AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0777260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0777260 MtrunA17_Chr5g0432341 48.750 80 18 3 19 77 246 323 1.82e-13 63.2
Msa0777260 MtrunA17_Chr5g0432331 48.750 80 18 3 19 77 277 354 4.42e-13 62.4
Msa0777260 MtrunA17_Chr5g0432401 45.455 77 19 3 19 74 211 285 5.76e-13 61.6
Msa0777260 MtrunA17_Chr5g0432361 41.463 82 25 3 14 74 29 108 2.72e-12 57.0
Msa0777260 MtrunA17_Chr5g0432351 47.436 78 18 3 19 75 246 321 9.00e-12 58.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 8 sgRNAs with CRISPR-Local

Find 126 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGATTTATTGTACAAAA+AGG 0.207420 5_2:+56116495 Msa0777260:CDS
TATTAGAACCATATATTATA+AGG 0.252483 5_2:+56116477 Msa0777260:CDS
GCCTATTACTGGCAGAATAA+TGG 0.270633 5_2:+56116658 Msa0777260:CDS
CAATAAATCCTTATAATATA+TGG 0.294284 5_2:-56116485 None:intergenic
CCCATTATTCTGCCAGTAAT+AGG 0.308962 5_2:-56116659 None:intergenic
CCTATTACTGGCAGAATAAT+GGG 0.377412 5_2:+56116659 Msa0777260:CDS
AGTAACATGAAGCCTATTAC+TGG 0.410932 5_2:+56116647 Msa0777260:CDS
GCAGAATAATGGGTGAGATT+AGG 0.482122 5_2:+56116669 Msa0777260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AATAATACTTTCATATATAT+TGG - chr5_2:56115378-56115397 None:intergenic 10.0%
!! TTTATGTTAGTATAAATTAT+AGG + chr5_2:56116448-56116467 Msa0777260:intron 10.0%
!! AATAATACTTTCATATATAT+TGG - chr5_2:56115378-56115397 None:intergenic 10.0%
!! TTTATGTTAGTATAAATTAT+AGG + chr5_2:56116448-56116467 Msa0777260:intron 10.0%
!! AGTTATGTAATATTATATGT+TGG + chr5_2:56115206-56115225 Msa0777260:intron 15.0%
!!! CTTTGTATTATTTAAGTTAT+AGG + chr5_2:56115234-56115253 Msa0777260:intron 15.0%
!!! AATTTGGAACTTTAAATAAA+AGG + chr5_2:56115445-56115464 Msa0777260:intron 15.0%
!! TAAATAATAATAGATTCACA+TGG - chr5_2:56116094-56116113 None:intergenic 15.0%
!! ATGATTAAAAAATTAATCAG+TGG - chr5_2:56116301-56116320 None:intergenic 15.0%
!! TATTAGAACCATATATTATA+AGG + chr5_2:56116477-56116496 Msa0777260:CDS 15.0%
!! CAATAAATCCTTATAATATA+TGG - chr5_2:56116488-56116507 None:intergenic 15.0%
!! AGTTATGTAATATTATATGT+TGG + chr5_2:56115206-56115225 Msa0777260:intron 15.0%
!!! CTTTGTATTATTTAAGTTAT+AGG + chr5_2:56115234-56115253 Msa0777260:intron 15.0%
!!! AATTTGGAACTTTAAATAAA+AGG + chr5_2:56115445-56115464 Msa0777260:intron 15.0%
!! TAAATAATAATAGATTCACA+TGG - chr5_2:56116094-56116113 None:intergenic 15.0%
!! ATGATTAAAAAATTAATCAG+TGG - chr5_2:56116301-56116320 None:intergenic 15.0%
!! TATTAGAACCATATATTATA+AGG + chr5_2:56116477-56116496 Msa0777260:CDS 15.0%
!! CAATAAATCCTTATAATATA+TGG - chr5_2:56116488-56116507 None:intergenic 15.0%
!! CAAATTAATTCTAATTACTC+TGG - chr5_2:56115638-56115657 None:intergenic 20.0%
!! GAAAGAATAATACATACATT+TGG + chr5_2:56115668-56115687 Msa0777260:intron 20.0%
!!! TTGAAAATTGAGAGTATTTT+TGG - chr5_2:56115858-56115877 None:intergenic 20.0%
!!! TATGTACATTTTGTATTGTA+GGG - chr5_2:56116424-56116443 None:intergenic 20.0%
!! TAAGGATTTATTGTACAAAA+AGG + chr5_2:56116495-56116514 Msa0777260:CDS 20.0%
!! AAGGATTTATTGTACAAAAA+GGG + chr5_2:56116496-56116515 Msa0777260:CDS 20.0%
!! CAAATTAATTCTAATTACTC+TGG - chr5_2:56115638-56115657 None:intergenic 20.0%
!! GAAAGAATAATACATACATT+TGG + chr5_2:56115668-56115687 Msa0777260:intron 20.0%
!!! TTGAAAATTGAGAGTATTTT+TGG - chr5_2:56115858-56115877 None:intergenic 20.0%
!!! TATGTACATTTTGTATTGTA+GGG - chr5_2:56116424-56116443 None:intergenic 20.0%
!! TAAGGATTTATTGTACAAAA+AGG + chr5_2:56116495-56116514 Msa0777260:CDS 20.0%
!! AAGGATTTATTGTACAAAAA+GGG + chr5_2:56116496-56116515 Msa0777260:CDS 20.0%
!!! CTTTTTTCTTTTCGAATTCA+CGG - chr5_2:56115123-56115142 None:intergenic 25.0%
!! AAAAGGTCTAAAACGTAATA+AGG + chr5_2:56115138-56115157 Msa0777260:intron 25.0%
!! AAAGGTCTAAAACGTAATAA+GGG + chr5_2:56115139-56115158 Msa0777260:intron 25.0%
!! GATGTTGAGTTTTTATGTTA+AGG + chr5_2:56115311-56115330 Msa0777260:intron 25.0%
! TATGTTAAGGTTCAATTGTT+TGG + chr5_2:56115324-56115343 Msa0777260:intron 25.0%
! ATGTTAAGGTTCAATTGTTT+GGG + chr5_2:56115325-56115344 Msa0777260:intron 25.0%
!!! GAGAATTTGACTTGTAAAAA+GGG - chr5_2:56115506-56115525 None:intergenic 25.0%
!!! TGAGAATTTGACTTGTAAAA+AGG - chr5_2:56115507-56115526 None:intergenic 25.0%
!!! CTCTGGTCTTTATTATTTTT+TGG - chr5_2:56115621-56115640 None:intergenic 25.0%
!!! AATTGAGAGTATTTTTGGAA+AGG - chr5_2:56115853-56115872 None:intergenic 25.0%
!! ATTAGGGTTTTTGTTACAAT+AGG + chr5_2:56116251-56116270 Msa0777260:intron 25.0%
!! ACTAACGATAGACTTTATTT+CGG + chr5_2:56116359-56116378 Msa0777260:intron 25.0%
!! ATGTACATTTTGTATTGTAG+GGG - chr5_2:56116423-56116442 None:intergenic 25.0%
!! CTATGTACATTTTGTATTGT+AGG - chr5_2:56116425-56116444 None:intergenic 25.0%
!! GAGCTTTTTAATAAAGATGA+TGG + chr5_2:56116538-56116557 Msa0777260:CDS 25.0%
!!! TGGTTTTGAAAGTGATAAAT+TGG + chr5_2:56116558-56116577 Msa0777260:CDS 25.0%
!! TATGCTTTTACTAATGACTT+TGG + chr5_2:56116606-56116625 Msa0777260:intron 25.0%
!!! CTTTTTTCTTTTCGAATTCA+CGG - chr5_2:56115123-56115142 None:intergenic 25.0%
!! AAAAGGTCTAAAACGTAATA+AGG + chr5_2:56115138-56115157 Msa0777260:intron 25.0%
!! AAAGGTCTAAAACGTAATAA+GGG + chr5_2:56115139-56115158 Msa0777260:intron 25.0%
!! GATGTTGAGTTTTTATGTTA+AGG + chr5_2:56115311-56115330 Msa0777260:intron 25.0%
! TATGTTAAGGTTCAATTGTT+TGG + chr5_2:56115324-56115343 Msa0777260:intron 25.0%
! ATGTTAAGGTTCAATTGTTT+GGG + chr5_2:56115325-56115344 Msa0777260:intron 25.0%
!!! GAGAATTTGACTTGTAAAAA+GGG - chr5_2:56115506-56115525 None:intergenic 25.0%
!!! TGAGAATTTGACTTGTAAAA+AGG - chr5_2:56115507-56115526 None:intergenic 25.0%
!!! CTCTGGTCTTTATTATTTTT+TGG - chr5_2:56115621-56115640 None:intergenic 25.0%
!!! AATTGAGAGTATTTTTGGAA+AGG - chr5_2:56115853-56115872 None:intergenic 25.0%
!! ATTAGGGTTTTTGTTACAAT+AGG + chr5_2:56116251-56116270 Msa0777260:intron 25.0%
!! ACTAACGATAGACTTTATTT+CGG + chr5_2:56116359-56116378 Msa0777260:intron 25.0%
!! ATGTACATTTTGTATTGTAG+GGG - chr5_2:56116423-56116442 None:intergenic 25.0%
!! CTATGTACATTTTGTATTGT+AGG - chr5_2:56116425-56116444 None:intergenic 25.0%
!! GAGCTTTTTAATAAAGATGA+TGG + chr5_2:56116538-56116557 Msa0777260:CDS 25.0%
!!! TGGTTTTGAAAGTGATAAAT+TGG + chr5_2:56116558-56116577 Msa0777260:CDS 25.0%
!! TATGCTTTTACTAATGACTT+TGG + chr5_2:56116606-56116625 Msa0777260:intron 25.0%
CGTGAATTCGAAAAGAAAAA+AGG + chr5_2:56115121-56115140 Msa0777260:intron 30.0%
! AAGGTCTAAAACGTAATAAG+GGG + chr5_2:56115140-56115159 Msa0777260:intron 30.0%
TTCCTCTGTGCTTAATTATA+AGG - chr5_2:56115742-56115761 None:intergenic 30.0%
TGTTACAATAGGAGCTATAA+AGG + chr5_2:56116262-56116281 Msa0777260:intron 30.0%
CGTGAATTCGAAAAGAAAAA+AGG + chr5_2:56115121-56115140 Msa0777260:intron 30.0%
! AAGGTCTAAAACGTAATAAG+GGG + chr5_2:56115140-56115159 Msa0777260:intron 30.0%
TTCCTCTGTGCTTAATTATA+AGG - chr5_2:56115742-56115761 None:intergenic 30.0%
TGTTACAATAGGAGCTATAA+AGG + chr5_2:56116262-56116281 Msa0777260:intron 30.0%
!! TTCAAATTTTGACACTCGAC+AGG - chr5_2:56115275-56115294 None:intergenic 35.0%
GCGATGATCAATGCTTAATT+TGG + chr5_2:56115429-56115448 Msa0777260:intron 35.0%
GTCCTTATAATTAAGCACAG+AGG + chr5_2:56115737-56115756 Msa0777260:intron 35.0%
! ACTACCTCTTTCAGCATTTT+TGG + chr5_2:56115816-56115835 Msa0777260:intron 35.0%
! CTACCTCTTTCAGCATTTTT+GGG + chr5_2:56115817-56115836 Msa0777260:intron 35.0%
ACATAAACCAATTGCTACTG+CGG - chr5_2:56116167-56116186 None:intergenic 35.0%
TGGTTTATGTCAAATCCCTT+TGG + chr5_2:56116177-56116196 Msa0777260:intron 35.0%
GGTTTATGTCAAATCCCTTT+GGG + chr5_2:56116178-56116197 Msa0777260:intron 35.0%
GTTTATGTCAAATCCCTTTG+GGG + chr5_2:56116179-56116198 Msa0777260:intron 35.0%
TTTATGTCAAATCCCTTTGG+GGG + chr5_2:56116180-56116199 Msa0777260:intron 35.0%
TAATCTTGAGAGTCTCCAAA+TGG - chr5_2:56116235-56116254 None:intergenic 35.0%
ATTTGGAGACTCTCAAGATT+AGG + chr5_2:56116234-56116253 Msa0777260:intron 35.0%
TTTGGAGACTCTCAAGATTA+GGG + chr5_2:56116235-56116254 Msa0777260:intron 35.0%
AGTAACATGAAGCCTATTAC+TGG + chr5_2:56116647-56116666 Msa0777260:CDS 35.0%
CCTATTACTGGCAGAATAAT+GGG + chr5_2:56116659-56116678 Msa0777260:CDS 35.0%
!! TTCAAATTTTGACACTCGAC+AGG - chr5_2:56115275-56115294 None:intergenic 35.0%
GCGATGATCAATGCTTAATT+TGG + chr5_2:56115429-56115448 Msa0777260:intron 35.0%
GTCCTTATAATTAAGCACAG+AGG + chr5_2:56115737-56115756 Msa0777260:intron 35.0%
! ACTACCTCTTTCAGCATTTT+TGG + chr5_2:56115816-56115835 Msa0777260:intron 35.0%
! CTACCTCTTTCAGCATTTTT+GGG + chr5_2:56115817-56115836 Msa0777260:intron 35.0%
ACATAAACCAATTGCTACTG+CGG - chr5_2:56116167-56116186 None:intergenic 35.0%
TGGTTTATGTCAAATCCCTT+TGG + chr5_2:56116177-56116196 Msa0777260:intron 35.0%
GGTTTATGTCAAATCCCTTT+GGG + chr5_2:56116178-56116197 Msa0777260:intron 35.0%
GTTTATGTCAAATCCCTTTG+GGG + chr5_2:56116179-56116198 Msa0777260:intron 35.0%
TTTATGTCAAATCCCTTTGG+GGG + chr5_2:56116180-56116199 Msa0777260:intron 35.0%
TAATCTTGAGAGTCTCCAAA+TGG - chr5_2:56116235-56116254 None:intergenic 35.0%
ATTTGGAGACTCTCAAGATT+AGG + chr5_2:56116234-56116253 Msa0777260:intron 35.0%
TTTGGAGACTCTCAAGATTA+GGG + chr5_2:56116235-56116254 Msa0777260:intron 35.0%
AGTAACATGAAGCCTATTAC+TGG + chr5_2:56116647-56116666 Msa0777260:CDS 35.0%
CCTATTACTGGCAGAATAAT+GGG + chr5_2:56116659-56116678 Msa0777260:CDS 35.0%
! GCATTGATCATCGCATCAAA+AGG - chr5_2:56115423-56115442 None:intergenic 40.0%
AAGAAATCCGCAGTAGCAAT+TGG + chr5_2:56116157-56116176 Msa0777260:intron 40.0%
GCCTATTACTGGCAGAATAA+TGG + chr5_2:56116658-56116677 Msa0777260:CDS 40.0%
CCCATTATTCTGCCAGTAAT+AGG - chr5_2:56116662-56116681 None:intergenic 40.0%
!! GCAGAATAATGGGTGAGATT+AGG + chr5_2:56116669-56116688 Msa0777260:CDS 40.0%
! GCATTGATCATCGCATCAAA+AGG - chr5_2:56115423-56115442 None:intergenic 40.0%
AAGAAATCCGCAGTAGCAAT+TGG + chr5_2:56116157-56116176 Msa0777260:intron 40.0%
GCCTATTACTGGCAGAATAA+TGG + chr5_2:56116658-56116677 Msa0777260:CDS 40.0%
CCCATTATTCTGCCAGTAAT+AGG - chr5_2:56116662-56116681 None:intergenic 40.0%
!! GCAGAATAATGGGTGAGATT+AGG + chr5_2:56116669-56116688 Msa0777260:CDS 40.0%
CTGCCCAAAAATGCTGAAAG+AGG - chr5_2:56115823-56115842 None:intergenic 45.0%
TCTCCAAATGGAGACTTCCA+TGG - chr5_2:56116223-56116242 None:intergenic 45.0%
CTGCCCAAAAATGCTGAAAG+AGG - chr5_2:56115823-56115842 None:intergenic 45.0%
TCTCCAAATGGAGACTTCCA+TGG - chr5_2:56116223-56116242 None:intergenic 45.0%
!!! TGTATATATATATTTTTTTA+AGG + chr5_2:56116017-56116036 Msa0777260:intron 5.0%
!!! TGTATATATATATTTTTTTA+AGG + chr5_2:56116017-56116036 Msa0777260:intron 5.0%
TGTAGTAGCAGCTTCAGCCA+TGG + chr5_2:56116203-56116222 Msa0777260:intron 50.0%
CAGCCATGGAAGTCTCCATT+TGG + chr5_2:56116217-56116236 Msa0777260:intron 50.0%
TGTAGTAGCAGCTTCAGCCA+TGG + chr5_2:56116203-56116222 Msa0777260:intron 50.0%
CAGCCATGGAAGTCTCCATT+TGG + chr5_2:56116217-56116236 Msa0777260:intron 50.0%
GCTGCTACTACACCCCCAAA+GGG - chr5_2:56116195-56116214 None:intergenic 55.0%
AGCTGCTACTACACCCCCAA+AGG - chr5_2:56116196-56116215 None:intergenic 55.0%
GCTGCTACTACACCCCCAAA+GGG - chr5_2:56116195-56116214 None:intergenic 55.0%
AGCTGCTACTACACCCCCAA+AGG - chr5_2:56116196-56116215 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_2 gene 56114983 56116721 56114983 ID=Msa0777260;Name=Msa0777260
chr5_2 mRNA 56114983 56116721 56114983 ID=Msa0777260-mRNA-1;Parent=Msa0777260;Name=Msa0777260-mRNA-1;_AED=0.55;_eAED=0.55;_QI=0|0|0|0.5|0|0|4|0|77
chr5_2 exon 56114983 56114988 56114983 ID=Msa0777260-mRNA-1:exon:16613;Parent=Msa0777260-mRNA-1
chr5_2 exon 56115256 56115295 56115256 ID=Msa0777260-mRNA-1:exon:16614;Parent=Msa0777260-mRNA-1
chr5_2 exon 56116470 56116579 56116470 ID=Msa0777260-mRNA-1:exon:16615;Parent=Msa0777260-mRNA-1
chr5_2 exon 56116644 56116721 56116644 ID=Msa0777260-mRNA-1:exon:16616;Parent=Msa0777260-mRNA-1
chr5_2 CDS 56114983 56114988 56114983 ID=Msa0777260-mRNA-1:cds;Parent=Msa0777260-mRNA-1
chr5_2 CDS 56115256 56115295 56115256 ID=Msa0777260-mRNA-1:cds;Parent=Msa0777260-mRNA-1
chr5_2 CDS 56116470 56116579 56116470 ID=Msa0777260-mRNA-1:cds;Parent=Msa0777260-mRNA-1
chr5_2 CDS 56116644 56116721 56116644 ID=Msa0777260-mRNA-1:cds;Parent=Msa0777260-mRNA-1
Gene Sequence

>Msa0777260

ATGGACGTTCAAATGACATCGACCTGTCGAGTGTCAAAATTTGAAAGAATCTTTATTAGAACCATATATTATAAGGATTTATTGTACAAAAAGGGTCTCTTTGATTCTGATCAAGAGCTTTTTAATAAAGATGATGGTTTTGAAAGTGATAAATTGATGAGTAACATGAAGCCTATTACTGGCAGAATAATGGGTGAGATTAGGCACAATTGCAGAAAAGTAAACTATATATGA

Protein sequence

>Msa0777260

MDVQMTSTCRVSKFERIFIRTIYYKDLLYKKGLFDSDQELFNKDDGFESDKLMSNMKPITGRIMGEIRHNCRKVNYI*