AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1078910

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1078910 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
Msa1078910 AT5G03120.1 40.625 64 31 1 16 72 10 73 7.15e-12 55.8
Msa1078910 AT5G03120.2 40.625 64 31 1 16 72 10 73 1.88e-11 55.5

Find 30 sgRNAs with CRISPR-Local

Find 114 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATCATTGTGTGATTTAT+AGG 0.229909 7_2:+77934100 None:intergenic
GACAAACCTCTAGAGAAATA+TGG 0.278570 7_2:+77933939 None:intergenic
AGATCATTGTGTGATTTATA+GGG 0.390485 7_2:+77934101 None:intergenic
AGCATCAACACCCGTAGCTT+TGG 0.412256 7_2:+77933459 None:intergenic
ACAAACCTCTAGAGAAATAT+GGG 0.461398 7_2:+77933940 None:intergenic
AAGAAAGAGAAAGAAACAAT+TGG 0.485064 7_2:+77933974 None:intergenic
GAAACAATTGGCGATGAAGA+TGG 0.489266 7_2:+77933986 None:intergenic
GGCACAAACGAGTGAGTCTC+AGG 0.492086 7_2:+77933547 None:intergenic
GACATGCACAAATTTCTTGA+GGG 0.493470 7_2:+77934029 None:intergenic
AAATTTGTGCATGTCATACA+TGG 0.499981 7_2:-77934021 Msa1078910:exon
ATTTATGAGATCGATTATAG+AGG 0.512251 7_2:-77933571 Msa1078910:CDS
GGCTTACCATGGGAATGATC+AGG 0.514926 7_2:+77933520 None:intergenic
TGCAGCTGCAACCAAAGCTA+CGG 0.523815 7_2:-77933470 Msa1078910:CDS
GATTTATAGGGTGGAAAGAA+AGG 0.525657 7_2:+77934113 None:intergenic
GACTAATGTATGCAAGTTCA+CGG 0.529375 7_2:+77934171 None:intergenic
TGATGCTACCATGAAACAAA+AGG 0.546319 7_2:-77933443 Msa1078910:CDS
TGACATGCACAAATTTCTTG+AGG 0.548150 7_2:+77934028 None:intergenic
TCATTGTGTGATTTATAGGG+TGG 0.550522 7_2:+77934104 None:intergenic
CTCTTGTCATGAGCTGAATG+AGG 0.554978 7_2:+77933499 None:intergenic
ACTCTCCCATATTTCTCTAG+AGG 0.566327 7_2:-77933945 Msa1078910:intron
GAGCTGAATGAGGCTTACCA+TGG 0.584782 7_2:+77933509 None:intergenic
GCAGCTGCAACCAAAGCTAC+GGG 0.602211 7_2:-77933469 Msa1078910:CDS
CCATGGGAATGATCAGGTGG+AGG 0.610610 7_2:+77933526 None:intergenic
CCTCCACCTGATCATTCCCA+TGG 0.611138 7_2:-77933526 Msa1078910:CDS
ACAATTGGCGATGAAGATGG+AGG 0.611543 7_2:+77933989 None:intergenic
AGCTGAATGAGGCTTACCAT+GGG 0.626115 7_2:+77933510 None:intergenic
GAAGAAACATAACATGGTCA+AGG 0.648058 7_2:+77934193 None:intergenic
CAATTGGCGATGAAGATGGA+GGG 0.648695 7_2:+77933990 None:intergenic
TTCACGGAAGAAACATAACA+TGG 0.691093 7_2:+77934187 None:intergenic
TTACCATGGGAATGATCAGG+TGG 0.701175 7_2:+77933523 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTATAAAATTTATGAGAG+TGG + chr7_2:77933753-77933772 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr7_2:77933865-77933884 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr7_2:77934014-77934033 Msa1078910:CDS 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr7_2:77934017-77934036 Msa1078910:exon 15.0%
!! TATTATAAAATTTATGAGAG+TGG + chr7_2:77933753-77933772 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr7_2:77933865-77933884 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr7_2:77934014-77934033 Msa1078910:CDS 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr7_2:77934017-77934036 Msa1078910:exon 15.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr7_2:77933834-77933853 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr7_2:77934022-77934041 Msa1078910:exon 20.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr7_2:77933834-77933853 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr7_2:77934022-77934041 Msa1078910:exon 20.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr7_2:77933503-77933522 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr7_2:77933504-77933523 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr7_2:77933535-77933554 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr7_2:77933536-77933555 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr7_2:77933662-77933681 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr7_2:77933750-77933769 None:intergenic 25.0%
!! GTCAATTTTCTCTTGTAAAT+AGG - chr7_2:77933963-77933982 Msa1078910:CDS 25.0%
!! TTTTCTCTTGTAAATAGGAT+CGG - chr7_2:77933968-77933987 Msa1078910:CDS 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr7_2:77934062-77934081 Msa1078910:five_prime_UTR 25.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr7_2:77933503-77933522 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr7_2:77933504-77933523 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr7_2:77933535-77933554 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr7_2:77933536-77933555 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr7_2:77933662-77933681 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr7_2:77933750-77933769 None:intergenic 25.0%
!! GTCAATTTTCTCTTGTAAAT+AGG - chr7_2:77933963-77933982 Msa1078910:CDS 25.0%
!! TTTTCTCTTGTAAATAGGAT+CGG - chr7_2:77933968-77933987 Msa1078910:CDS 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr7_2:77934062-77934081 Msa1078910:five_prime_UTR 25.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr7_2:77933494-77933513 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr7_2:77933502-77933521 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr7_2:77933612-77933631 Msa1078910:intron 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr7_2:77933696-77933715 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG + chr7_2:77933721-77933740 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr7_2:77933860-77933879 None:intergenic 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr7_2:77933992-77934011 Msa1078910:CDS 30.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr7_2:77933494-77933513 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr7_2:77933502-77933521 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr7_2:77933612-77933631 Msa1078910:intron 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr7_2:77933696-77933715 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG + chr7_2:77933721-77933740 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr7_2:77933860-77933879 None:intergenic 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr7_2:77933992-77934011 Msa1078910:CDS 30.0%
TTCACGGAAGAAACATAACA+TGG + chr7_2:77933449-77933468 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr7_2:77933465-77933484 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr7_2:77933523-77933542 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr7_2:77933532-77933551 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr7_2:77933607-77933626 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr7_2:77933608-77933627 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr7_2:77933697-77933716 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr7_2:77933743-77933762 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr7_2:77933838-77933857 Msa1078910:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr7_2:77934190-77934209 Msa1078910:five_prime_UTR 35.0%
TTCACGGAAGAAACATAACA+TGG + chr7_2:77933449-77933468 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr7_2:77933465-77933484 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr7_2:77933523-77933542 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr7_2:77933532-77933551 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr7_2:77933607-77933626 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr7_2:77933608-77933627 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr7_2:77933697-77933716 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr7_2:77933743-77933762 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr7_2:77933838-77933857 Msa1078910:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr7_2:77934190-77934209 Msa1078910:five_prime_UTR 35.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr7_2:77933488-77933507 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr7_2:77933650-77933669 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr7_2:77933688-77933707 Msa1078910:intron 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG + chr7_2:77933735-77933754 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr7_2:77933856-77933875 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr7_2:77933857-77933876 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr7_2:77933971-77933990 Msa1078910:CDS 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr7_2:77933972-77933991 Msa1078910:CDS 40.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr7_2:77933488-77933507 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr7_2:77933650-77933669 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr7_2:77933688-77933707 Msa1078910:intron 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG + chr7_2:77933735-77933754 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr7_2:77933856-77933875 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr7_2:77933857-77933876 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr7_2:77933971-77933990 Msa1078910:CDS 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr7_2:77933972-77933991 Msa1078910:CDS 40.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr7_2:77933487-77933506 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr7_2:77933489-77933508 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr7_2:77933646-77933665 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr7_2:77933647-77933666 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG + chr7_2:77933736-77933755 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr7_2:77934031-77934050 Msa1078910:exon 45.0%
TTACCATGGGAATGATCAGG+TGG + chr7_2:77934113-77934132 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr7_2:77934126-77934145 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr7_2:77934137-77934156 None:intergenic 45.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr7_2:77933487-77933506 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr7_2:77933489-77933508 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr7_2:77933646-77933665 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr7_2:77933647-77933666 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG + chr7_2:77933736-77933755 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr7_2:77934031-77934050 Msa1078910:exon 45.0%
TTACCATGGGAATGATCAGG+TGG + chr7_2:77934113-77934132 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr7_2:77934126-77934145 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr7_2:77934137-77934156 None:intergenic 45.0%
GGCTTACCATGGGAATGATC+AGG + chr7_2:77934116-77934135 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr7_2:77934127-77934146 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr7_2:77934163-77934182 Msa1078910:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr7_2:77934177-77934196 None:intergenic 50.0%
GGCTTACCATGGGAATGATC+AGG + chr7_2:77934116-77934135 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr7_2:77934127-77934146 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr7_2:77934163-77934182 Msa1078910:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr7_2:77934177-77934196 None:intergenic 50.0%
GGCACAAACGAGTGAGTCTC+AGG + chr7_2:77934089-77934108 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr7_2:77934110-77934129 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr7_2:77934107-77934126 Msa1078910:five_prime_UTR 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr7_2:77934164-77934183 Msa1078910:five_prime_UTR 55.0%
GGCACAAACGAGTGAGTCTC+AGG + chr7_2:77934089-77934108 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr7_2:77934110-77934129 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr7_2:77934107-77934126 Msa1078910:five_prime_UTR 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr7_2:77934164-77934183 Msa1078910:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 77933441 77934214 77933441 ID=Msa1078910;Name=Msa1078910
chr7_2 mRNA 77933441 77934214 77933441 ID=Msa1078910-mRNA-1;Parent=Msa1078910;Name=Msa1078910-mRNA-1;_AED=0.12;_eAED=0.12;_QI=181|0|0.5|1|0|0|2|0|81
chr7_2 exon 77933441 77933595 77933441 ID=Msa1078910-mRNA-1:exon:19320;Parent=Msa1078910-mRNA-1
chr7_2 exon 77933946 77934214 77933946 ID=Msa1078910-mRNA-1:exon:19319;Parent=Msa1078910-mRNA-1
chr7_2 five_prime_UTR 77934034 77934214 77934034 ID=Msa1078910-mRNA-1:five_prime_utr;Parent=Msa1078910-mRNA-1
chr7_2 CDS 77933946 77934033 77933946 ID=Msa1078910-mRNA-1:cds;Parent=Msa1078910-mRNA-1
chr7_2 CDS 77933441 77933595 77933441 ID=Msa1078910-mRNA-1:cds;Parent=Msa1078910-mRNA-1
Gene Sequence

>Msa1078910

ATGTCATACATGGATCTAAGACCCTCCATCTTCATCGCCAATTGTTTCTTTCTCTTTCTTATACTCACTCTCCCATATTTCTCTAGAGAAATTTATGAGATCGATTATAGAGGTCCTGAGACTCACTCGTTTGTGCCTCCACCTGATCATTCCCATGGTAAGCCTCATTCAGCTCATGACAAGAGCTCTACTGCAGCTGCAACCAAAGCTACGGGTGTTGATGCTACCATGAAACAAAAGGCA
Protein sequence

>Msa1078910

MSYMDLRPSIFIANCFFLFLILTLPYFSREIYEIDYRGPETHSFVPPPDHSHGKPHSAHDKSSTAAATKATGVDATMKQKA