AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0111510


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0111510 MtrunA17_Chr1g0169741 88.172 93 9 1 1 91 110 202 9.09e-55 168
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0111510 AT4G13720.2 75.000 92 21 1 1 90 122 213 1.06e-44 143
Msa0111510 AT4G13720.1 75.000 92 21 1 1 90 109 200 1.59e-44 142

Find 10 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCAAGAGGACCCAATGATTT+TGG 0.178011 1_3:+25345278 Msa0111510:CDS
AAATCATTGGGTCCTCTTGC+AGG 0.318605 1_3:-25345275 None:intergenic
GGGATCCCATCCAAAATCAT+TGG 0.403416 1_3:-25345288 None:intergenic
ATCTTTAGTTCATAGCCATC+AGG 0.438044 1_3:-25345320 None:intergenic
AGGTCTCAACAATCTGTTGA+TGG 0.476377 1_3:+25344844 None:intergenic
GGATCCCATCCAAAATCATT+GGG 0.509802 1_3:-25345287 None:intergenic
ACGCATCTTTCAGATTTGAA+AGG 0.571486 1_3:-25345490 None:intergenic
GGGAAGATTGTTCCTGCAAG+AGG 0.597623 1_3:+25345263 Msa0111510:CDS
ACTGTCTGAACCAATTGCAA+AGG 0.625537 1_3:-25344906 None:intergenic
CAAGTGCAAGAGATTTGCAG+CGG 0.688996 1_3:-25345437 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TATGCATACATAATTGTTTT+TGG - chr1_3:25344990-25345009 None:intergenic 20.0%
!! ATTTACATGTTAATATTGTG+AGG + chr1_3:25345021-25345040 Msa0111510:intron 20.0%
!!! TCAATGAGTAAATTTTATGA+CGG + chr1_3:25345049-25345068 Msa0111510:intron 20.0%
!! TAAAAGTCAGGTTAAATATA+AGG - chr1_3:25345203-25345222 None:intergenic 20.0%
!!! AATTTTGTTCTTTTCTTCTT+TGG - chr1_3:25345412-25345431 None:intergenic 20.0%
! AACAGAACTCAGATTAAAAA+CGG - chr1_3:25344965-25344984 None:intergenic 25.0%
!! AGAATAACACGTTTTTACAA+GGG - chr1_3:25345098-25345117 None:intergenic 25.0%
!! AAGAATAACACGTTTTTACA+AGG - chr1_3:25345099-25345118 None:intergenic 25.0%
!! TAACTCATTTTATGCTTGTA+TGG + chr1_3:25345237-25345256 Msa0111510:intron 25.0%
! TGTGTATTTTCCTTTGCAAT+TGG + chr1_3:25344896-25344915 Msa0111510:CDS 30.0%
! GTTTTTCCTGAAAATGTGAT+AGG - chr1_3:25344935-25344954 None:intergenic 30.0%
TGCGTTAAAGATGAAATAGT+TGG + chr1_3:25345136-25345155 Msa0111510:intron 30.0%
! TCATTTTATGCTTGTATGGT+AGG + chr1_3:25345241-25345260 Msa0111510:intron 30.0%
! CATTTTATGCTTGTATGGTA+GGG + chr1_3:25345242-25345261 Msa0111510:intron 30.0%
! ATTTTATGCTTGTATGGTAG+GGG + chr1_3:25345243-25345262 Msa0111510:intron 30.0%
TTAGCTCATGCAAATAACTA+TGG - chr1_3:25345350-25345369 None:intergenic 30.0%
ACAATTGTAGTTATGCATAG+AGG + chr1_3:25345385-25345404 Msa0111510:intron 30.0%
! AGTGAACCTATCACATTTTC+AGG + chr1_3:25344926-25344945 Msa0111510:CDS 35.0%
!! CACATTTTCAGGAAAAACAC+TGG + chr1_3:25344937-25344956 Msa0111510:CDS 35.0%
TCATCTTTAACGCACTAGTT+TGG - chr1_3:25345130-25345149 None:intergenic 35.0%
CATCACTCATCATAAAAGTC+AGG - chr1_3:25345215-25345234 None:intergenic 35.0%
!! TAGCCATCAGGTTGAAAAAT+GGG - chr1_3:25345311-25345330 None:intergenic 35.0%
!! ATAGCCATCAGGTTGAAAAA+TGG - chr1_3:25345312-25345331 None:intergenic 35.0%
! ATCTTTAGTTCATAGCCATC+AGG - chr1_3:25345323-25345342 None:intergenic 35.0%
! AAATCACATTTTGCTGAAGC+TGG + chr1_3:25345462-25345481 Msa0111510:CDS 35.0%
ACTGTCTGAACCAATTGCAA+AGG - chr1_3:25344909-25344928 None:intergenic 40.0%
! TTTAACGCACTAGTTTGGTC+AGG - chr1_3:25345125-25345144 None:intergenic 40.0%
TGGCACGTCTGTAAAACAAT+AGG + chr1_3:25345156-25345175 Msa0111510:intron 40.0%
! AGGACCCAATGATTTTGGAT+GGG + chr1_3:25345283-25345302 Msa0111510:CDS 40.0%
GGATCCCATCCAAAATCATT+GGG - chr1_3:25345290-25345309 None:intergenic 40.0%
!! GATCCCATTTTTCAACCTGA+TGG + chr1_3:25345305-25345324 Msa0111510:CDS 40.0%
AAATCATTGGGTCCTCTTGC+AGG - chr1_3:25345278-25345297 None:intergenic 45.0%
! GCAAGAGGACCCAATGATTT+TGG + chr1_3:25345278-25345297 Msa0111510:CDS 45.0%
! GAGGACCCAATGATTTTGGA+TGG + chr1_3:25345282-25345301 Msa0111510:CDS 45.0%
GGGATCCCATCCAAAATCAT+TGG - chr1_3:25345291-25345310 None:intergenic 45.0%
CAAGTGCAAGAGATTTGCAG+CGG - chr1_3:25345440-25345459 None:intergenic 45.0%
GGGAAGATTGTTCCTGCAAG+AGG + chr1_3:25345263-25345282 Msa0111510:CDS 50.0%
Chromosome Type Strat End Strand Name
chr1_3 gene 25344846 25345500 25344846 ID=Msa0111510;Name=Msa0111510
chr1_3 mRNA 25344846 25345500 25344846 ID=Msa0111510-mRNA-1;Parent=Msa0111510;Name=Msa0111510-mRNA-1;_AED=0.16;_eAED=0.21;_QI=17|0|0|1|0.5|0.33|3|0|91
chr1_3 exon 25344846 25344958 25344846 ID=Msa0111510-mRNA-1:exon:8683;Parent=Msa0111510-mRNA-1
chr1_3 exon 25345263 25345343 25345263 ID=Msa0111510-mRNA-1:exon:8684;Parent=Msa0111510-mRNA-1
chr1_3 exon 25345405 25345500 25345405 ID=Msa0111510-mRNA-1:exon:8685;Parent=Msa0111510-mRNA-1
chr1_3 five_prime_UTR 25344846 25344862 25344846 ID=Msa0111510-mRNA-1:five_prime_utr;Parent=Msa0111510-mRNA-1
chr1_3 CDS 25344863 25344958 25344863 ID=Msa0111510-mRNA-1:cds;Parent=Msa0111510-mRNA-1
chr1_3 CDS 25345263 25345343 25345263 ID=Msa0111510-mRNA-1:cds;Parent=Msa0111510-mRNA-1
chr1_3 CDS 25345405 25345500 25345405 ID=Msa0111510-mRNA-1:cds;Parent=Msa0111510-mRNA-1
Gene Sequence

>Msa0111510

ATGGCATATGATGATAAATCAGCTTATGCATTATGTGTATTTTCCTTTGCAATTGGTTCAGACAGTGAACCTATCACATTTTCAGGAAAAACACTGGGGAAGATTGTTCCTGCAAGAGGACCCAATGATTTTGGATGGGATCCCATTTTTCAACCTGATGGCTATGAACTAAAGATTAGGTCCAAAGAAGAAAAGAACAAAATTTCTCACCGCTGCAAATCTCTTGCACTTGTGAAATCACATTTTGCTGAAGCTGGATATACCTTTCAAATC

Protein sequence

>Msa0111510

MAYDDKSAYALCVFSFAIGSDSEPITFSGKTLGKIVPARGPNDFGWDPIFQPDGYELKIRSKEEKNKISHRCKSLALVKSHFAEAGYTFQI