTACTTT+GGG + chr2_3:45098370-45098389 Msa0293650:CDS 35.0%
TGACATCTTCAGCAGCTTTA+CGG + chr2_3:45097383-45097402 Msa0293650:CDS 40.0%
AAACAATCTTCGACGACACT+TGG + chr2_3:45097408-45097427 Msa0293650:CDS 40.0%
ATGTTTGATGTGCAGCATAC+AGG + chr2_3:45097615-45097634 Msa0293650:intron 40.0%
CATACAGGAGTTAATGCTGT+TGG + chr2_3:45097630-45097649 Msa0293650:CDS 40.0%
AGCTTCGTCAATCAATGTGA+AGG + chr2_3:45097653-45097672 Msa0293650:CDS 40.0%
!! GTTTCTGAAGCGTTATCACT+TGG + chr2_3:45097687-45097706 Msa0293650:CDS 40.0%
TACGGATTTCAGTCGTGAAA+AGG - chr2_3:45097793-45097812 None:intergenic 40.0%
!! GAAGGTATTGTGAGAGAGAA+CGG + chr2_3:45097886-45097905 Msa0293650:CDS 40.0%
AAATTGAATGCACAGACCGA+AGG - chr2_3:45097973-45097992 None:intergenic 40.0%
TGAGTAACGATCCTGCAAAT+TGG + chr2_3:45098167-45098186 Msa0293650:intron 40.0%
! TTCTTTTCCAGCCAATTTGC+AGG - chr2_3:45098181-45098200 None:intergenic 40.0%
! GCATATGTTGTGAGTGCTTT+TGG + chr2_3:45098427-45098446 Msa0293650:CDS 40.0%
TGACATCTTCAGCAGCTTTA+CGG + chr2_3:45097383-45097402 Msa0293650:CDS 40.0%
AAACAATCTTCGACGACACT+TGG + chr2_3:45097408-45097427 Msa0293650:CDS 40.0%
ATGTTTGATGTGCAGCATAC+AGG + chr2_3:45097615-45097634 Msa0293650:intron 40.0%
CATACAGGAGTTAATGCTGT+TGG + chr2_3:45097630-45097649 Msa0293650:CDS 40.0%
AGCTTCGTCAATCAATGTGA+AGG + chr2_3:45097653-45097672 Msa0293650:CDS 40.0%
!! GTTTCTGAAGCGTTATCACT+TGG + chr2_3:45097687-45097706 Msa0293650:CDS 40.0%
TACGGATTTCAGTCGTGAAA+AGG - chr2_3:45097793-45097812 None:intergenic 40.0%
!! GAAGGTATTGTGAGAGAGAA+CGG + chr2_3:45097886-45097905 Msa0293650:CDS 40.0%
AAATTGAATGCACAGACCGA+AGG - chr2_3:45097973-45097992 None:intergenic 40.0%
TGAGTAACGATCCTGCAAAT+TGG + chr2_3:45098167-45098186 Msa0293650:intron 40.0%
! TTCTTTTCCAGCCAATTTGC+AGG - chr2_3:45098181-45098200 None:intergenic 40.0%
! GCATATGTTGTGAGTGCTTT+TGG + chr2_3:45098427-45098446 Msa0293650:CDS 40.0%
TTCGTCTGACACAGTCAACA+AGG + chr2_3:45097432-45097451 Msa0293650:CDS 45.0%
CTGACACAGTCAACAAGGTA+CGG + chr2_3:45097437-45097456 Msa0293650:intron 45.0%
CAATGTGAAGGTAGCTTCAG+AGG + chr2_3:45097665-45097684 Msa0293650:CDS 45.0%
CAAACTGCGAAAGAGGTTGA+AGG + chr2_3:45097868-45097887 Msa0293650:CDS 45.0%
TAACGATCCTGCAAATTGGC+TGG + chr2_3:45098171-45098190 Msa0293650:intron 45.0%
AGCTCAGAAAACAGCTCGAA+GGG + chr2_3:45098399-45098418 Msa0293650:CDS 45.0%
TTCGTCTGACACAGTCAACA+AGG + chr2_3:45097432-45097451 Msa0293650:CDS 45.0%
CTGACACAGTCAACAAGGTA+CGG + chr2_3:45097437-45097456 Msa0293650:intron 45.0%
CAATGTGAAGGTAGCTTCAG+AGG + chr2_3:45097665-45097684 Msa0293650:CDS 45.0%
CAAACTGCGAAAGAGGTTGA+AGG + chr2_3:45097868-45097887 Msa0293650:CDS 45.0%
TAACGATCCTGCAAATTGGC+TGG + chr2_3:45098171-45098190 Msa0293650:intron 45.0%
AGCTCAGAAAACAGCTCGAA+GGG + chr2_3:45098399-45098418 Msa0293650:CDS 45.0%
TTAGATGGCGTGCCTATCGT+AGG + chr2_3:45097934-45097953 Msa0293650:CDS 50.0%
ATGAAATGCCTGCGCCTAAC+TGG + chr2_3:45098033-45098052 Msa0293650:intron 50.0%
CCACAAGTAGCTAGCCAGTT+AGG - chr2_3:45098050-45098069 None:intergenic 50.0%
! CCTAACTGGCTAGCTACTTG+TGG + chr2_3:45098047-45098066 Msa0293650:intron 50.0%
!! CGAGCTGTTTTCTGAGCTCT+GGG - chr2_3:45098397-45098416 None:intergenic 50.0%
!! TCGAGCTGTTTTCTGAGCTC+TGG - chr2_3:45098398-45098417 None:intergenic 50.0%
GAGCTCAGAAAACAGCTCGA+AGG + chr2_3:45098398-45098417 Msa0293650:CDS 50.0%
TTAGATGGCGTGCCTATCGT+AGG + chr2_3:45097934-45097953 Msa0293650:CDS 50.0%
ATGAAATGCCTGCGCCTAAC+TGG + chr2_3:45098033-45098052 Msa0293650:intron 50.0%
CCACAAGTAGCTAGCCAGTT+AGG - chr2_3:45098050-45098069 None:intergenic 50.0%
! CCTAACTGGCTAGCTACTTG+TGG + chr2_3:45098047-45098066 Msa0293650:intron 50.0%
!! CGAGCTGTTTTCTGAGCTCT+GGG - chr2_3:45098397-45098416 None:intergenic 50.0%
!! TCGAGCTGTTTTCTGAGCTC+TGG - chr2_3:45098398-45098417 None:intergenic 50.0%
GAGCTCAGAAAACAGCTCGA+AGG + chr2_3:45098398-45098417 Msa0293650:CDS 50.0%
GTAGCTAGCCAGTTAGGCGC+AGG - chr2_3:45098044-45098063 None:intergenic 60.0%
GTAGCTAGCCAGTTAGGCGC+AGG - chr2_3:45098044-45098063 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr2_3 gene 45097382 45098510 45097382 ID=Msa0293650;Name=Msa0293650
chr2_3 mRNA 45097382 45098510 45097382 ID=Msa0293650-mRNA-1;Parent=Msa0293650;Name=Msa0293650-mRNA-1;_AED=0.11;_eAED=0.11;_QI=0|0|0|1|1|0.75|4|0|153
chr2_3 exon 45097382 45097453 45097382 ID=Msa0293650-mRNA-1:exon:14071;Parent=Msa0293650-mRNA-1
chr2_3 exon 45097630 45097750 45097630 ID=Msa0293650-mRNA-1:exon:14072;Parent=Msa0293650-mRNA-1
chr2_3 exon 45097845 45097955 45097845 ID=Msa0293650-mRNA-1:exon:14073;Parent=Msa0293650-mRNA-1
chr2_3 exon 45098353 45098510 45098353 ID=Msa0293650-mRNA-1:exon:14074;Parent=Msa0293650-mRNA-1
chr2_3 CDS 45097382 45097453 45097382 ID=Msa0293650-mRNA-1:cds;Parent=Msa0293650-mRNA-1
chr2_3 CDS 45097630 45097750 45097630 ID=Msa0293650-mRNA-1:cds;Parent=Msa0293650-mRNA-1
chr2_3 CDS 45097845 45097955 45097845 ID=Msa0293650-mRNA-1:cds;Parent=Msa0293650-mRNA-1
chr2_3 CDS 45098353 45098510 45098353 ID=Msa0293650-mRNA-1:cds;Parent=Msa0293650-mRNA-1
Gene Sequence

>Msa0293650

ATGACATCTTCAGCAGCTTTACGGATAAACAATCTTCGACGACACTTGGATTCGTCTGACACAGTCAACAAGCATACAGGAGTTAATGCTGTTGGAGCTTCGTCAATCAATGTGAAGGTAGCTTCAGAGGTTTCTGAAGCGTTATCACTTGGGCGTGCAGTTGTTGCTCTAGAATCTACCATCATTTCACATGGGATGCCATATCCTCAAAATTTGCAAACTGCGAAAGAGGTTGAAGGTATTGTGAGAGAGAACGGTGCAGTTCCTGCAACTATTGCAATTTTAGATGGCGTGCCTATCGTAGGTCTAAGTTGGGAAGAACTTGAAAGGTTAGCTACTTTGGGACCCAGAGCTCAGAAAACAGCTCGAAGGGATATTGCATATGTTGTGAGTGCTTTTGGTTTCGCCATAGATCATATTTATGTATGCATATGTCGATATGATTGTCTTTTATATCCTTAG

Protein sequence

>Msa0293650

MTSSAALRINNLRRHLDSSDTVNKHTGVNAVGASSINVKVASEVSEALSLGRAVVALESTIISHGMPYPQNLQTAKEVEGIVRENGAVPATIAILDGVPIVGLSWEELERLATLGPRAQKTARRDIAYVVSAFGFAIDHIYVCICRYDCLLYP*