AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1140690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1140690 MtrunA17_Chr6g0481301 77.990 209 5 3 1 168 162 370 4.63e-95 280
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 32 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTTTCCACTTAAACCTTCT+AGG 0.230863 7_4:+12943124 None:intergenic
AAAAGAGAGAGTCAAGAAAA+TGG 0.291854 7_4:-12943217 Msa1140690:CDS
GAGTTATAGAGTTGATAGTT+TGG 0.410150 7_4:-12943426 Msa1140690:CDS
TTCAAATGGAGAAGCCTAGA+AGG 0.411732 7_4:-12943138 Msa1140690:CDS
TCAAGGGTAGATACATGGTT+TGG 0.416509 7_4:-12943275 Msa1140690:intron
GAAAGTATTGCGAGTCTTCG+AGG 0.458677 7_4:-12943528 Msa1140690:CDS
AAAGAGTTTGCTCGAGGTGT+TGG 0.462590 7_4:-12943489 Msa1140690:intron
TGGCGGTGAAGGGATAGCTT+TGG 0.465544 7_4:-12943170 Msa1140690:CDS
TTTGGAAGTTCATGTTCAAA+TGG 0.473753 7_4:-12943152 Msa1140690:CDS
GGAAGAAAGGTCATAGTTTG+TGG 0.489302 7_4:-12943069 Msa1140690:CDS
AGATACATGGTTTGGAGAAG+AGG 0.492157 7_4:-12943267 Msa1140690:CDS
AAAGGGAAGAATGGCGGTGA+AGG 0.500248 7_4:-12943181 Msa1140690:CDS
AGGTTTAAGTGGAAAGAAGA+AGG 0.501263 7_4:-12943118 Msa1140690:CDS
GGTTCATGAGGTTGGTGTCA+TGG 0.507161 7_4:-12943554 Msa1140690:CDS
AAGAAGAAGGAAATTCATCT+AGG 0.520316 7_4:-12943105 Msa1140690:CDS
AGTCAAGAAAATGGTTGTAT+CGG 0.537463 7_4:-12943208 Msa1140690:CDS
GATCTTCAAGGGTAGATACA+TGG 0.550147 7_4:-12943280 Msa1140690:intron
AATGGTTGTATCGGCAACAA+AGG 0.550602 7_4:-12943199 Msa1140690:CDS
AGAAGCCTAGAAGGTTTAAG+TGG 0.552094 7_4:-12943129 Msa1140690:CDS
GATCAAGATCAAGCGCAAGT+TGG 0.564528 7_4:+12943004 None:intergenic
CAAAGAGCTTGCGTCCGAGT+CGG 0.566207 7_4:-12943393 Msa1140690:intron
ATCGGCAACAAAGGGAAGAA+TGG 0.569240 7_4:-12943190 Msa1140690:CDS
ATGGTTGTATCGGCAACAAA+GGG 0.570595 7_4:-12943198 Msa1140690:CDS
AAGGGAAGAATGGCGGTGAA+GGG 0.589106 7_4:-12943180 Msa1140690:CDS
ACATGGACTTGTTGCTGTGT+GGG 0.595042 7_4:-12943033 Msa1140690:CDS
AATTGCTTCAACATCAACCA+TGG 0.625609 7_4:+12943618 None:intergenic
TCTCTTAATGAAAACCGACT+CGG 0.642791 7_4:+12943379 None:intergenic
AACATGGACTTGTTGCTGTG+TGG 0.658532 7_4:-12943034 Msa1140690:CDS
GGAACAAGGAGTATTATGAG+AGG 0.665037 7_4:-12943246 Msa1140690:CDS
GTTACAAAAGAGTTTGCTCG+AGG 0.680580 7_4:-12943495 Msa1140690:intron
GGCAACAAAGGGAAGAATGG+CGG 0.694360 7_4:-12943187 Msa1140690:CDS
TGGTTTGGAGAAGAGGAACA+AGG 0.704148 7_4:-12943260 Msa1140690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GAATGTTATGTATGATTTTT+TGG - chr7_4:12943053-12943072 Msa1140690:CDS 20.0%
!!! GTATGATTTTTTGGTTCATG+AGG - chr7_4:12943062-12943081 Msa1140690:CDS 30.0%
!! GAGTTATAGAGTTGATAGTT+TGG - chr7_4:12943202-12943221 Msa1140690:CDS 30.0%
! GTTTTCATTAAGAGAAAACC+CGG - chr7_4:12943257-12943276 Msa1140690:CDS 30.0%
ATCAGAGTTTATCTATTGCA+TGG - chr7_4:12943315-12943334 Msa1140690:intron 30.0%
TCAGAGTTTATCTATTGCAT+GGG - chr7_4:12943316-12943335 Msa1140690:intron 30.0%
GGAAAATTGAAGATCTTCAA+GGG - chr7_4:12943337-12943356 Msa1140690:intron 30.0%
AAAAGAGAGAGTCAAGAAAA+TGG - chr7_4:12943411-12943430 Msa1140690:CDS 30.0%
AGTCAAGAAAATGGTTGTAT+CGG - chr7_4:12943420-12943439 Msa1140690:CDS 30.0%
TTTGGAAGTTCATGTTCAAA+TGG - chr7_4:12943476-12943495 Msa1140690:CDS 30.0%
AAGAAGAAGGAAATTCATCT+AGG - chr7_4:12943523-12943542 Msa1140690:CDS 30.0%
!!! GATTTTTTGGTTCATGAGGT+TGG - chr7_4:12943066-12943085 Msa1140690:CDS 35.0%
!! GTTTTGTTGAATGAGAATGC+TGG - chr7_4:12943176-12943195 Msa1140690:CDS 35.0%
TCTCTTAATGAAAACCGACT+CGG + chr7_4:12943252-12943271 None:intergenic 35.0%
GGGAAAATTGAAGATCTTCA+AGG - chr7_4:12943336-12943355 Msa1140690:intron 35.0%
TCTTTCCACTTAAACCTTCT+AGG + chr7_4:12943507-12943526 None:intergenic 35.0%
AGGTTTAAGTGGAAAGAAGA+AGG - chr7_4:12943510-12943529 Msa1140690:intron 35.0%
! TCATCTAGGAAGAATTTTGC+TGG - chr7_4:12943537-12943556 Msa1140690:CDS 35.0%
! CATCTAGGAAGAATTTTGCT+GGG - chr7_4:12943538-12943557 Msa1140690:CDS 35.0%
! AAGAATTTTGCTGGGAAGAA+AGG - chr7_4:12943546-12943565 Msa1140690:CDS 35.0%
GTGGAAAAAGTTGAAGAACA+TGG - chr7_4:12943578-12943597 Msa1140690:CDS 35.0%
! GTTACAAAAGAGTTTGCTCG+AGG - chr7_4:12943133-12943152 Msa1140690:CDS 40.0%
TAAGTGTGTGCTGAAGATGA+GGG - chr7_4:12943289-12943308 Msa1140690:intron 40.0%
GATCTTCAAGGGTAGATACA+TGG - chr7_4:12943348-12943367 Msa1140690:intron 40.0%
TCAAGGGTAGATACATGGTT+TGG - chr7_4:12943353-12943372 Msa1140690:intron 40.0%
! AGATACATGGTTTGGAGAAG+AGG - chr7_4:12943361-12943380 Msa1140690:intron 40.0%
!! GGAACAAGGAGTATTATGAG+AGG - chr7_4:12943382-12943401 Msa1140690:intron 40.0%
! AATGGTTGTATCGGCAACAA+AGG - chr7_4:12943429-12943448 Msa1140690:CDS 40.0%
! ATGGTTGTATCGGCAACAAA+GGG - chr7_4:12943430-12943449 Msa1140690:CDS 40.0%
TTCAAATGGAGAAGCCTAGA+AGG - chr7_4:12943490-12943509 Msa1140690:intron 40.0%
AGAAGCCTAGAAGGTTTAAG+TGG - chr7_4:12943499-12943518 Msa1140690:intron 40.0%
GGAAGAAAGGTCATAGTTTG+TGG - chr7_4:12943559-12943578 Msa1140690:CDS 40.0%
!! GAAAGTATTGCGAGTCTTCG+AGG - chr7_4:12943100-12943119 Msa1140690:CDS 45.0%
! AAAGAGTTTGCTCGAGGTGT+TGG - chr7_4:12943139-12943158 Msa1140690:CDS 45.0%
ACACACTTAGCTAACTCACC+GGG + chr7_4:12943278-12943297 None:intergenic 45.0%
CACACACTTAGCTAACTCAC+CGG + chr7_4:12943279-12943298 None:intergenic 45.0%
CTAAGTGTGTGCTGAAGATG+AGG - chr7_4:12943288-12943307 Msa1140690:intron 45.0%
! TGGTTTGGAGAAGAGGAACA+AGG - chr7_4:12943368-12943387 Msa1140690:intron 45.0%
ATCGGCAACAAAGGGAAGAA+TGG - chr7_4:12943438-12943457 Msa1140690:CDS 45.0%
!! AACATGGACTTGTTGCTGTG+TGG - chr7_4:12943594-12943613 Msa1140690:CDS 45.0%
!! ACATGGACTTGTTGCTGTGT+GGG - chr7_4:12943595-12943614 Msa1140690:CDS 45.0%
!! GGTTCATGAGGTTGGTGTCA+TGG - chr7_4:12943074-12943093 Msa1140690:CDS 50.0%
GGCAACAAAGGGAAGAATGG+CGG - chr7_4:12943441-12943460 Msa1140690:CDS 50.0%
AAAGGGAAGAATGGCGGTGA+AGG - chr7_4:12943447-12943466 Msa1140690:CDS 50.0%
AAGGGAAGAATGGCGGTGAA+GGG - chr7_4:12943448-12943467 Msa1140690:CDS 50.0%
CAAAGAGCTTGCGTCCGAGT+CGG - chr7_4:12943235-12943254 Msa1140690:CDS 55.0%
GTGTGTGCTGAAGATGAGGG+AGG - chr7_4:12943292-12943311 Msa1140690:intron 55.0%
TGGCGGTGAAGGGATAGCTT+TGG - chr7_4:12943458-12943477 Msa1140690:CDS 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 12943012 12943638 12943012 ID=Msa1140690;Name=Msa1140690
chr7_4 mRNA 12943012 12943638 12943012 ID=Msa1140690-mRNA-1;Parent=Msa1140690;Name=Msa1140690-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|0|0|1|0.5|0.66|3|0|168
chr7_4 exon 12943522 12943638 12943522 ID=Msa1140690-mRNA-1:exon:3106;Parent=Msa1140690-mRNA-1
chr7_4 exon 12943394 12943507 12943394 ID=Msa1140690-mRNA-1:exon:3105;Parent=Msa1140690-mRNA-1
chr7_4 exon 12943012 12943287 12943012 ID=Msa1140690-mRNA-1:exon:3104;Parent=Msa1140690-mRNA-1
chr7_4 CDS 12943522 12943638 12943522 ID=Msa1140690-mRNA-1:cds;Parent=Msa1140690-mRNA-1
chr7_4 CDS 12943394 12943507 12943394 ID=Msa1140690-mRNA-1:cds;Parent=Msa1140690-mRNA-1
chr7_4 CDS 12943012 12943287 12943012 ID=Msa1140690-mRNA-1:cds;Parent=Msa1140690-mRNA-1
Gene Sequence

>Msa1140690

ATGGTTGATGTTGAAGCAATTGTAGCTGAGCTTGTGATTAAGAATGTTATGTATGATTTTTTGGTTCATGAGGTTGGTGTCATGGAGAGAAAGTATTGCGAGTCTTCGAGGAAAAAAAGTTTGCTCGAGGTGTTGGAATCTGAGAGACTTGTTTTGTTGAATGAGAATGCTGGTTTGAGTTATAGAGTTGATAGTTTGGTTGAAGAGAACAAAGAGCTTGCGTCCGAGTCGATACATGGTTTGGAGAAGAGGAACAAGGAGTATTATGAGAGGCTTTTGAAAAGAGAGAGTCAAGAAAATGGTTGTATCGGCAACAAAGGGAAGAATGGCGGTGAAGGGATAGCTTTGGAAGTTCATGTTCAAATGGAGAAGCCTAGAAGGTTTAAGTGGAAAGAAGAAGGAAATTCATCTAGGAAGAATTTTGCTGGGAAGAAAGGTCATAGTTTGTGGAAAAAGTTGAAGAACATGGACTTGTTGCTGTGTGGGACAAATCCAACTTGCGCTTGA

Protein sequence

>Msa1140690

MVDVEAIVAELVIKNVMYDFLVHEVGVMERKYCESSRKKSLLEVLESERLVLLNENAGLSYRVDSLVEENKELASESIHGLEKRNKEYYERLLKRESQENGCIGNKGKNGGEGIALEVHVQMEKPRRFKWKEEGNSSRKNFAGKKGHSLWKKLKNMDLLLCGTNPTCA*