AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0968330


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0968330 MtrunA17_Chr7g0263811 84.091 88 7 3 1 81 1 88 6.93e-46 141
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0968330 AT5G03120.1 40.625 64 31 1 16 72 10 73 7.15e-12 55.8
Msa0968330 AT5G03120.2 40.625 64 31 1 16 72 10 73 1.88e-11 55.5

Find 30 sgRNAs with CRISPR-Local

Find 112 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATCATTGTGTGATTTAT+AGG 0.229909 6_3:+98659820 None:intergenic
GACAAACCTCTAGAGAAATA+TGG 0.278570 6_3:+98659659 None:intergenic
AGATCATTGTGTGATTTATA+GGG 0.390485 6_3:+98659821 None:intergenic
AGCATCAACACCCGTAGCTT+TGG 0.412256 6_3:+98659179 None:intergenic
ACAAACCTCTAGAGAAATAT+GGG 0.461398 6_3:+98659660 None:intergenic
AAGAAAGAGAAAGAAACAAT+TGG 0.485064 6_3:+98659694 None:intergenic
GAAACAATTGGCGATGAAGA+TGG 0.489266 6_3:+98659706 None:intergenic
GGCACAAACGAGTGAGTCTC+AGG 0.492086 6_3:+98659267 None:intergenic
GACATGCACAAATTTCTTGA+GGG 0.493470 6_3:+98659749 None:intergenic
AAATTTGTGCATGTCATACA+TGG 0.499981 6_3:-98659741 Msa0968330:exon
ATTTATGAGATCGATTATAG+AGG 0.512251 6_3:-98659291 Msa0968330:CDS
GGCTTACCATGGGAATGATC+AGG 0.514926 6_3:+98659240 None:intergenic
TGCAGCTGCAACCAAAGCTA+CGG 0.523815 6_3:-98659190 Msa0968330:CDS
GATTTATAGGGTGGAAAGAA+AGG 0.525657 6_3:+98659833 None:intergenic
GACTAATGTATGCAAGTTCA+CGG 0.529375 6_3:+98659891 None:intergenic
TGATGCTACCATGAAACAAA+AGG 0.546319 6_3:-98659163 Msa0968330:CDS
TGACATGCACAAATTTCTTG+AGG 0.548150 6_3:+98659748 None:intergenic
TCATTGTGTGATTTATAGGG+TGG 0.550522 6_3:+98659824 None:intergenic
CTCTTGTCATGAGCTGAATG+AGG 0.554978 6_3:+98659219 None:intergenic
ACTCTCCCATATTTCTCTAG+AGG 0.566327 6_3:-98659665 Msa0968330:intron
GAGCTGAATGAGGCTTACCA+TGG 0.584782 6_3:+98659229 None:intergenic
GCAGCTGCAACCAAAGCTAC+GGG 0.602211 6_3:-98659189 Msa0968330:CDS
CCATGGGAATGATCAGGTGG+AGG 0.610610 6_3:+98659246 None:intergenic
CCTCCACCTGATCATTCCCA+TGG 0.611138 6_3:-98659246 Msa0968330:CDS
ACAATTGGCGATGAAGATGG+AGG 0.611543 6_3:+98659709 None:intergenic
AGCTGAATGAGGCTTACCAT+GGG 0.626115 6_3:+98659230 None:intergenic
GAAGAAACATAACATGGTCA+AGG 0.648058 6_3:+98659913 None:intergenic
CAATTGGCGATGAAGATGGA+GGG 0.648695 6_3:+98659710 None:intergenic
TTCACGGAAGAAACATAACA+TGG 0.691093 6_3:+98659907 None:intergenic
TTACCATGGGAATGATCAGG+TGG 0.701175 6_3:+98659243 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTATAAAATTTATGAGAG+TGG + chr6_3:98659473-98659492 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr6_3:98659585-98659604 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr6_3:98659734-98659753 Msa0968330:CDS 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr6_3:98659737-98659756 Msa0968330:exon 15.0%
!! TATTATAAAATTTATGAGAG+TGG + chr6_3:98659473-98659492 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr6_3:98659585-98659604 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr6_3:98659734-98659753 Msa0968330:CDS 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr6_3:98659737-98659756 Msa0968330:exon 15.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr6_3:98659554-98659573 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr6_3:98659742-98659761 Msa0968330:exon 20.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr6_3:98659554-98659573 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr6_3:98659742-98659761 Msa0968330:exon 20.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr6_3:98659223-98659242 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr6_3:98659224-98659243 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr6_3:98659255-98659274 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr6_3:98659256-98659275 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr6_3:98659382-98659401 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr6_3:98659470-98659489 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr6_3:98659782-98659801 Msa0968330:five_prime_UTR 25.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr6_3:98659223-98659242 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr6_3:98659224-98659243 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr6_3:98659255-98659274 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr6_3:98659256-98659275 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr6_3:98659382-98659401 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr6_3:98659470-98659489 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr6_3:98659782-98659801 Msa0968330:five_prime_UTR 25.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr6_3:98659214-98659233 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr6_3:98659222-98659241 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr6_3:98659332-98659351 Msa0968330:intron 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr6_3:98659416-98659435 None:intergenic 30.0%
GAAAGACGGTTTGTAAAATT+CGG + chr6_3:98659441-98659460 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr6_3:98659580-98659599 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG - chr6_3:98659683-98659702 Msa0968330:CDS 30.0%
CTTTCTCTTGTAAATAGGAT+CGG - chr6_3:98659688-98659707 Msa0968330:CDS 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr6_3:98659712-98659731 Msa0968330:CDS 30.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr6_3:98659214-98659233 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr6_3:98659222-98659241 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr6_3:98659332-98659351 Msa0968330:intron 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr6_3:98659416-98659435 None:intergenic 30.0%
GAAAGACGGTTTGTAAAATT+CGG + chr6_3:98659441-98659460 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr6_3:98659580-98659599 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG - chr6_3:98659683-98659702 Msa0968330:CDS 30.0%
CTTTCTCTTGTAAATAGGAT+CGG - chr6_3:98659688-98659707 Msa0968330:CDS 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr6_3:98659712-98659731 Msa0968330:CDS 30.0%
TTCACGGAAGAAACATAACA+TGG + chr6_3:98659169-98659188 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr6_3:98659185-98659204 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr6_3:98659243-98659262 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr6_3:98659252-98659271 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr6_3:98659327-98659346 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr6_3:98659328-98659347 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr6_3:98659417-98659436 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr6_3:98659463-98659482 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr6_3:98659558-98659577 Msa0968330:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr6_3:98659910-98659929 Msa0968330:five_prime_UTR 35.0%
TTCACGGAAGAAACATAACA+TGG + chr6_3:98659169-98659188 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr6_3:98659185-98659204 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr6_3:98659243-98659262 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr6_3:98659252-98659271 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr6_3:98659327-98659346 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr6_3:98659328-98659347 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr6_3:98659417-98659436 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr6_3:98659463-98659482 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr6_3:98659558-98659577 Msa0968330:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr6_3:98659910-98659929 Msa0968330:five_prime_UTR 35.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr6_3:98659208-98659227 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr6_3:98659370-98659389 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr6_3:98659408-98659427 Msa0968330:intron 40.0%
! AGTGGTGGAAATTGGAAAGA+CGG + chr6_3:98659455-98659474 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr6_3:98659576-98659595 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr6_3:98659577-98659596 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr6_3:98659691-98659710 Msa0968330:CDS 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr6_3:98659692-98659711 Msa0968330:CDS 40.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr6_3:98659208-98659227 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr6_3:98659370-98659389 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr6_3:98659408-98659427 Msa0968330:intron 40.0%
! AGTGGTGGAAATTGGAAAGA+CGG + chr6_3:98659455-98659474 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr6_3:98659576-98659595 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr6_3:98659577-98659596 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr6_3:98659691-98659710 Msa0968330:CDS 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr6_3:98659692-98659711 Msa0968330:CDS 40.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr6_3:98659207-98659226 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr6_3:98659209-98659228 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr6_3:98659366-98659385 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr6_3:98659367-98659386 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr6_3:98659751-98659770 Msa0968330:exon 45.0%
TTACCATGGGAATGATCAGG+TGG + chr6_3:98659833-98659852 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr6_3:98659846-98659865 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr6_3:98659857-98659876 None:intergenic 45.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr6_3:98659207-98659226 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr6_3:98659209-98659228 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr6_3:98659366-98659385 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr6_3:98659367-98659386 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr6_3:98659751-98659770 Msa0968330:exon 45.0%
TTACCATGGGAATGATCAGG+TGG + chr6_3:98659833-98659852 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr6_3:98659846-98659865 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr6_3:98659857-98659876 None:intergenic 45.0%
GGCTTACCATGGGAATGATC+AGG + chr6_3:98659836-98659855 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr6_3:98659847-98659866 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr6_3:98659883-98659902 Msa0968330:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr6_3:98659897-98659916 None:intergenic 50.0%
GGCTTACCATGGGAATGATC+AGG + chr6_3:98659836-98659855 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr6_3:98659847-98659866 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr6_3:98659883-98659902 Msa0968330:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr6_3:98659897-98659916 None:intergenic 50.0%
GGCACAAACGAGTGAGTCTC+AGG + chr6_3:98659809-98659828 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr6_3:98659830-98659849 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr6_3:98659827-98659846 Msa0968330:five_prime_UTR 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr6_3:98659884-98659903 Msa0968330:five_prime_UTR 55.0%
GGCACAAACGAGTGAGTCTC+AGG + chr6_3:98659809-98659828 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr6_3:98659830-98659849 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr6_3:98659827-98659846 Msa0968330:five_prime_UTR 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr6_3:98659884-98659903 Msa0968330:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr6_3 gene 98659161 98659934 98659161 ID=Msa0968330;Name=Msa0968330
chr6_3 mRNA 98659161 98659934 98659161 ID=Msa0968330-mRNA-1;Parent=Msa0968330;Name=Msa0968330-mRNA-1;_AED=0.11;_eAED=0.11;_QI=181|0|0.5|1|0|0|2|0|81
chr6_3 exon 98659161 98659315 98659161 ID=Msa0968330-mRNA-1:exon:18555;Parent=Msa0968330-mRNA-1
chr6_3 exon 98659666 98659934 98659666 ID=Msa0968330-mRNA-1:exon:18554;Parent=Msa0968330-mRNA-1
chr6_3 five_prime_UTR 98659754 98659934 98659754 ID=Msa0968330-mRNA-1:five_prime_utr;Parent=Msa0968330-mRNA-1
chr6_3 CDS 98659666 98659753 98659666 ID=Msa0968330-mRNA-1:cds;Parent=Msa0968330-mRNA-1
chr6_3 CDS 98659161 98659315 98659161 ID=Msa0968330-mRNA-1:cds;Parent=Msa0968330-mRNA-1
Gene Sequence

>Msa0968330

ATGTCATACATGGATCTAAGACCCTCCATCTTCATCGCCAATTGTTTCTTTCTCTTTCTTATACTCACTCTCCCATATTTCTCTAGAGAAATTTATGAGATCGATTATAGAGGTCCTGAGACTCACTCGTTTGTGCCTCCACCTGATCATTCCCATGGTAAGCCTCATTCAGCTCATGACAAGAGCTCTACTGCAGCTGCAACCAAAGCTACGGGTGTTGATGCTACCATGAAACAAAAGGCA

Protein sequence

>Msa0968330

MSYMDLRPSIFIANCFFLFLILTLPYFSREIYEIDYRGPETHSFVPPPDHSHGKPHSAHDKSSTAAATKATGVDATMKQKA