AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268360


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268360 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268360 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268360 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268360 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268360 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268360 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268360 MtrunA17_Chr6g0451331 90.323 31 3 0 24 54 41 71 5.28e-14 61.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268360 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268360 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 27 sgRNAs with CRISPR-Local

Find 50 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 2_2:+70200828 Msa0268360:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:-70201090 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:-70200794 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:+70200745 Msa0268360:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:+70200693 Msa0268360:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:+70200786 Msa0268360:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:-70200793 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:+70201148 Msa0268360:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:-70200861 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:-70201096 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:-70200751 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:+70200702 Msa0268360:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:-70201079 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:+70201149 Msa0268360:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:+70200677 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:+70200807 Msa0268360:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:-70200856 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:-70200855 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:+70200806 Msa0268360:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:+70200790 Msa0268360:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:-70200857 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:-70201157 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:+70200684 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:+70200785 Msa0268360:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:-70200789 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:-70200790 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:+70201150 Msa0268360:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr2_2:70200938-70200957 Msa0268360:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr2_2:70201128-70201147 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr2_2:70201129-70201148 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr2_2:70200887-70200906 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr2_2:70200941-70200960 Msa0268360:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr2_2:70201042-70201061 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr2_2:70200745-70200764 Msa0268360:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr2_2:70200754-70200773 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr2_2:70200864-70200883 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr2_2:70200888-70200907 Msa0268360:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr2_2:70200914-70200933 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr2_2:70200993-70201012 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr2_2:70200828-70200847 Msa0268360:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr2_2:70200859-70200878 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr2_2:70200860-70200879 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr2_2:70200870-70200889 Msa0268360:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr2_2:70200900-70200919 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr2_2:70200988-70201007 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr2_2:70200988-70201007 Msa0268360:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr2_2:70200994-70201013 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr2_2:70200992-70201011 Msa0268360:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr2_2:70201082-70201101 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr2_2:70201093-70201112 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr2_2:70201099-70201118 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr2_2:70200785-70200804 Msa0268360:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr2_2:70200796-70200815 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr2_2:70200797-70200816 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr2_2:70200858-70200877 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr2_2:70200905-70200924 Msa0268360:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr2_2:70200969-70200988 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr2_2:70200976-70200995 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr2_2:70201032-70201051 Msa0268360:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr2_2:70201038-70201057 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr2_2:70201039-70201058 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr2_2:70201160-70201179 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr2_2:70200786-70200805 Msa0268360:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr2_2:70200806-70200825 Msa0268360:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr2_2:70200807-70200826 Msa0268360:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr2_2:70200961-70200980 Msa0268360:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr2_2:70201031-70201050 Msa0268360:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr2_2:70201148-70201167 Msa0268360:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr2_2:70201149-70201168 Msa0268360:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr2_2:70201150-70201169 Msa0268360:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr2_2:70200792-70200811 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr2_2:70201002-70201021 Msa0268360:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr2_2:70200693-70200712 Msa0268360:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr2_2:70200793-70200812 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr2_2:70200790-70200809 Msa0268360:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr2_2:70201010-70201029 Msa0268360:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr2_2:70200702-70200721 Msa0268360:exon 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70200691 70201224 70200691 ID=Msa0268360;Name=Msa0268360
chr2_2 mRNA 70200691 70201224 70200691 ID=Msa0268360-mRNA-1;Parent=Msa0268360;Name=Msa0268360-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70200691 70200868 70200691 ID=Msa0268360-mRNA-1:exon:22544;Parent=Msa0268360-mRNA-1
chr2_2 exon 70201074 70201224 70201074 ID=Msa0268360-mRNA-1:exon:22545;Parent=Msa0268360-mRNA-1
chr2_2 five_prime_UTR 70200691 70200707 70200691 ID=Msa0268360-mRNA-1:five_prime_utr;Parent=Msa0268360-mRNA-1
chr2_2 CDS 70200708 70200868 70200708 ID=Msa0268360-mRNA-1:cds;Parent=Msa0268360-mRNA-1
chr2_2 CDS 70201074 70201224 70201074 ID=Msa0268360-mRNA-1:cds;Parent=Msa0268360-mRNA-1
Gene Sequence

>Msa0268360

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268360

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN