AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0357380


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 23 sgRNAs with CRISPR-Local

Find 104 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AATTAAACTTGACCGAACTA+TGG 0.324856 3_1:-39437961 Msa0357380:three_prime_UTR
TGAATTTGAAGTGGACGATT+TGG 0.365773 3_1:-39438047 Msa0357380:three_prime_UTR
CCTCTTGAATTTCATCATCT+AGG 0.384014 3_1:+39438083 None:intergenic
CAAGATAAATTTGAATGAGT+TGG 0.400423 3_1:-39438013 Msa0357380:three_prime_UTR
GTTGGTTCGCGTAGGAATAC+TGG 0.404620 3_1:-39438949 Msa0357380:CDS
TATCAATGAAGATGTTGAAA+AGG 0.471255 3_1:-39438211 Msa0357380:CDS
GCACTTGATCTAGCTTGAAA+AGG 0.475883 3_1:+39438898 None:intergenic
AAAATAACAAAACCATAGTT+CGG 0.496331 3_1:+39437949 None:intergenic
CTATGCTTTAAAATGCAAGA+AGG 0.510840 3_1:-39438979 None:intergenic
GAAATTCTCGAGGGCAACAT+AGG 0.514832 3_1:-39438147 Msa0357380:CDS
AGGATGATATAGATGATAAG+AGG 0.519091 3_1:-39438110 Msa0357380:CDS
ATGCAAGAAGGATTAGATGT+TGG 0.539382 3_1:-39438967 Msa0357380:CDS
CATCGATGATGAATTTGAAG+TGG 0.587100 3_1:-39438056 Msa0357380:three_prime_UTR
GATAGATGAGGAATTGCAAG+AGG 0.601318 3_1:-39438184 Msa0357380:CDS
ACTGGTCAAAGTTCTGCTGA+AGG 0.601331 3_1:-39438931 Msa0357380:CDS
ATAAATTTGAATGAGTTGGA+TGG 0.622667 3_1:-39438009 Msa0357380:three_prime_UTR
GATTAGATGTTGGTTCGCGT+AGG 0.623215 3_1:-39438957 Msa0357380:CDS
CATAGGTGATGAATTTCAAG+AGG 0.627468 3_1:-39438130 Msa0357380:CDS
TGATATAGATGATAAGAGGA+CGG 0.634825 3_1:-39438106 Msa0357380:CDS
CGTAGATGATGAAATTCTCG+AGG 0.645005 3_1:-39438157 Msa0357380:CDS
CCTAGATGATGAAATTCAAG+AGG 0.646389 3_1:-39438083 Msa0357380:exon
TGAAAAGGATGAGATAGATG+AGG 0.656088 3_1:-39438196 Msa0357380:CDS
GTAGATGATGAAATTCTCGA+GGG 0.693006 3_1:-39438156 Msa0357380:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAAAACAAATTTCCTATTTG+CGG - chr3_1:39438463-39438482 Msa0357380:intron 20.0%
!! AAAATAACAAAACCATAGTT+CGG + chr3_1:39438886-39438905 None:intergenic 20.0%
!! TAAAACAAATTTCCTATTTG+CGG - chr3_1:39438463-39438482 Msa0357380:intron 20.0%
!! AAAATAACAAAACCATAGTT+CGG + chr3_1:39438886-39438905 None:intergenic 20.0%
!!! AATTTTGTTTCTGCATTTTG+TGG - chr3_1:39438316-39438335 Msa0357380:intron 25.0%
! AAGTTACGGAAACTTAAATA+TGG - chr3_1:39438407-39438426 Msa0357380:intron 25.0%
! AGTTACGGAAACTTAAATAT+GGG - chr3_1:39438408-39438427 Msa0357380:intron 25.0%
! TGTAATGATAGAATAAGGAA+GGG - chr3_1:39438433-39438452 Msa0357380:intron 25.0%
!!! TTTTGGTTTTTATTTGTGTG+AGG - chr3_1:39438512-39438531 Msa0357380:intron 25.0%
! TATCAATGAAGATGTTGAAA+AGG - chr3_1:39438621-39438640 Msa0357380:intron 25.0%
! CAAGATAAATTTGAATGAGT+TGG - chr3_1:39438819-39438838 Msa0357380:intron 25.0%
!! ATAAATTTGAATGAGTTGGA+TGG - chr3_1:39438823-39438842 Msa0357380:intron 25.0%
!!! TATGGTTTTGTTATTTTGCT+AGG - chr3_1:39438889-39438908 Msa0357380:CDS 25.0%
!!! AATTTTGTTTCTGCATTTTG+TGG - chr3_1:39438316-39438335 Msa0357380:intron 25.0%
! AAGTTACGGAAACTTAAATA+TGG - chr3_1:39438407-39438426 Msa0357380:intron 25.0%
! AGTTACGGAAACTTAAATAT+GGG - chr3_1:39438408-39438427 Msa0357380:intron 25.0%
! TGTAATGATAGAATAAGGAA+GGG - chr3_1:39438433-39438452 Msa0357380:intron 25.0%
!!! TTTTGGTTTTTATTTGTGTG+AGG - chr3_1:39438512-39438531 Msa0357380:intron 25.0%
! TATCAATGAAGATGTTGAAA+AGG - chr3_1:39438621-39438640 Msa0357380:intron 25.0%
! CAAGATAAATTTGAATGAGT+TGG - chr3_1:39438819-39438838 Msa0357380:intron 25.0%
!! ATAAATTTGAATGAGTTGGA+TGG - chr3_1:39438823-39438842 Msa0357380:intron 25.0%
!!! TATGGTTTTGTTATTTTGCT+AGG - chr3_1:39438889-39438908 Msa0357380:CDS 25.0%
! AAGTGCTAAGTTGAAAAAGA+TGG - chr3_1:39437951-39437970 Msa0357380:three_prime_UTR 30.0%
GTGTGAACTTATGATTATGT+TGG - chr3_1:39438229-39438248 Msa0357380:intron 30.0%
GAACTTATGATTATGTTGGT+TGG - chr3_1:39438233-39438252 Msa0357380:intron 30.0%
CTTCCTTATTCTATCATTAC+AGG + chr3_1:39438434-39438453 None:intergenic 30.0%
CTGTAATGATAGAATAAGGA+AGG - chr3_1:39438432-39438451 Msa0357380:intron 30.0%
!!! GTGTGTTTTACTTGTTGTTT+TGG - chr3_1:39438495-39438514 Msa0357380:intron 30.0%
ACATCAACCATAGATATTGT+TGG + chr3_1:39438576-39438595 None:intergenic 30.0%
AGGATGATATAGATGATAAG+AGG - chr3_1:39438722-39438741 Msa0357380:intron 30.0%
TGATATAGATGATAAGAGGA+CGG - chr3_1:39438726-39438745 Msa0357380:intron 30.0%
AATTAAACTTGACCGAACTA+TGG - chr3_1:39438871-39438890 Msa0357380:intron 30.0%
! AAGTGCTAAGTTGAAAAAGA+TGG - chr3_1:39437951-39437970 Msa0357380:three_prime_UTR 30.0%
GTGTGAACTTATGATTATGT+TGG - chr3_1:39438229-39438248 Msa0357380:intron 30.0%
GAACTTATGATTATGTTGGT+TGG - chr3_1:39438233-39438252 Msa0357380:intron 30.0%
CTTCCTTATTCTATCATTAC+AGG + chr3_1:39438434-39438453 None:intergenic 30.0%
CTGTAATGATAGAATAAGGA+AGG - chr3_1:39438432-39438451 Msa0357380:intron 30.0%
!!! GTGTGTTTTACTTGTTGTTT+TGG - chr3_1:39438495-39438514 Msa0357380:intron 30.0%
ACATCAACCATAGATATTGT+TGG + chr3_1:39438576-39438595 None:intergenic 30.0%
AGGATGATATAGATGATAAG+AGG - chr3_1:39438722-39438741 Msa0357380:intron 30.0%
TGATATAGATGATAAGAGGA+CGG - chr3_1:39438726-39438745 Msa0357380:intron 30.0%
AATTAAACTTGACCGAACTA+TGG - chr3_1:39438871-39438890 Msa0357380:intron 30.0%
ATGCAAGAAGGATTAGATGT+TGG - chr3_1:39437865-39437884 Msa0357380:three_prime_UTR 35.0%
ACAACTTCTACAATCTCATG+AGG + chr3_1:39438048-39438067 None:intergenic 35.0%
GAGATTGTAGAAGTTGTAGA+CGG - chr3_1:39438051-39438070 Msa0357380:three_prime_UTR 35.0%
ACACGCAAGTTAACAATTTC+AGG + chr3_1:39438189-39438208 None:intergenic 35.0%
GAATTGTTTAAGTGTGTCCA+AGG - chr3_1:39438258-39438277 Msa0357380:intron 35.0%
ACACAATCAAAATCCAACCT+TGG + chr3_1:39438278-39438297 None:intergenic 35.0%
! TGTTTCTGTGTTGCATAACA+TGG - chr3_1:39438381-39438400 Msa0357380:intron 35.0%
!! CATAGATATTGTTGGTTCAG+AGG + chr3_1:39438568-39438587 None:intergenic 35.0%
CTCTGAACCAACAATATCTA+TGG - chr3_1:39438566-39438585 Msa0357380:intron 35.0%
!! TTTGTTGTTCTTATGCAGCA+AGG - chr3_1:39438598-39438617 Msa0357380:intron 35.0%
TGAAAAGGATGAGATAGATG+AGG - chr3_1:39438636-39438655 Msa0357380:intron 35.0%
GTAGATGATGAAATTCTCGA+GGG - chr3_1:39438676-39438695 Msa0357380:intron 35.0%
CATAGGTGATGAATTTCAAG+AGG - chr3_1:39438702-39438721 Msa0357380:intron 35.0%
CCTCTTGAATTTCATCATCT+AGG + chr3_1:39438752-39438771 None:intergenic 35.0%
CCTAGATGATGAAATTCAAG+AGG - chr3_1:39438749-39438768 Msa0357380:intron 35.0%
CATCGATGATGAATTTGAAG+TGG - chr3_1:39438776-39438795 Msa0357380:intron 35.0%
! TGAATTTGAAGTGGACGATT+TGG - chr3_1:39438785-39438804 Msa0357380:intron 35.0%
ATGCAAGAAGGATTAGATGT+TGG - chr3_1:39437865-39437884 Msa0357380:three_prime_UTR 35.0%
ACAACTTCTACAATCTCATG+AGG + chr3_1:39438048-39438067 None:intergenic 35.0%
GAGATTGTAGAAGTTGTAGA+CGG - chr3_1:39438051-39438070 Msa0357380:three_prime_UTR 35.0%
ACACGCAAGTTAACAATTTC+AGG + chr3_1:39438189-39438208 None:intergenic 35.0%
GAATTGTTTAAGTGTGTCCA+AGG - chr3_1:39438258-39438277 Msa0357380:intron 35.0%
ACACAATCAAAATCCAACCT+TGG + chr3_1:39438278-39438297 None:intergenic 35.0%
! TGTTTCTGTGTTGCATAACA+TGG - chr3_1:39438381-39438400 Msa0357380:intron 35.0%
!! CATAGATATTGTTGGTTCAG+AGG + chr3_1:39438568-39438587 None:intergenic 35.0%
CTCTGAACCAACAATATCTA+TGG - chr3_1:39438566-39438585 Msa0357380:intron 35.0%
!! TTTGTTGTTCTTATGCAGCA+AGG - chr3_1:39438598-39438617 Msa0357380:intron 35.0%
TGAAAAGGATGAGATAGATG+AGG - chr3_1:39438636-39438655 Msa0357380:intron 35.0%
GTAGATGATGAAATTCTCGA+GGG - chr3_1:39438676-39438695 Msa0357380:intron 35.0%
CATAGGTGATGAATTTCAAG+AGG - chr3_1:39438702-39438721 Msa0357380:intron 35.0%
CCTCTTGAATTTCATCATCT+AGG + chr3_1:39438752-39438771 None:intergenic 35.0%
CCTAGATGATGAAATTCAAG+AGG - chr3_1:39438749-39438768 Msa0357380:intron 35.0%
CATCGATGATGAATTTGAAG+TGG - chr3_1:39438776-39438795 Msa0357380:intron 35.0%
! TGAATTTGAAGTGGACGATT+TGG - chr3_1:39438785-39438804 Msa0357380:intron 35.0%
! GCACTTGATCTAGCTTGAAA+AGG + chr3_1:39437937-39437956 None:intergenic 40.0%
TGTTTAAGTGTGTCCAAGGT+TGG - chr3_1:39438262-39438281 Msa0357380:intron 40.0%
GCATAACATGGCACAAGTTA+CGG - chr3_1:39438393-39438412 Msa0357380:intron 40.0%
GGGCCTGTAATGATAGAATA+AGG - chr3_1:39438428-39438447 Msa0357380:intron 40.0%
CACACAACATAACCGCAAAT+AGG + chr3_1:39438478-39438497 None:intergenic 40.0%
GATAGATGAGGAATTGCAAG+AGG - chr3_1:39438648-39438667 Msa0357380:intron 40.0%
CGTAGATGATGAAATTCTCG+AGG - chr3_1:39438675-39438694 Msa0357380:intron 40.0%
! GCACTTGATCTAGCTTGAAA+AGG + chr3_1:39437937-39437956 None:intergenic 40.0%
TGTTTAAGTGTGTCCAAGGT+TGG - chr3_1:39438262-39438281 Msa0357380:intron 40.0%
GCATAACATGGCACAAGTTA+CGG - chr3_1:39438393-39438412 Msa0357380:intron 40.0%
GGGCCTGTAATGATAGAATA+AGG - chr3_1:39438428-39438447 Msa0357380:intron 40.0%
CACACAACATAACCGCAAAT+AGG + chr3_1:39438478-39438497 None:intergenic 40.0%
GATAGATGAGGAATTGCAAG+AGG - chr3_1:39438648-39438667 Msa0357380:intron 40.0%
CGTAGATGATGAAATTCTCG+AGG - chr3_1:39438675-39438694 Msa0357380:intron 40.0%
!! GATTAGATGTTGGTTCGCGT+AGG - chr3_1:39437875-39437894 Msa0357380:three_prime_UTR 45.0%
ACTGGTCAAAGTTCTGCTGA+AGG - chr3_1:39437901-39437920 Msa0357380:three_prime_UTR 45.0%
AAAGTTGCATGAGAAGCTGC+AGG - chr3_1:39438005-39438024 Msa0357380:three_prime_UTR 45.0%
AAGTTGCATGAGAAGCTGCA+GGG - chr3_1:39438006-39438025 Msa0357380:three_prime_UTR 45.0%
!! TGTTGGTTCAGAGGACAATC+AGG + chr3_1:39438559-39438578 None:intergenic 45.0%
GAAATTCTCGAGGGCAACAT+AGG - chr3_1:39438685-39438704 Msa0357380:intron 45.0%
!! GATTAGATGTTGGTTCGCGT+AGG - chr3_1:39437875-39437894 Msa0357380:three_prime_UTR 45.0%
ACTGGTCAAAGTTCTGCTGA+AGG - chr3_1:39437901-39437920 Msa0357380:three_prime_UTR 45.0%
AAAGTTGCATGAGAAGCTGC+AGG - chr3_1:39438005-39438024 Msa0357380:three_prime_UTR 45.0%
AAGTTGCATGAGAAGCTGCA+GGG - chr3_1:39438006-39438025 Msa0357380:three_prime_UTR 45.0%
!! TGTTGGTTCAGAGGACAATC+AGG + chr3_1:39438559-39438578 None:intergenic 45.0%
GAAATTCTCGAGGGCAACAT+AGG - chr3_1:39438685-39438704 Msa0357380:intron 45.0%
!! GTTGGTTCGCGTAGGAATAC+TGG - chr3_1:39437883-39437902 Msa0357380:three_prime_UTR 50.0%
!! GTTGGTTCGCGTAGGAATAC+TGG - chr3_1:39437883-39437902 Msa0357380:three_prime_UTR 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 39437865 39438989 39437865 ID=Msa0357380;Name=Msa0357380
chr3_1 mRNA 39437865 39438989 39437865 ID=Msa0357380-mRNA-1;Parent=Msa0357380;Name=Msa0357380-mRNA-1;_AED=0.33;_eAED=0.35;_QI=0|0|0.5|1|1|1|2|236|81
chr3_1 exon 39437865 39438238 39437865 ID=Msa0357380-mRNA-1:exon:7048;Parent=Msa0357380-mRNA-1
chr3_1 exon 39438882 39438989 39438882 ID=Msa0357380-mRNA-1:exon:7047;Parent=Msa0357380-mRNA-1
chr3_1 CDS 39438882 39438989 39438882 ID=Msa0357380-mRNA-1:cds;Parent=Msa0357380-mRNA-1
chr3_1 CDS 39438101 39438238 39438101 ID=Msa0357380-mRNA-1:cds;Parent=Msa0357380-mRNA-1
chr3_1 three_prime_UTR 39437865 39438100 39437865 ID=Msa0357380-mRNA-1:three_prime_utr;Parent=Msa0357380-mRNA-1
Gene Sequence

>Msa0357380

ATGCAAGAAGGATTAGATGTTGGTTCGCGTAGGAATACTGGTCAAAGTTCTGCTGAAGGATTAGATTTACCTTTTCAAGCTAGATCAAGTGCTAAGTTGAAAAAGATGCAAGGTATCAATGAAGATGTTGAAAAGGATGAGATAGATGAGGAATTGCAAGAGGAAGACGTAGATGATGAAATTCTCGAGGGCAACATAGGTGATGAATTTCAAGAGGATGATATAGATGATAAGAGGACGGCCTAG

Protein sequence

>Msa0357380

MQEGLDVGSRRNTGQSSAEGLDLPFQARSSAKLKKMQGINEDVEKDEIDEELQEEDVDDEILEGNIGDEFQEDDIDDKRTA*