AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1170050


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1170050 MtrunA17_Chr7g0263811 84.946 93 5 4 1 89 1 88 4.10e-48 148
Msa1170050 MtrunA17_Chr1g0181521 75.676 37 8 1 23 58 18 54 4.40e-13 60.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1170050 AT5G03120.2 43.678 87 42 2 16 102 10 89 5.03e-17 70.9
Msa1170050 AT5G03120.1 47.692 65 33 1 16 80 10 73 4.37e-16 67.4

Find 35 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGATCATTGTGTGATTTAT+AGG 0.229909 7_4:+63152170 None:intergenic
GACAAACCTCTAGAGAAATA+TGG 0.278570 7_4:+63152009 None:intergenic
AGATCATTGTGTGATTTATA+GGG 0.390485 7_4:+63152171 None:intergenic
AGCATCAACACCCGTAGCTT+TGG 0.412256 7_4:+63151529 None:intergenic
TCATTATCATCACAGGATCT+AGG 0.434501 7_4:-63151466 Msa1170050:CDS
ACAAACCTCTAGAGAAATAT+GGG 0.461398 7_4:+63152010 None:intergenic
TTATTTCGTATAAAAGATCA+AGG 0.471757 7_4:-63151438 Msa1170050:exon
AAGAAAGAGAAAGAAACAAT+TGG 0.485064 7_4:+63152044 None:intergenic
GAAACAATTGGCGATGAAGA+TGG 0.489266 7_4:+63152056 None:intergenic
GGCACAAACGAGTGAGTCTC+AGG 0.492086 7_4:+63151617 None:intergenic
TTTAGGTGGATCGGAAGCAT+TGG 0.492339 7_4:-63151672 Msa1170050:intron
GACATGCACAAATTTCTTGA+GGG 0.493470 7_4:+63152099 None:intergenic
AAATTTGTGCATGTCATACA+TGG 0.499981 7_4:-63152091 Msa1170050:exon
ATTTATGAGATCGATTATAG+AGG 0.512251 7_4:-63151641 Msa1170050:CDS
GGCTTACCATGGGAATGATC+AGG 0.514926 7_4:+63151590 None:intergenic
TGCAGCTGCAACCAAAGCTA+CGG 0.523815 7_4:-63151540 Msa1170050:CDS
GATTTATAGGGTGGAAAGAA+AGG 0.525657 7_4:+63152183 None:intergenic
GACTAATGTATGCAAGTTCA+CGG 0.529375 7_4:+63152241 None:intergenic
TGATGCTACCATGAAACAAA+AGG 0.546319 7_4:-63151513 Msa1170050:CDS
TGACATGCACAAATTTCTTG+AGG 0.548150 7_4:+63152098 None:intergenic
TCATTGTGTGATTTATAGGG+TGG 0.550522 7_4:+63152174 None:intergenic
CTCTTGTCATGAGCTGAATG+AGG 0.554978 7_4:+63151569 None:intergenic
CAACTACTCATTATCATCAC+AGG 0.565467 7_4:-63151473 Msa1170050:CDS
ACTCTCCCATATTTCTCTAG+AGG 0.566327 7_4:-63152015 Msa1170050:intron
GAGCTGAATGAGGCTTACCA+TGG 0.584782 7_4:+63151579 None:intergenic
GCAGCTGCAACCAAAGCTAC+GGG 0.602211 7_4:-63151539 Msa1170050:CDS
CCATGGGAATGATCAGGTGG+AGG 0.610610 7_4:+63151596 None:intergenic
CCTCCACCTGATCATTCCCA+TGG 0.611138 7_4:-63151596 Msa1170050:CDS
ACAATTGGCGATGAAGATGG+AGG 0.611543 7_4:+63152059 None:intergenic
AGCTGAATGAGGCTTACCAT+GGG 0.626115 7_4:+63151580 None:intergenic
TATTTCGTATAAAAGATCAA+GGG 0.639495 7_4:-63151437 Msa1170050:exon
GAAGAAACATAACATGGTCA+AGG 0.648058 7_4:+63152263 None:intergenic
CAATTGGCGATGAAGATGGA+GGG 0.648695 7_4:+63152060 None:intergenic
TTCACGGAAGAAACATAACA+TGG 0.691093 7_4:+63152257 None:intergenic
TTACCATGGGAATGATCAGG+TGG 0.701175 7_4:+63151593 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TATTATAAAATTTATGAGAG+TGG + chr7_4:63151725-63151744 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr7_4:63151837-63151856 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr7_4:63151986-63152005 Msa1170050:intron 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr7_4:63151989-63152008 Msa1170050:intron 15.0%
!! TATTATAAAATTTATGAGAG+TGG + chr7_4:63151725-63151744 None:intergenic 15.0%
!! ATTAATTGTCTATTGTAAAT+AGG + chr7_4:63151837-63151856 None:intergenic 15.0%
!!! GTGTTATGTTTTTAAATTTT+AGG - chr7_4:63151986-63152005 Msa1170050:intron 15.0%
!!! TTATGTTTTTAAATTTTAGG+TGG - chr7_4:63151989-63152008 Msa1170050:intron 15.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr7_4:63151806-63151825 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr7_4:63151994-63152013 Msa1170050:intron 20.0%
!! TTATTTCGTATAAAAGATCA+AGG - chr7_4:63152237-63152256 Msa1170050:five_prime_UTR 20.0%
!! TATTTCGTATAAAAGATCAA+GGG - chr7_4:63152238-63152257 Msa1170050:five_prime_UTR 20.0%
!! GAGTAATATTGTAGAAAAAA+AGG + chr7_4:63151806-63151825 None:intergenic 20.0%
!!! TTTTTAAATTTTAGGTGGAT+CGG - chr7_4:63151994-63152013 Msa1170050:intron 20.0%
!! TTATTTCGTATAAAAGATCA+AGG - chr7_4:63152237-63152256 Msa1170050:five_prime_UTR 20.0%
!! TATTTCGTATAAAAGATCAA+GGG - chr7_4:63152238-63152257 Msa1170050:five_prime_UTR 20.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr7_4:63151475-63151494 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr7_4:63151476-63151495 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr7_4:63151507-63151526 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr7_4:63151508-63151527 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr7_4:63151634-63151653 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr7_4:63151722-63151741 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr7_4:63152034-63152053 Msa1170050:CDS 25.0%
! AGGAAATGAAAAAAGAAGAA+GGG + chr7_4:63151475-63151494 None:intergenic 25.0%
! AAGGAAATGAAAAAAGAAGA+AGG + chr7_4:63151476-63151495 None:intergenic 25.0%
! AGATCATTGTGTGATTTATA+GGG + chr7_4:63151507-63151526 None:intergenic 25.0%
! AAGATCATTGTGTGATTTAT+AGG + chr7_4:63151508-63151527 None:intergenic 25.0%
! AAGAAAGAGAAAGAAACAAT+TGG + chr7_4:63151634-63151653 None:intergenic 25.0%
! TATAAAATTTATGAGAGTGG+TGG + chr7_4:63151722-63151741 None:intergenic 25.0%
! ATTTATGAGATCGATTATAG+AGG - chr7_4:63152034-63152053 Msa1170050:CDS 25.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr7_4:63151466-63151485 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr7_4:63151474-63151493 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr7_4:63151584-63151603 Msa1170050:CDS 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr7_4:63151668-63151687 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG + chr7_4:63151693-63151712 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr7_4:63151832-63151851 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG - chr7_4:63151935-63151954 Msa1170050:intron 30.0%
CTTTCTCTTGTAAATAGGAT+CGG - chr7_4:63151940-63151959 Msa1170050:intron 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr7_4:63151964-63151983 Msa1170050:intron 30.0%
!! AAAACTTGCCTTTTGTTTCA+TGG + chr7_4:63152173-63152192 None:intergenic 30.0%
! AAAAAGAAGAAGGGGTTTTA+AGG + chr7_4:63151466-63151485 None:intergenic 30.0%
GGAAATGAAAAAAGAAGAAG+GGG + chr7_4:63151474-63151493 None:intergenic 30.0%
AAATTTGTGCATGTCATACA+TGG - chr7_4:63151584-63151603 Msa1170050:CDS 30.0%
! ACAAACCTCTAGAGAAATAT+GGG + chr7_4:63151668-63151687 None:intergenic 30.0%
GAAAGAGGGTTTGTAAAATT+CGG + chr7_4:63151693-63151712 None:intergenic 30.0%
TTGTCTATTGTAAATAGGAC+CGG + chr7_4:63151832-63151851 None:intergenic 30.0%
GTCAACTTTCTCTTGTAAAT+AGG - chr7_4:63151935-63151954 Msa1170050:intron 30.0%
CTTTCTCTTGTAAATAGGAT+CGG - chr7_4:63151940-63151959 Msa1170050:intron 30.0%
!! GGGAGTATTAATTTGTTTCT+TGG - chr7_4:63151964-63151983 Msa1170050:intron 30.0%
!! AAAACTTGCCTTTTGTTTCA+TGG + chr7_4:63152173-63152192 None:intergenic 30.0%
TTCACGGAAGAAACATAACA+TGG + chr7_4:63151421-63151440 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr7_4:63151437-63151456 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr7_4:63151495-63151514 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr7_4:63151504-63151523 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr7_4:63151579-63151598 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr7_4:63151580-63151599 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr7_4:63151669-63151688 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr7_4:63151715-63151734 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr7_4:63151810-63151829 Msa1170050:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr7_4:63152162-63152181 Msa1170050:five_prime_UTR 35.0%
CAACTACTCATTATCATCAC+AGG - chr7_4:63152202-63152221 Msa1170050:five_prime_UTR 35.0%
TCATTATCATCACAGGATCT+AGG - chr7_4:63152209-63152228 Msa1170050:five_prime_UTR 35.0%
TTCACGGAAGAAACATAACA+TGG + chr7_4:63151421-63151440 None:intergenic 35.0%
GACTAATGTATGCAAGTTCA+CGG + chr7_4:63151437-63151456 None:intergenic 35.0%
GATTTATAGGGTGGAAAGAA+AGG + chr7_4:63151495-63151514 None:intergenic 35.0%
TCATTGTGTGATTTATAGGG+TGG + chr7_4:63151504-63151523 None:intergenic 35.0%
GACATGCACAAATTTCTTGA+GGG + chr7_4:63151579-63151598 None:intergenic 35.0%
TGACATGCACAAATTTCTTG+AGG + chr7_4:63151580-63151599 None:intergenic 35.0%
! GACAAACCTCTAGAGAAATA+TGG + chr7_4:63151669-63151688 None:intergenic 35.0%
! TTTATGAGAGTGGTGGAAAT+TGG + chr7_4:63151715-63151734 None:intergenic 35.0%
TTCTACAATATTACTCCCTC+CGG - chr7_4:63151810-63151829 Msa1170050:intron 35.0%
TGATGCTACCATGAAACAAA+AGG - chr7_4:63152162-63152181 Msa1170050:five_prime_UTR 35.0%
CAACTACTCATTATCATCAC+AGG - chr7_4:63152202-63152221 Msa1170050:five_prime_UTR 35.0%
TCATTATCATCACAGGATCT+AGG - chr7_4:63152209-63152228 Msa1170050:five_prime_UTR 35.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr7_4:63151460-63151479 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr7_4:63151622-63151641 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr7_4:63151660-63151679 Msa1170050:CDS 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG + chr7_4:63151707-63151726 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr7_4:63151828-63151847 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr7_4:63151829-63151848 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr7_4:63151943-63151962 Msa1170050:intron 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr7_4:63151944-63151963 Msa1170050:intron 40.0%
!!! AAGAAGGGGTTTTAAGGAGT+GGG + chr7_4:63151460-63151479 None:intergenic 40.0%
GAAACAATTGGCGATGAAGA+TGG + chr7_4:63151622-63151641 None:intergenic 40.0%
ACTCTCCCATATTTCTCTAG+AGG - chr7_4:63151660-63151679 Msa1170050:CDS 40.0%
! AGTGGTGGAAATTGGAAAGA+GGG + chr7_4:63151707-63151726 None:intergenic 40.0%
CTATTGTAAATAGGACCGGA+GGG + chr7_4:63151828-63151847 None:intergenic 40.0%
TCTATTGTAAATAGGACCGG+AGG + chr7_4:63151829-63151848 None:intergenic 40.0%
TCTCTTGTAAATAGGATCGG+AGG - chr7_4:63151943-63151962 Msa1170050:intron 40.0%
CTCTTGTAAATAGGATCGGA+GGG - chr7_4:63151944-63151963 Msa1170050:intron 40.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr7_4:63151459-63151478 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr7_4:63151461-63151480 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr7_4:63151618-63151637 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr7_4:63151619-63151638 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG + chr7_4:63151708-63151727 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr7_4:63152003-63152022 Msa1170050:intron 45.0%
TTACCATGGGAATGATCAGG+TGG + chr7_4:63152085-63152104 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr7_4:63152098-63152117 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr7_4:63152109-63152128 None:intergenic 45.0%
!!! AGAAGGGGTTTTAAGGAGTG+GGG + chr7_4:63151459-63151478 None:intergenic 45.0%
!!! GAAGAAGGGGTTTTAAGGAG+TGG + chr7_4:63151461-63151480 None:intergenic 45.0%
CAATTGGCGATGAAGATGGA+GGG + chr7_4:63151618-63151637 None:intergenic 45.0%
ACAATTGGCGATGAAGATGG+AGG + chr7_4:63151619-63151638 None:intergenic 45.0%
! GAGTGGTGGAAATTGGAAAG+AGG + chr7_4:63151708-63151727 None:intergenic 45.0%
! TTTAGGTGGATCGGAAGCAT+TGG - chr7_4:63152003-63152022 Msa1170050:intron 45.0%
TTACCATGGGAATGATCAGG+TGG + chr7_4:63152085-63152104 None:intergenic 45.0%
AGCTGAATGAGGCTTACCAT+GGG + chr7_4:63152098-63152117 None:intergenic 45.0%
CTCTTGTCATGAGCTGAATG+AGG + chr7_4:63152109-63152128 None:intergenic 45.0%
GGCTTACCATGGGAATGATC+AGG + chr7_4:63152088-63152107 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr7_4:63152099-63152118 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr7_4:63152135-63152154 Msa1170050:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr7_4:63152149-63152168 None:intergenic 50.0%
GGCTTACCATGGGAATGATC+AGG + chr7_4:63152088-63152107 None:intergenic 50.0%
GAGCTGAATGAGGCTTACCA+TGG + chr7_4:63152099-63152118 None:intergenic 50.0%
TGCAGCTGCAACCAAAGCTA+CGG - chr7_4:63152135-63152154 Msa1170050:five_prime_UTR 50.0%
AGCATCAACACCCGTAGCTT+TGG + chr7_4:63152149-63152168 None:intergenic 50.0%
GGCACAAACGAGTGAGTCTC+AGG + chr7_4:63152061-63152080 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr7_4:63152082-63152101 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr7_4:63152079-63152098 Msa1170050:CDS 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr7_4:63152136-63152155 Msa1170050:five_prime_UTR 55.0%
GGCACAAACGAGTGAGTCTC+AGG + chr7_4:63152061-63152080 None:intergenic 55.0%
CCATGGGAATGATCAGGTGG+AGG + chr7_4:63152082-63152101 None:intergenic 55.0%
CCTCCACCTGATCATTCCCA+TGG - chr7_4:63152079-63152098 Msa1170050:CDS 55.0%
GCAGCTGCAACCAAAGCTAC+GGG - chr7_4:63152136-63152155 Msa1170050:five_prime_UTR 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 63151413 63152284 63151413 ID=Msa1170050;Name=Msa1170050
chr7_4 mRNA 63151413 63152284 63151413 ID=Msa1170050-mRNA-1;Parent=Msa1170050;Name=Msa1170050-mRNA-1;_AED=0.00;_eAED=0.00;_QI=181|1|1|1|1|1|2|35|109
chr7_4 exon 63151413 63151689 63151413 ID=Msa1170050-mRNA-1:exon:20153;Parent=Msa1170050-mRNA-1
chr7_4 exon 63152016 63152284 63152016 ID=Msa1170050-mRNA-1:exon:20152;Parent=Msa1170050-mRNA-1
chr7_4 five_prime_UTR 63152104 63152284 63152104 ID=Msa1170050-mRNA-1:five_prime_utr;Parent=Msa1170050-mRNA-1
chr7_4 CDS 63152016 63152103 63152016 ID=Msa1170050-mRNA-1:cds;Parent=Msa1170050-mRNA-1
chr7_4 CDS 63151448 63151689 63151448 ID=Msa1170050-mRNA-1:cds;Parent=Msa1170050-mRNA-1
chr7_4 three_prime_UTR 63151413 63151447 63151413 ID=Msa1170050-mRNA-1:three_prime_utr;Parent=Msa1170050-mRNA-1
Gene Sequence

>Msa1170050

ATGTCATACATGGATCTAAGACCCTCCATCTTCATCGCCAATTGTTTCTTTCTCTTTCTTATACTCACTCTCCCATATTTCTCTAGAGGTGGATCGGAAGCATTGGATTCAGAAATTTATGAGATCGATTATAGAGGTCCTGAGACTCACTCGTTTGTGCCTCCACCTGATCATTCCCATGGTAAGCCTCATTCAGCTCATGACAAGAGCTCTACTGCAGCTGCAACCAAAGCTACGGGTGTTGATGCTACCATGAAACAAAAGGCAAGTTTTGAATTAAATCAACTACTCATTATCATCACAGGATCTAGGAAATTTTATTTCGTATAA

Protein sequence

>Msa1170050

MSYMDLRPSIFIANCFFLFLILTLPYFSRGGSEALDSEIYEIDYRGPETHSFVPPPDHSHGKPHSAHDKSSTAAATKATGVDATMKQKASFELNQLLIIITGSRKFYFV*