AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0865280


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0865280 MtrunA17_Chr5g0448271 90.678 118 11 0 1 118 1 118 2.81e-68 201
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0865280 AT4G13500.1 79.487 78 16 0 41 118 48 125 1.20e-40 131
Msa0865280 AT2G05310.1 78.205 78 17 0 41 118 48 125 1.33e-40 131

Find 30 sgRNAs with CRISPR-Local

Find 96 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTTCCTTATATTATCTTATT+TGG 0.144829 5_4:-65947082 Msa0865280:CDS
ATCAAAGTTTGTGCTCAATT+AGG 0.317774 5_4:-65947446 Msa0865280:intron
TTTGTTATTACATACTGTTC+TGG 0.320587 5_4:+65947226 None:intergenic
AGAAGTGCTTACAATAAAAT+TGG 0.324738 5_4:+65946939 None:intergenic
TGTGACCTCATCTATCTAAT+TGG 0.325517 5_4:+65947001 None:intergenic
TGAGAAAGTGAAGGTGAATT+AGG 0.344148 5_4:+65947503 None:intergenic
ATACCAAATAAGATAATATA+AGG 0.355873 5_4:+65947079 None:intergenic
AAATTGTTTATAAATGTTAC+CGG 0.376329 5_4:+65946766 None:intergenic
TACTCGTCCTCTACCGGAAC+TGG 0.385067 5_4:+65946803 None:intergenic
TAAGGAAGTGGCGTCATCAT+TGG 0.409790 5_4:+65947097 None:intergenic
ACACATTACAAGGAAGTGTT+TGG 0.437192 5_4:+65946971 None:intergenic
GCATGTATCATATCCAGTTC+CGG 0.470278 5_4:-65946816 Msa0865280:three_prime_UTR
TTACAAGGAAGTGTTTGGTT+TGG 0.478552 5_4:+65946976 None:intergenic
GAGTAAGAATATACTTTATC+CGG 0.490368 5_4:-65946785 Msa0865280:three_prime_UTR
TCCCCGAAAACTACTTCTCT+TGG 0.492880 5_4:-65947470 Msa0865280:CDS
TGCAGATATTGGCAGTCAGC+AGG 0.493463 5_4:-65947139 Msa0865280:intron
AGAAGATAGAAGAGTTACTT+TGG 0.494989 5_4:+65947553 None:intergenic
GCAATGGCTAAGATTACAAA+AGG 0.495139 5_4:+65947049 None:intergenic
GATAACAAGTGATGAAATGA+TGG 0.507285 5_4:-65947637 None:intergenic
ATCATATCCAGTTCCGGTAG+AGG 0.545395 5_4:-65946810 Msa0865280:three_prime_UTR
TATTCTTACTCGTCCTCTAC+CGG 0.549007 5_4:+65946797 None:intergenic
AATAAGATAATATAAGGAAG+TGG 0.555321 5_4:+65947085 None:intergenic
GAACTGGATATGATACATGC+TGG 0.561899 5_4:+65946819 None:intergenic
TAGAAGAGTTACTTTGGCAA+TGG 0.565993 5_4:+65947559 None:intergenic
CGAGATGAAGAATCCAAGAA+AGG 0.576483 5_4:-65947283 Msa0865280:CDS
CCAACCATTTACAAAAGCAA+TGG 0.600902 5_4:+65947033 None:intergenic
CAGTCAGCAGGAGAGAGAGA+AGG 0.609827 5_4:-65947127 Msa0865280:CDS
AGGTACCAATTAGATAGATG+AGG 0.649220 5_4:-65947006 Msa0865280:exon
GTGAGAATGAACACATTACA+AGG 0.650557 5_4:+65946961 None:intergenic
GCAATGGTGTGAGAAAGTGA+AGG 0.753305 5_4:+65947494 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAAATAAAAATAGATAGA+TGG + chr5_4:65946977-65946996 None:intergenic 10.0%
!! ATTAAATAAAAATAGATAGA+TGG + chr5_4:65946977-65946996 None:intergenic 10.0%
!! ATACCAAATAAGATAATATA+AGG + chr5_4:65947303-65947322 None:intergenic 15.0%
!! AAATTGTTTATAAATGTTAC+CGG + chr5_4:65947616-65947635 None:intergenic 15.0%
!! ATACCAAATAAGATAATATA+AGG + chr5_4:65947303-65947322 None:intergenic 15.0%
!! AAATTGTTTATAAATGTTAC+CGG + chr5_4:65947616-65947635 None:intergenic 15.0%
!!! TTTTGTTGAATTGAATTGAA+TGG + chr5_4:65946792-65946811 None:intergenic 20.0%
!! TATGATTAATATGATTGTGT+TGG - chr5_4:65947052-65947071 Msa0865280:CDS 20.0%
!! TGTTGGTATATATTTGTATT+AGG - chr5_4:65947069-65947088 Msa0865280:CDS 20.0%
!! AATAAGATAATATAAGGAAG+TGG + chr5_4:65947297-65947316 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG - chr5_4:65947297-65947316 Msa0865280:intron 20.0%
!!! TTACTTTTTCACATATGTAA+CGG - chr5_4:65947508-65947527 Msa0865280:CDS 20.0%
!!! TTTTGTTGAATTGAATTGAA+TGG + chr5_4:65946792-65946811 None:intergenic 20.0%
!! TATGATTAATATGATTGTGT+TGG - chr5_4:65947052-65947071 Msa0865280:CDS 20.0%
!! TGTTGGTATATATTTGTATT+AGG - chr5_4:65947069-65947088 Msa0865280:CDS 20.0%
!! AATAAGATAATATAAGGAAG+TGG + chr5_4:65947297-65947316 None:intergenic 20.0%
!! CTTCCTTATATTATCTTATT+TGG - chr5_4:65947297-65947316 Msa0865280:intron 20.0%
!!! TTACTTTTTCACATATGTAA+CGG - chr5_4:65947508-65947527 Msa0865280:CDS 20.0%
! TGGTATATATTTGTATTAGG+TGG - chr5_4:65947072-65947091 Msa0865280:CDS 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG + chr5_4:65947112-65947131 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG + chr5_4:65947156-65947175 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG + chr5_4:65947204-65947223 None:intergenic 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG - chr5_4:65947353-65947372 Msa0865280:intron 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG + chr5_4:65947443-65947462 None:intergenic 25.0%
! GAGTAAGAATATACTTTATC+CGG - chr5_4:65947594-65947613 Msa0865280:five_prime_UTR 25.0%
! TGGTATATATTTGTATTAGG+TGG - chr5_4:65947072-65947091 Msa0865280:CDS 25.0%
!!! TTTCTTTTTTTCTCCTTTCT+TGG + chr5_4:65947112-65947131 None:intergenic 25.0%
!!! TTTGTTATTACATACTGTTC+TGG + chr5_4:65947156-65947175 None:intergenic 25.0%
! CACTTTGATTAGTAAAAACA+TGG + chr5_4:65947204-65947223 None:intergenic 25.0%
!! TTTTGTAAATGGTTGGATTA+AGG - chr5_4:65947353-65947372 Msa0865280:intron 25.0%
!!! AGAAGTGCTTACAATAAAAT+TGG + chr5_4:65947443-65947462 None:intergenic 25.0%
! GAGTAAGAATATACTTTATC+CGG - chr5_4:65947594-65947613 Msa0865280:five_prime_UTR 25.0%
AGAAGATAGAAGAGTTACTT+TGG + chr5_4:65946829-65946848 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+TGG + chr5_4:65946852-65946871 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG + chr5_4:65946859-65946878 None:intergenic 30.0%
! ATACCAAGAGAAGTAGTTTT+CGG + chr5_4:65946915-65946934 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG - chr5_4:65946933-65946952 Msa0865280:three_prime_UTR 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG - chr5_4:65947342-65947361 Msa0865280:intron 30.0%
AGAAGATAGAAGAGTTACTT+TGG + chr5_4:65946829-65946848 None:intergenic 30.0%
!!! AATGAAGTTTTGAAGGTAAG+TGG + chr5_4:65946852-65946871 None:intergenic 30.0%
!! AGGAAGAAATGAAGTTTTGA+AGG + chr5_4:65946859-65946878 None:intergenic 30.0%
! ATACCAAGAGAAGTAGTTTT+CGG + chr5_4:65946915-65946934 None:intergenic 30.0%
ATCAAAGTTTGTGCTCAATT+AGG - chr5_4:65946933-65946952 Msa0865280:three_prime_UTR 30.0%
!! TTAGCCATTGCTTTTGTAAA+TGG - chr5_4:65947342-65947361 Msa0865280:intron 30.0%
! TAGAAGAGTTACTTTGGCAA+TGG + chr5_4:65946823-65946842 None:intergenic 35.0%
TGAGAAAGTGAAGGTGAATT+AGG + chr5_4:65946879-65946898 None:intergenic 35.0%
! TACCAAGAGAAGTAGTTTTC+GGG + chr5_4:65946914-65946933 None:intergenic 35.0%
! TTTTGTGATGCTGCAGATAT+TGG - chr5_4:65947229-65947248 Msa0865280:intron 35.0%
GCAATGGCTAAGATTACAAA+AGG + chr5_4:65947333-65947352 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG + chr5_4:65947349-65947368 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG - chr5_4:65947346-65947365 Msa0865280:intron 35.0%
AGGTACCAATTAGATAGATG+AGG - chr5_4:65947373-65947392 Msa0865280:intron 35.0%
TGTGACCTCATCTATCTAAT+TGG + chr5_4:65947381-65947400 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG + chr5_4:65947406-65947425 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG + chr5_4:65947411-65947430 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG + chr5_4:65947421-65947440 None:intergenic 35.0%
! TAGAAGAGTTACTTTGGCAA+TGG + chr5_4:65946823-65946842 None:intergenic 35.0%
TGAGAAAGTGAAGGTGAATT+AGG + chr5_4:65946879-65946898 None:intergenic 35.0%
! TACCAAGAGAAGTAGTTTTC+GGG + chr5_4:65946914-65946933 None:intergenic 35.0%
! TTTTGTGATGCTGCAGATAT+TGG - chr5_4:65947229-65947248 Msa0865280:intron 35.0%
GCAATGGCTAAGATTACAAA+AGG + chr5_4:65947333-65947352 None:intergenic 35.0%
CCAACCATTTACAAAAGCAA+TGG + chr5_4:65947349-65947368 None:intergenic 35.0%
!! CCATTGCTTTTGTAAATGGT+TGG - chr5_4:65947346-65947365 Msa0865280:intron 35.0%
AGGTACCAATTAGATAGATG+AGG - chr5_4:65947373-65947392 Msa0865280:intron 35.0%
TGTGACCTCATCTATCTAAT+TGG + chr5_4:65947381-65947400 None:intergenic 35.0%
!! TTACAAGGAAGTGTTTGGTT+TGG + chr5_4:65947406-65947425 None:intergenic 35.0%
!! ACACATTACAAGGAAGTGTT+TGG + chr5_4:65947411-65947430 None:intergenic 35.0%
GTGAGAATGAACACATTACA+AGG + chr5_4:65947421-65947440 None:intergenic 35.0%
! ACCAAGAGAAGTAGTTTTCG+GGG + chr5_4:65946913-65946932 None:intergenic 40.0%
CGAGATGAAGAATCCAAGAA+AGG - chr5_4:65947096-65947115 Msa0865280:CDS 40.0%
GAACTGGATATGATACATGC+TGG + chr5_4:65947563-65947582 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG - chr5_4:65947563-65947582 Msa0865280:CDS 40.0%
TATTCTTACTCGTCCTCTAC+CGG + chr5_4:65947585-65947604 None:intergenic 40.0%
! ACCAAGAGAAGTAGTTTTCG+GGG + chr5_4:65946913-65946932 None:intergenic 40.0%
CGAGATGAAGAATCCAAGAA+AGG - chr5_4:65947096-65947115 Msa0865280:CDS 40.0%
GAACTGGATATGATACATGC+TGG + chr5_4:65947563-65947582 None:intergenic 40.0%
GCATGTATCATATCCAGTTC+CGG - chr5_4:65947563-65947582 Msa0865280:CDS 40.0%
TATTCTTACTCGTCCTCTAC+CGG + chr5_4:65947585-65947604 None:intergenic 40.0%
GCAATGGTGTGAGAAAGTGA+AGG + chr5_4:65946888-65946907 None:intergenic 45.0%
!! AAGAGAAGTAGTTTTCGGGG+AGG + chr5_4:65946910-65946929 None:intergenic 45.0%
TCCCCGAAAACTACTTCTCT+TGG - chr5_4:65946909-65946928 Msa0865280:three_prime_UTR 45.0%
TAAGGAAGTGGCGTCATCAT+TGG + chr5_4:65947285-65947304 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG - chr5_4:65947569-65947588 Msa0865280:CDS 45.0%
GCAATGGTGTGAGAAAGTGA+AGG + chr5_4:65946888-65946907 None:intergenic 45.0%
!! AAGAGAAGTAGTTTTCGGGG+AGG + chr5_4:65946910-65946929 None:intergenic 45.0%
TCCCCGAAAACTACTTCTCT+TGG - chr5_4:65946909-65946928 Msa0865280:three_prime_UTR 45.0%
TAAGGAAGTGGCGTCATCAT+TGG + chr5_4:65947285-65947304 None:intergenic 45.0%
ATCATATCCAGTTCCGGTAG+AGG - chr5_4:65947569-65947588 Msa0865280:CDS 45.0%
!! AGTAGTTTTCGGGGAGGCAA+TGG + chr5_4:65946904-65946923 None:intergenic 50.0%
TGCAGATATTGGCAGTCAGC+AGG - chr5_4:65947240-65947259 Msa0865280:intron 50.0%
!! AGTAGTTTTCGGGGAGGCAA+TGG + chr5_4:65946904-65946923 None:intergenic 50.0%
TGCAGATATTGGCAGTCAGC+AGG - chr5_4:65947240-65947259 Msa0865280:intron 50.0%
CAGTCAGCAGGAGAGAGAGA+AGG - chr5_4:65947252-65947271 Msa0865280:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG + chr5_4:65947579-65947598 None:intergenic 55.0%
CAGTCAGCAGGAGAGAGAGA+AGG - chr5_4:65947252-65947271 Msa0865280:CDS 55.0%
TACTCGTCCTCTACCGGAAC+TGG + chr5_4:65947579-65947598 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr5_4 gene 65946756 65947645 65946756 ID=Msa0865280;Name=Msa0865280
chr5_4 mRNA 65946756 65947645 65946756 ID=Msa0865280-mRNA-1;Parent=Msa0865280;Name=Msa0865280-mRNA-1;_AED=0.06;_eAED=0.06;_QI=57|1|1|1|1|1|3|256|118
chr5_4 exon 65946756 65947156 65946756 ID=Msa0865280-mRNA-1:exon:20846;Parent=Msa0865280-mRNA-1
chr5_4 exon 65947241 65947310 65947241 ID=Msa0865280-mRNA-1:exon:20845;Parent=Msa0865280-mRNA-1
chr5_4 exon 65947447 65947645 65947447 ID=Msa0865280-mRNA-1:exon:20844;Parent=Msa0865280-mRNA-1
chr5_4 five_prime_UTR 65947589 65947645 65947589 ID=Msa0865280-mRNA-1:five_prime_utr;Parent=Msa0865280-mRNA-1
chr5_4 CDS 65947447 65947588 65947447 ID=Msa0865280-mRNA-1:cds;Parent=Msa0865280-mRNA-1
chr5_4 CDS 65947241 65947310 65947241 ID=Msa0865280-mRNA-1:cds;Parent=Msa0865280-mRNA-1
chr5_4 CDS 65947012 65947156 65947012 ID=Msa0865280-mRNA-1:cds;Parent=Msa0865280-mRNA-1
chr5_4 three_prime_UTR 65946756 65947011 65946756 ID=Msa0865280-mRNA-1:three_prime_utr;Parent=Msa0865280-mRNA-1
Gene Sequence

>Msa0865280

ATGTCTACCATTGCCAAAGTAACTCTTCTATCTTCTCCACTTACCTTCAAAACTTCATTTCTTCCTAATTCACCTTCACTTTCTCACACCATTGCCTCCCCGAAAACTACTTCTCTTGGTATCAAAGTTTGTGCTCAATTAGGTGGTCGAGATGAAGAATCCAAGAAAGGAGAAAAAAAGAAATTTATAACTAGAGAACAAGAACCAGAACAATATTGGCAGTCAGCAGGAGAGAGAGAAGGAGAGAATCCAATGATGACGCCACTTCCTTATATTATCTTATTTGGTATGTCAACTCCTTTTGTAATCTTAGCCATTGCTTTTGTAAATGGTTGGATTAAGGTACCAATTAGATAG

Protein sequence

>Msa0865280

MSTIAKVTLLSSPLTFKTSFLPNSPSLSHTIASPKTTSLGIKVCAQLGGRDEESKKGEKKKFITREQEPEQYWQSAGEREGENPMMTPLPYIILFGMSTPFVILAIAFVNGWIKVPIR*