AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0471360

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0471360 MtrunA17_Chr3g0126121 83.871 31 5 0 1 31 138 168 3.44e-13 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 26 sgRNAs with CRISPR-Local

Find 136 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCCTTAACAAATTCAAATT+TGG 0.154699 3_3:-73534170 Msa0471360:five_prime_UTR
AACCAAATTTGAATTTGTTA+AGG 0.324351 3_3:+73534168 None:intergenic
AGTGTGTACTGTATATAGTT+TGG 0.325358 3_3:-73533123 Msa0471360:three_prime_UTR
ACCAAATTTGAATTTGTTAA+GGG 0.329032 3_3:+73534169 None:intergenic
GCGGCAGTAAATCCTTTGTT+TGG 0.397158 3_3:-73534096 Msa0471360:five_prime_UTR
CTTTGAAACCATGGCATGGA+TGG 0.431560 3_3:-73533845 Msa0471360:CDS
AATCCTTTGTTTGGCTCACT+AGG 0.459588 3_3:-73534087 Msa0471360:intron
AGAAAGTGTATAACTTGGAC+AGG 0.511125 3_3:-73533195 Msa0471360:CDS
TTTGCAGAAAGTGTATAACT+TGG 0.513854 3_3:-73533200 Msa0471360:intron
GTTATTTACATGAAAACAGC+AGG 0.522414 3_3:+73533092 None:intergenic
CTCACTGTCGGACACGAGAC+AGG 0.522800 3_3:-73534335 Msa0471360:five_prime_UTR
TTTGCAACTTTGCATCCAGC+TGG 0.527690 3_3:-73533026 None:intergenic
TGTCATTGCATTGCAGAGGT+TGG 0.543373 3_3:-73534212 Msa0471360:five_prime_UTR
ACAATGCTGATGTGAAATCC+AGG 0.552433 3_3:+73533937 None:intergenic
TGTGCCACTATGTAGATCCC+TGG 0.554714 3_3:-73533955 Msa0471360:intron
ATGATGCAACTTTGAAACCA+TGG 0.590512 3_3:-73533854 Msa0471360:CDS
AATGCAAAGAAGAGAGTTAG+CGG 0.596549 3_3:-73534115 Msa0471360:five_prime_UTR
ACATATAGTTAGTTACACAT+TGG 0.616095 3_3:-73534282 Msa0471360:five_prime_UTR
GATGCAATCCATCCATGCCA+TGG 0.623186 3_3:+73533837 None:intergenic
TGTCGATATTGTCTCACTGT+CGG 0.627209 3_3:-73534347 Msa0471360:five_prime_UTR
CAATGCTGATGTGAAATCCA+GGG 0.628144 3_3:+73533938 None:intergenic
TTCAAGTCAGAAACTAGCAA+AGG 0.631092 3_3:-73534139 Msa0471360:five_prime_UTR
TATGTGTCATTGCATTGCAG+AGG 0.634437 3_3:-73534216 Msa0471360:five_prime_UTR
GCAACTTTGAAACCATGGCA+TGG 0.637985 3_3:-73533849 Msa0471360:CDS
TCACCTAGTGAGCCAAACAA+AGG 0.662600 3_3:+73534084 None:intergenic
TGAGACAATATCGACACATG+TGG 0.695949 3_3:+73534354 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAAATAAATAAATATTCATC+AGG + chr3_3:73534196-73534215 None:intergenic 10.0%
!! AAAATAAATAAATATTCATC+AGG + chr3_3:73534196-73534215 None:intergenic 10.0%
!! ATTTCAAGAAAAATAAATTG+TGG - chr3_3:73533371-73533390 Msa0471360:intron 15.0%
!! AAAAAAAAAAAAGGAAGAAA+TGG + chr3_3:73533625-73533644 None:intergenic 15.0%
!! ATTTCAAGAAAAATAAATTG+TGG - chr3_3:73533371-73533390 Msa0471360:intron 15.0%
!! AAAAAAAAAAAAGGAAGAAA+TGG + chr3_3:73533625-73533644 None:intergenic 15.0%
!!! ACCAAATTTGAATTTGTTAA+GGG + chr3_3:73533247-73533266 None:intergenic 20.0%
!!! AACCAAATTTGAATTTGTTA+AGG + chr3_3:73533248-73533267 None:intergenic 20.0%
!! AAAAGATCCTAAAAAGAATA+TGG - chr3_3:73533515-73533534 Msa0471360:intron 20.0%
!! AGTGGGAAAAAAAAAAAAAA+AGG + chr3_3:73533634-73533653 None:intergenic 20.0%
!!! CTTTCTATTATTTTGAGTTT+AGG + chr3_3:73533807-73533826 None:intergenic 20.0%
!! CTAAACTCAAAATAATAGAA+AGG - chr3_3:73533805-73533824 Msa0471360:intron 20.0%
!!! ACCAAATTTGAATTTGTTAA+GGG + chr3_3:73533247-73533266 None:intergenic 20.0%
!!! AACCAAATTTGAATTTGTTA+AGG + chr3_3:73533248-73533267 None:intergenic 20.0%
!! AAAAGATCCTAAAAAGAATA+TGG - chr3_3:73533515-73533534 Msa0471360:intron 20.0%
!! AGTGGGAAAAAAAAAAAAAA+AGG + chr3_3:73533634-73533653 None:intergenic 20.0%
!!! CTTTCTATTATTTTGAGTTT+AGG + chr3_3:73533807-73533826 None:intergenic 20.0%
!! CTAAACTCAAAATAATAGAA+AGG - chr3_3:73533805-73533824 Msa0471360:intron 20.0%
! ACATATAGTTAGTTACACAT+TGG - chr3_3:73533131-73533150 Msa0471360:three_prime_UTR 25.0%
! TCCCTTAACAAATTCAAATT+TGG - chr3_3:73533243-73533262 Msa0471360:intron 25.0%
!! TTTGGTAACTATTGAAAAGT+GGG + chr3_3:73533651-73533670 None:intergenic 25.0%
!!! TTTTGGTAACTATTGAAAAG+TGG + chr3_3:73533652-73533671 None:intergenic 25.0%
!! ATAACTTTACTCTTTTGAAC+CGG - chr3_3:73533915-73533934 Msa0471360:five_prime_UTR 25.0%
! ACTAACAGAATTAATATTGC+AGG - chr3_3:73533955-73533974 Msa0471360:intron 25.0%
!!! AATCTGCATTTTTTCCATTA+GGG + chr3_3:73534053-73534072 None:intergenic 25.0%
!!! AAATCTGCATTTTTTCCATT+AGG + chr3_3:73534054-73534073 None:intergenic 25.0%
! ACATATAGTTAGTTACACAT+TGG - chr3_3:73533131-73533150 Msa0471360:three_prime_UTR 25.0%
! TCCCTTAACAAATTCAAATT+TGG - chr3_3:73533243-73533262 Msa0471360:intron 25.0%
!! TTTGGTAACTATTGAAAAGT+GGG + chr3_3:73533651-73533670 None:intergenic 25.0%
!!! TTTTGGTAACTATTGAAAAG+TGG + chr3_3:73533652-73533671 None:intergenic 25.0%
!! ATAACTTTACTCTTTTGAAC+CGG - chr3_3:73533915-73533934 Msa0471360:five_prime_UTR 25.0%
! ACTAACAGAATTAATATTGC+AGG - chr3_3:73533955-73533974 Msa0471360:intron 25.0%
!!! AATCTGCATTTTTTCCATTA+GGG + chr3_3:73534053-73534072 None:intergenic 25.0%
!!! AAATCTGCATTTTTTCCATT+AGG + chr3_3:73534054-73534073 None:intergenic 25.0%
! ACAACTCGCAATTTCAATTT+TGG + chr3_3:73533669-73533688 None:intergenic 30.0%
! TAACTTTACTCTTTTGAACC+GGG - chr3_3:73533916-73533935 Msa0471360:five_prime_UTR 30.0%
AACAGAATTAATATTGCAGG+TGG - chr3_3:73533958-73533977 Msa0471360:intron 30.0%
! TCCATGAAAGTTTTTGTATC+AGG + chr3_3:73533998-73534017 None:intergenic 30.0%
TCAAGCTTACTAGAATACAA+TGG + chr3_3:73534111-73534130 None:intergenic 30.0%
! TTTGCAGAAAGTGTATAACT+TGG - chr3_3:73534213-73534232 Msa0471360:five_prime_UTR 30.0%
AGTGTGTACTGTATATAGTT+TGG - chr3_3:73534290-73534309 Msa0471360:five_prime_UTR 30.0%
GTTATTTACATGAAAACAGC+AGG + chr3_3:73534324-73534343 None:intergenic 30.0%
! ACAACTCGCAATTTCAATTT+TGG + chr3_3:73533669-73533688 None:intergenic 30.0%
! TAACTTTACTCTTTTGAACC+GGG - chr3_3:73533916-73533935 Msa0471360:five_prime_UTR 30.0%
AACAGAATTAATATTGCAGG+TGG - chr3_3:73533958-73533977 Msa0471360:intron 30.0%
! TCCATGAAAGTTTTTGTATC+AGG + chr3_3:73533998-73534017 None:intergenic 30.0%
TCAAGCTTACTAGAATACAA+TGG + chr3_3:73534111-73534130 None:intergenic 30.0%
! TTTGCAGAAAGTGTATAACT+TGG - chr3_3:73534213-73534232 Msa0471360:five_prime_UTR 30.0%
AGTGTGTACTGTATATAGTT+TGG - chr3_3:73534290-73534309 Msa0471360:five_prime_UTR 30.0%
GTTATTTACATGAAAACAGC+AGG + chr3_3:73534324-73534343 None:intergenic 30.0%
TTCAAGTCAGAAACTAGCAA+AGG - chr3_3:73533274-73533293 Msa0471360:intron 35.0%
AATGCAAAGAAGAGAGTTAG+CGG - chr3_3:73533298-73533317 Msa0471360:intron 35.0%
! GCTTGCTCCATATTCTTTTT+AGG + chr3_3:73533525-73533544 None:intergenic 35.0%
!! ATGATGCAACTTTGAAACCA+TGG - chr3_3:73533559-73533578 Msa0471360:intron 35.0%
TGACATTGAACTGTTGAGTA+TGG - chr3_3:73533688-73533707 Msa0471360:intron 35.0%
GCTCATAGCTACTAATAAGT+GGG - chr3_3:73533710-73533729 Msa0471360:intron 35.0%
ACAATGCCCAACTTGTATTA+CGG + chr3_3:73533780-73533799 None:intergenic 35.0%
AATTTCGTTACCAAACATCG+TGG - chr3_3:73533872-73533891 Msa0471360:CDS 35.0%
AAACAATGAACCACGATGTT+TGG + chr3_3:73533885-73533904 None:intergenic 35.0%
GCCTGATACAAAAACTTTCA+TGG - chr3_3:73533994-73534013 Msa0471360:intron 35.0%
CAATGGATATCCTCAAGAAA+AGG + chr3_3:73534094-73534113 None:intergenic 35.0%
TCATCAGGTATGTATATGAC+AGG + chr3_3:73534181-73534200 None:intergenic 35.0%
! AGAAAGTGTATAACTTGGAC+AGG - chr3_3:73534218-73534237 Msa0471360:five_prime_UTR 35.0%
TTCAAGTCAGAAACTAGCAA+AGG - chr3_3:73533274-73533293 Msa0471360:intron 35.0%
AATGCAAAGAAGAGAGTTAG+CGG - chr3_3:73533298-73533317 Msa0471360:intron 35.0%
! GCTTGCTCCATATTCTTTTT+AGG + chr3_3:73533525-73533544 None:intergenic 35.0%
!! ATGATGCAACTTTGAAACCA+TGG - chr3_3:73533559-73533578 Msa0471360:intron 35.0%
TGACATTGAACTGTTGAGTA+TGG - chr3_3:73533688-73533707 Msa0471360:intron 35.0%
GCTCATAGCTACTAATAAGT+GGG - chr3_3:73533710-73533729 Msa0471360:intron 35.0%
ACAATGCCCAACTTGTATTA+CGG + chr3_3:73533780-73533799 None:intergenic 35.0%
AATTTCGTTACCAAACATCG+TGG - chr3_3:73533872-73533891 Msa0471360:CDS 35.0%
AAACAATGAACCACGATGTT+TGG + chr3_3:73533885-73533904 None:intergenic 35.0%
GCCTGATACAAAAACTTTCA+TGG - chr3_3:73533994-73534013 Msa0471360:intron 35.0%
CAATGGATATCCTCAAGAAA+AGG + chr3_3:73534094-73534113 None:intergenic 35.0%
TCATCAGGTATGTATATGAC+AGG + chr3_3:73534181-73534200 None:intergenic 35.0%
! AGAAAGTGTATAACTTGGAC+AGG - chr3_3:73534218-73534237 Msa0471360:five_prime_UTR 35.0%
TGAGACAATATCGACACATG+TGG + chr3_3:73533062-73533081 None:intergenic 40.0%
TGTCGATATTGTCTCACTGT+CGG - chr3_3:73533066-73533085 Msa0471360:three_prime_UTR 40.0%
! TATGTGTCATTGCATTGCAG+AGG - chr3_3:73533197-73533216 Msa0471360:intron 40.0%
! AATCCTTTGTTTGGCTCACT+AGG - chr3_3:73533326-73533345 Msa0471360:intron 40.0%
AAATCCAGGGATCTACATAG+TGG + chr3_3:73533465-73533484 None:intergenic 40.0%
CAATGCTGATGTGAAATCCA+GGG + chr3_3:73533478-73533497 None:intergenic 40.0%
ACAATGCTGATGTGAAATCC+AGG + chr3_3:73533479-73533498 None:intergenic 40.0%
GGCTCATAGCTACTAATAAG+TGG - chr3_3:73533709-73533728 Msa0471360:intron 40.0%
CCTGATTACAACATTACCTC+TGG + chr3_3:73533756-73533775 None:intergenic 40.0%
CCAGAGGTAATGTTGTAATC+AGG - chr3_3:73533753-73533772 Msa0471360:intron 40.0%
ATCAGGACCGTAATACAAGT+TGG - chr3_3:73533770-73533789 Msa0471360:intron 40.0%
TCAGGACCGTAATACAAGTT+GGG - chr3_3:73533771-73533790 Msa0471360:intron 40.0%
GTTCATGTTAAATCGCAACC+CGG + chr3_3:73533937-73533956 None:intergenic 40.0%
! AGTCTTCGTCTTTTTCTCTG+AGG + chr3_3:73534024-73534043 None:intergenic 40.0%
CATCAATTGTTCATGCTCAC+TGG - chr3_3:73534151-73534170 Msa0471360:five_prime_UTR 40.0%
TGAGACAATATCGACACATG+TGG + chr3_3:73533062-73533081 None:intergenic 40.0%
TGTCGATATTGTCTCACTGT+CGG - chr3_3:73533066-73533085 Msa0471360:three_prime_UTR 40.0%
! TATGTGTCATTGCATTGCAG+AGG - chr3_3:73533197-73533216 Msa0471360:intron 40.0%
! AATCCTTTGTTTGGCTCACT+AGG - chr3_3:73533326-73533345 Msa0471360:intron 40.0%
AAATCCAGGGATCTACATAG+TGG + chr3_3:73533465-73533484 None:intergenic 40.0%
CAATGCTGATGTGAAATCCA+GGG + chr3_3:73533478-73533497 None:intergenic 40.0%
ACAATGCTGATGTGAAATCC+AGG + chr3_3:73533479-73533498 None:intergenic 40.0%
GGCTCATAGCTACTAATAAG+TGG - chr3_3:73533709-73533728 Msa0471360:intron 40.0%
CCTGATTACAACATTACCTC+TGG + chr3_3:73533756-73533775 None:intergenic 40.0%
CCAGAGGTAATGTTGTAATC+AGG - chr3_3:73533753-73533772 Msa0471360:intron 40.0%
ATCAGGACCGTAATACAAGT+TGG - chr3_3:73533770-73533789 Msa0471360:intron 40.0%
TCAGGACCGTAATACAAGTT+GGG - chr3_3:73533771-73533790 Msa0471360:intron 40.0%
GTTCATGTTAAATCGCAACC+CGG + chr3_3:73533937-73533956 None:intergenic 40.0%
! AGTCTTCGTCTTTTTCTCTG+AGG + chr3_3:73534024-73534043 None:intergenic 40.0%
CATCAATTGTTCATGCTCAC+TGG - chr3_3:73534151-73534170 Msa0471360:five_prime_UTR 40.0%
TGTCATTGCATTGCAGAGGT+TGG - chr3_3:73533201-73533220 Msa0471360:intron 45.0%
GCGGCAGTAAATCCTTTGTT+TGG - chr3_3:73533317-73533336 Msa0471360:intron 45.0%
TCACCTAGTGAGCCAAACAA+AGG + chr3_3:73533332-73533351 None:intergenic 45.0%
!! GCAACTTTGAAACCATGGCA+TGG - chr3_3:73533564-73533583 Msa0471360:intron 45.0%
!! CTTTGAAACCATGGCATGGA+TGG - chr3_3:73533568-73533587 Msa0471360:intron 45.0%
! GTTGCTTGTGCCTTTTCTTG+AGG - chr3_3:73534081-73534100 Msa0471360:intron 45.0%
TGTCATTGCATTGCAGAGGT+TGG - chr3_3:73533201-73533220 Msa0471360:intron 45.0%
GCGGCAGTAAATCCTTTGTT+TGG - chr3_3:73533317-73533336 Msa0471360:intron 45.0%
TCACCTAGTGAGCCAAACAA+AGG + chr3_3:73533332-73533351 None:intergenic 45.0%
!! GCAACTTTGAAACCATGGCA+TGG - chr3_3:73533564-73533583 Msa0471360:intron 45.0%
!! CTTTGAAACCATGGCATGGA+TGG - chr3_3:73533568-73533587 Msa0471360:intron 45.0%
! GTTGCTTGTGCCTTTTCTTG+AGG - chr3_3:73534081-73534100 Msa0471360:intron 45.0%
! TGTGCCACTATGTAGATCCC+TGG - chr3_3:73533458-73533477 Msa0471360:intron 50.0%
GATGCAATCCATCCATGCCA+TGG + chr3_3:73533579-73533598 None:intergenic 50.0%
CACTATGCAGTCAGAGACGT+AGG - chr3_3:73533837-73533856 Msa0471360:CDS 50.0%
GTCAGAGACGTAGGCACAAT+TGG - chr3_3:73533846-73533865 Msa0471360:CDS 50.0%
CGAAGACTGTGACACCCTAA+TGG - chr3_3:73534036-73534055 Msa0471360:intron 50.0%
! TGTGCCACTATGTAGATCCC+TGG - chr3_3:73533458-73533477 Msa0471360:intron 50.0%
GATGCAATCCATCCATGCCA+TGG + chr3_3:73533579-73533598 None:intergenic 50.0%
CACTATGCAGTCAGAGACGT+AGG - chr3_3:73533837-73533856 Msa0471360:CDS 50.0%
GTCAGAGACGTAGGCACAAT+TGG - chr3_3:73533846-73533865 Msa0471360:CDS 50.0%
CGAAGACTGTGACACCCTAA+TGG - chr3_3:73534036-73534055 Msa0471360:intron 50.0%
CATTACCTCTGGACCGTAGC+TGG + chr3_3:73533745-73533764 None:intergenic 55.0%
CATTACCTCTGGACCGTAGC+TGG + chr3_3:73533745-73533764 None:intergenic 55.0%
CTCACTGTCGGACACGAGAC+AGG - chr3_3:73533078-73533097 Msa0471360:three_prime_UTR 60.0%
TGGGCAAGTCGCTCCAGCTA+CGG - chr3_3:73533729-73533748 Msa0471360:intron 60.0%
CTCACTGTCGGACACGAGAC+AGG - chr3_3:73533078-73533097 Msa0471360:three_prime_UTR 60.0%
TGGGCAAGTCGCTCCAGCTA+CGG - chr3_3:73533729-73533748 Msa0471360:intron 60.0%
TCGCTCCAGCTACGGTCCAG+AGG - chr3_3:73533737-73533756 Msa0471360:intron 65.0%
TCGCTCCAGCTACGGTCCAG+AGG - chr3_3:73533737-73533756 Msa0471360:intron 65.0%
Chromosome Type Strat End Strand Name
chr3_3 gene 73533029 73534406 73533029 ID=Msa0471360;Name=Msa0471360
chr3_3 mRNA 73533029 73534406 73533029 ID=Msa0471360-mRNA-1;Parent=Msa0471360;Name=Msa0471360-mRNA-1;_AED=0.18;_eAED=0.18;_QI=380|0.5|1|1|0|0.33|3|151|37
chr3_3 exon 73533029 73533215 73533029 ID=Msa0471360-mRNA-1:exon:18694;Parent=Msa0471360-mRNA-1
chr3_3 exon 73533824 73533962 73533824 ID=Msa0471360-mRNA-1:exon:18693;Parent=Msa0471360-mRNA-1
chr3_3 exon 73534088 73534406 73534088 ID=Msa0471360-mRNA-1:exon:18692;Parent=Msa0471360-mRNA-1
chr3_3 five_prime_UTR 73534088 73534406 73534088 ID=Msa0471360-mRNA-1:five_prime_utr;Parent=Msa0471360-mRNA-1
chr3_3 five_prime_UTR 73533902 73533962 73533902 ID=Msa0471360-mRNA-1:five_prime_utr;Parent=Msa0471360-mRNA-1
chr3_3 CDS 73533824 73533901 73533824 ID=Msa0471360-mRNA-1:cds;Parent=Msa0471360-mRNA-1
chr3_3 CDS 73533180 73533215 73533180 ID=Msa0471360-mRNA-1:cds;Parent=Msa0471360-mRNA-1
chr3_3 three_prime_UTR 73533029 73533179 73533029 ID=Msa0471360-mRNA-1:three_prime_utr;Parent=Msa0471360-mRNA-1
Gene Sequence

>Msa0471360

ATGGAGCAAGCAGTTCAAGAGTCTTATGATGCAACTTTGAAACCATGGCATGGATGGATTGCATCAGCTGCTTTCAGAAAAGTGTATAACTTGGACAGGCTTAAGTCAAATTGA
Protein sequence

>Msa0471360

MEQAVQESYDATLKPWHGWIASAAFRKVYNLDRLKSN*