AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0391350

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 122 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAATTGTGAAGAGAGAAAT+AGG 0.224146 3_2:+2900249 None:intergenic
TCTAAGACACCGGATCTATT+TGG 0.254975 3_2:-2900120 Msa0391350:CDS
ATGGGGAGTAGGAGTATTAC+TGG 0.335430 3_2:-2899154 Msa0391350:CDS
GGGAAGATGATCTAAGTCTA+AGG 0.342188 3_2:+2900207 None:intergenic
ATCTTCTAAGAGCTGCAATA+TGG 0.364246 3_2:-2900155 Msa0391350:CDS
GTCTAAGGGTGTGTTTGGTT+TGG 0.384467 3_2:+2900222 None:intergenic
ATGTCTCATGTCTGCCTCAC+TGG 0.394407 3_2:-2900183 Msa0391350:CDS
TCTAAGTCTAAGGGTGTGTT+TGG 0.395921 3_2:+2900217 None:intergenic
AAATAGATCCGGTGTCTTAG+AGG 0.427682 3_2:+2900122 None:intergenic
TTTAGGTAAGTATGGGGAGT+AGG 0.443906 3_2:-2899165 Msa0391350:intron
TCCTTTCAAGTGCTACTACA+AGG 0.488545 3_2:-2900076 Msa0391350:intron
ACCTTGTAGTAGCACTTGAA+AGG 0.540154 3_2:+2900075 None:intergenic
TCACCGCCACCAAATAGATC+CGG 0.557945 3_2:+2900111 None:intergenic
ACGAGCTTCCTCTAAGACAC+CGG 0.592995 3_2:-2900130 Msa0391350:CDS
AAGACACCGGATCTATTTGG+TGG 0.595439 3_2:-2900117 Msa0391350:CDS
GGAAGATGATCTAAGTCTAA+GGG 0.613582 3_2:+2900208 None:intergenic
GTGAGGCAGACATGAGACAT+GGG 0.618587 3_2:+2900186 None:intergenic
ACACCGGATCTATTTGGTGG+CGG 0.626807 3_2:-2900114 Msa0391350:CDS
TGGGGAGTAGGAGTATTACT+GGG 0.634686 3_2:-2899153 Msa0391350:CDS
AGTGAGGCAGACATGAGACA+TGG 0.648452 3_2:+2900185 None:intergenic
TGAGGCAGACATGAGACATG+GGG 0.699030 3_2:+2900187 None:intergenic
TTAGAAGATGTGCACCAGTG+AGG 0.702752 3_2:+2900169 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAACATTTAAAAAAAGTC+AGG + chr3_2:2899878-2899897 None:intergenic 15.0%
!! ATTGAAAATATTATACTACA+GGG + chr3_2:2900059-2900078 None:intergenic 15.0%
!! ATTAACATTTAAAAAAAGTC+AGG + chr3_2:2899878-2899897 None:intergenic 15.0%
!! ATTGAAAATATTATACTACA+GGG + chr3_2:2900059-2900078 None:intergenic 15.0%
!!! AAAAACATGTAAAAGCATAA+TGG + chr3_2:2899371-2899390 None:intergenic 20.0%
!! ATAACTTAATATGCATTGAA+TGG - chr3_2:2899732-2899751 Msa0391350:intron 20.0%
!! ATAACTTAATATGCATTGAA+TGG - chr3_2:2899732-2899751 Msa0391350:intron 20.0%
!! GATTGAAAATATTATACTAC+AGG + chr3_2:2900060-2900079 None:intergenic 20.0%
!!! AGTTTTAGTTTTTATGTATG+TGG - chr3_2:2900085-2900104 Msa0391350:CDS 20.0%
!!! AAAAACATGTAAAAGCATAA+TGG + chr3_2:2899371-2899390 None:intergenic 20.0%
!! ATAACTTAATATGCATTGAA+TGG - chr3_2:2899732-2899751 Msa0391350:intron 20.0%
!! ATAACTTAATATGCATTGAA+TGG - chr3_2:2899732-2899751 Msa0391350:intron 20.0%
!! GATTGAAAATATTATACTAC+AGG + chr3_2:2900060-2900079 None:intergenic 20.0%
!!! AGTTTTAGTTTTTATGTATG+TGG - chr3_2:2900085-2900104 Msa0391350:CDS 20.0%
! TTATTAACATTGAAACAGTC+GGG + chr3_2:2899716-2899735 None:intergenic 25.0%
! GTTATTAACATTGAAACAGT+CGG + chr3_2:2899717-2899736 None:intergenic 25.0%
! AAGAAAACAAAATGTGTAGA+TGG + chr3_2:2900204-2900223 None:intergenic 25.0%
!!! CTACACATTTTGTTTTCTTT+AGG - chr3_2:2900205-2900224 Msa0391350:exon 25.0%
!! TTGTTTTCTTTAGGTAAGTA+TGG - chr3_2:2900214-2900233 Msa0391350:five_prime_UTR 25.0%
!! TGTTTTCTTTAGGTAAGTAT+GGG - chr3_2:2900215-2900234 Msa0391350:five_prime_UTR 25.0%
! TTATTAACATTGAAACAGTC+GGG + chr3_2:2899716-2899735 None:intergenic 25.0%
! GTTATTAACATTGAAACAGT+CGG + chr3_2:2899717-2899736 None:intergenic 25.0%
! AAGAAAACAAAATGTGTAGA+TGG + chr3_2:2900204-2900223 None:intergenic 25.0%
!!! CTACACATTTTGTTTTCTTT+AGG - chr3_2:2900205-2900224 Msa0391350:exon 25.0%
!! TTGTTTTCTTTAGGTAAGTA+TGG - chr3_2:2900214-2900233 Msa0391350:five_prime_UTR 25.0%
!! TGTTTTCTTTAGGTAAGTAT+GGG - chr3_2:2900215-2900234 Msa0391350:five_prime_UTR 25.0%
ATTGATGAACTTCACTAACA+AGG + chr3_2:2899654-2899673 None:intergenic 30.0%
CTTAATATGCATTGAATGGT+AGG - chr3_2:2899736-2899755 Msa0391350:intron 30.0%
CAAGCTAAAAGAACTTTCTA+TGG - chr3_2:2899786-2899805 Msa0391350:intron 30.0%
CAACTGTCTACTAACAAATT+TGG - chr3_2:2899819-2899838 Msa0391350:intron 30.0%
CTTAATATGCATTGAATGGT+TGG - chr3_2:2899736-2899755 Msa0391350:intron 30.0%
ATGCAACAATTGTCTACTAA+TGG - chr3_2:2899979-2899998 Msa0391350:intron 30.0%
! GTTTTCTTTAGGTAAGTATG+GGG - chr3_2:2900216-2900235 Msa0391350:five_prime_UTR 30.0%
ATTGATGAACTTCACTAACA+AGG + chr3_2:2899654-2899673 None:intergenic 30.0%
CTTAATATGCATTGAATGGT+AGG - chr3_2:2899736-2899755 Msa0391350:intron 30.0%
CAAGCTAAAAGAACTTTCTA+TGG - chr3_2:2899786-2899805 Msa0391350:intron 30.0%
CAACTGTCTACTAACAAATT+TGG - chr3_2:2899819-2899838 Msa0391350:intron 30.0%
CTTAATATGCATTGAATGGT+TGG - chr3_2:2899736-2899755 Msa0391350:intron 30.0%
ATGCAACAATTGTCTACTAA+TGG - chr3_2:2899979-2899998 Msa0391350:intron 30.0%
! GTTTTCTTTAGGTAAGTATG+GGG - chr3_2:2900216-2900235 Msa0391350:five_prime_UTR 30.0%
GGAAGATGATCTAAGTCTAA+GGG + chr3_2:2899182-2899201 None:intergenic 35.0%
! ATCTTCTAAGAGCTGCAATA+TGG - chr3_2:2899232-2899251 Msa0391350:intron 35.0%
AGAAGTAAAGAACAGATCTG+AGG + chr3_2:2899342-2899361 None:intergenic 35.0%
GAAAATGATGAACAGAACGA+AGG + chr3_2:2899398-2899417 None:intergenic 35.0%
!! TAGTTTTGCTGTGTTTTTCC+TGG - chr3_2:2899477-2899496 Msa0391350:intron 35.0%
ATTTGAGCTCAAACATTTCC+AGG + chr3_2:2899498-2899517 None:intergenic 35.0%
TAGTAGTAGTAGTAGTAGTC+TGG - chr3_2:2899615-2899634 Msa0391350:intron 35.0%
CTGTCTACTAACAAATTTGG+TGG - chr3_2:2899822-2899841 Msa0391350:intron 35.0%
!!! TATTTTAGCTTGAATCGAGC+AGG + chr3_2:2899942-2899961 None:intergenic 35.0%
! TGTGCAATTCTTATTTAGCC+TGG - chr3_2:2900125-2900144 Msa0391350:CDS 35.0%
ATGGCATGTTCTTAGATCTT+GGG + chr3_2:2900185-2900204 None:intergenic 35.0%
GGAAGATGATCTAAGTCTAA+GGG + chr3_2:2899182-2899201 None:intergenic 35.0%
! ATCTTCTAAGAGCTGCAATA+TGG - chr3_2:2899232-2899251 Msa0391350:intron 35.0%
AGAAGTAAAGAACAGATCTG+AGG + chr3_2:2899342-2899361 None:intergenic 35.0%
GAAAATGATGAACAGAACGA+AGG + chr3_2:2899398-2899417 None:intergenic 35.0%
!! TAGTTTTGCTGTGTTTTTCC+TGG - chr3_2:2899477-2899496 Msa0391350:intron 35.0%
ATTTGAGCTCAAACATTTCC+AGG + chr3_2:2899498-2899517 None:intergenic 35.0%
TAGTAGTAGTAGTAGTAGTC+TGG - chr3_2:2899615-2899634 Msa0391350:intron 35.0%
CTGTCTACTAACAAATTTGG+TGG - chr3_2:2899822-2899841 Msa0391350:intron 35.0%
!!! TATTTTAGCTTGAATCGAGC+AGG + chr3_2:2899942-2899961 None:intergenic 35.0%
! TGTGCAATTCTTATTTAGCC+TGG - chr3_2:2900125-2900144 Msa0391350:CDS 35.0%
ATGGCATGTTCTTAGATCTT+GGG + chr3_2:2900185-2900204 None:intergenic 35.0%
! TCTAAGTCTAAGGGTGTGTT+TGG + chr3_2:2899173-2899192 None:intergenic 40.0%
GGGAAGATGATCTAAGTCTA+AGG + chr3_2:2899183-2899202 None:intergenic 40.0%
AAATAGATCCGGTGTCTTAG+AGG + chr3_2:2899268-2899287 None:intergenic 40.0%
! TCTAAGACACCGGATCTATT+TGG - chr3_2:2899267-2899286 Msa0391350:intron 40.0%
! TCCTTTCAAGTGCTACTACA+AGG - chr3_2:2899311-2899330 Msa0391350:intron 40.0%
ACCTTGTAGTAGCACTTGAA+AGG + chr3_2:2899315-2899334 None:intergenic 40.0%
CTTCACTAACAAGGATTGCA+GGG + chr3_2:2899645-2899664 None:intergenic 40.0%
ACTTCACTAACAAGGATTGC+AGG + chr3_2:2899646-2899665 None:intergenic 40.0%
GGAGAAGAATGGAAGCTAAA+TGG + chr3_2:2899695-2899714 None:intergenic 40.0%
TATGCATTGAATGGTTGGAG+TGG - chr3_2:2899905-2899924 Msa0391350:intron 40.0%
TATTATACTACAGGGTGTGC+TGG + chr3_2:2900051-2900070 None:intergenic 40.0%
ACCTAACAGACAATATGACC+AGG + chr3_2:2900146-2900165 None:intergenic 40.0%
GATGGCATGTTCTTAGATCT+TGG + chr3_2:2900186-2900205 None:intergenic 40.0%
TTTAGGTAAGTATGGGGAGT+AGG - chr3_2:2900222-2900241 Msa0391350:five_prime_UTR 40.0%
! TCTAAGTCTAAGGGTGTGTT+TGG + chr3_2:2899173-2899192 None:intergenic 40.0%
GGGAAGATGATCTAAGTCTA+AGG + chr3_2:2899183-2899202 None:intergenic 40.0%
AAATAGATCCGGTGTCTTAG+AGG + chr3_2:2899268-2899287 None:intergenic 40.0%
! TCTAAGACACCGGATCTATT+TGG - chr3_2:2899267-2899286 Msa0391350:intron 40.0%
! TCCTTTCAAGTGCTACTACA+AGG - chr3_2:2899311-2899330 Msa0391350:intron 40.0%
ACCTTGTAGTAGCACTTGAA+AGG + chr3_2:2899315-2899334 None:intergenic 40.0%
CTTCACTAACAAGGATTGCA+GGG + chr3_2:2899645-2899664 None:intergenic 40.0%
ACTTCACTAACAAGGATTGC+AGG + chr3_2:2899646-2899665 None:intergenic 40.0%
GGAGAAGAATGGAAGCTAAA+TGG + chr3_2:2899695-2899714 None:intergenic 40.0%
TATGCATTGAATGGTTGGAG+TGG - chr3_2:2899905-2899924 Msa0391350:intron 40.0%
TATTATACTACAGGGTGTGC+TGG + chr3_2:2900051-2900070 None:intergenic 40.0%
ACCTAACAGACAATATGACC+AGG + chr3_2:2900146-2900165 None:intergenic 40.0%
GATGGCATGTTCTTAGATCT+TGG + chr3_2:2900186-2900205 None:intergenic 40.0%
TTTAGGTAAGTATGGGGAGT+AGG - chr3_2:2900222-2900241 Msa0391350:five_prime_UTR 40.0%
! GTCTAAGGGTGTGTTTGGTT+TGG + chr3_2:2899168-2899187 None:intergenic 45.0%
TTAGAAGATGTGCACCAGTG+AGG + chr3_2:2899221-2899240 None:intergenic 45.0%
AAGACACCGGATCTATTTGG+TGG - chr3_2:2899270-2899289 Msa0391350:intron 45.0%
TGAAACAGTCGGGAGAAGAA+TGG + chr3_2:2899706-2899725 None:intergenic 45.0%
GCCTGGTCATATTGTCTGTT+AGG - chr3_2:2900142-2900161 Msa0391350:CDS 45.0%
!! ATGGGGAGTAGGAGTATTAC+TGG - chr3_2:2900233-2900252 Msa0391350:five_prime_UTR 45.0%
!! TGGGGAGTAGGAGTATTACT+GGG - chr3_2:2900234-2900253 Msa0391350:five_prime_UTR 45.0%
! GTCTAAGGGTGTGTTTGGTT+TGG + chr3_2:2899168-2899187 None:intergenic 45.0%
TTAGAAGATGTGCACCAGTG+AGG + chr3_2:2899221-2899240 None:intergenic 45.0%
AAGACACCGGATCTATTTGG+TGG - chr3_2:2899270-2899289 Msa0391350:intron 45.0%
TGAAACAGTCGGGAGAAGAA+TGG + chr3_2:2899706-2899725 None:intergenic 45.0%
GCCTGGTCATATTGTCTGTT+AGG - chr3_2:2900142-2900161 Msa0391350:CDS 45.0%
!! ATGGGGAGTAGGAGTATTAC+TGG - chr3_2:2900233-2900252 Msa0391350:five_prime_UTR 45.0%
!! TGGGGAGTAGGAGTATTACT+GGG - chr3_2:2900234-2900253 Msa0391350:five_prime_UTR 45.0%
TGAGGCAGACATGAGACATG+GGG + chr3_2:2899203-2899222 None:intergenic 50.0%
GTGAGGCAGACATGAGACAT+GGG + chr3_2:2899204-2899223 None:intergenic 50.0%
AGTGAGGCAGACATGAGACA+TGG + chr3_2:2899205-2899224 None:intergenic 50.0%
ATGTCTCATGTCTGCCTCAC+TGG - chr3_2:2899204-2899223 Msa0391350:intron 50.0%
!! ACGAGCTTCCTCTAAGACAC+CGG - chr3_2:2899257-2899276 Msa0391350:intron 50.0%
! ACACCGGATCTATTTGGTGG+CGG - chr3_2:2899273-2899292 Msa0391350:intron 50.0%
TCACCGCCACCAAATAGATC+CGG + chr3_2:2899279-2899298 None:intergenic 50.0%
ATACTACAGGGTGTGCTGGA+GGG + chr3_2:2900047-2900066 None:intergenic 50.0%
TATACTACAGGGTGTGCTGG+AGG + chr3_2:2900048-2900067 None:intergenic 50.0%
TGAGGCAGACATGAGACATG+GGG + chr3_2:2899203-2899222 None:intergenic 50.0%
GTGAGGCAGACATGAGACAT+GGG + chr3_2:2899204-2899223 None:intergenic 50.0%
AGTGAGGCAGACATGAGACA+TGG + chr3_2:2899205-2899224 None:intergenic 50.0%
ATGTCTCATGTCTGCCTCAC+TGG - chr3_2:2899204-2899223 Msa0391350:intron 50.0%
!! ACGAGCTTCCTCTAAGACAC+CGG - chr3_2:2899257-2899276 Msa0391350:intron 50.0%
! ACACCGGATCTATTTGGTGG+CGG - chr3_2:2899273-2899292 Msa0391350:intron 50.0%
TCACCGCCACCAAATAGATC+CGG + chr3_2:2899279-2899298 None:intergenic 50.0%
ATACTACAGGGTGTGCTGGA+GGG + chr3_2:2900047-2900066 None:intergenic 50.0%
TATACTACAGGGTGTGCTGG+AGG + chr3_2:2900048-2900067 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 2899141 2900268 2899141 ID=Msa0391350;Name=Msa0391350
chr3_2 mRNA 2899141 2900268 2899141 ID=Msa0391350-mRNA-1;Parent=Msa0391350;Name=Msa0391350-mRNA-1;_AED=0.52;_eAED=0.52;_QI=63|0|0.5|0.5|1|1|2|0|56
chr3_2 exon 2899141 2899182 2899141 ID=Msa0391350-mRNA-1:exon:956;Parent=Msa0391350-mRNA-1
chr3_2 exon 2900077 2900268 2900077 ID=Msa0391350-mRNA-1:exon:955;Parent=Msa0391350-mRNA-1
chr3_2 five_prime_UTR 2900206 2900268 2900206 ID=Msa0391350-mRNA-1:five_prime_utr;Parent=Msa0391350-mRNA-1
chr3_2 CDS 2900077 2900205 2900077 ID=Msa0391350-mRNA-1:cds;Parent=Msa0391350-mRNA-1
chr3_2 CDS 2899141 2899182 2899141 ID=Msa0391350-mRNA-1:cds;Parent=Msa0391350-mRNA-1
Gene Sequence

>Msa0391350

ATGTCTCATGTCTGCCTCACTGGTGCACATCTTCTAAGAGCTGCAATATGGACACGAGCTTCCTCTAAGACACCGGATCTATTTGGTGGCGGTGACAGCTTTGCTTTTCCTTTCAAGTGCTACTACAAGGTAAGTATGGGGAGTAGGAGTATTACTGGGATGCAAGTATGA
Protein sequence

>Msa0391350

MSHVCLTGAHLLRAAIWTRASSKTPDLFGGGDSFAFPFKCYYKVSMGSRSITGMQV*