AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268710 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268710 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268710 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268710 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268710 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268710 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268710 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
Msa0268710 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268710 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:+70371603 Msa0268710:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:-70371865 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:-70371569 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:+70371520 Msa0268710:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:+70371468 Msa0268710:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:+70371561 Msa0268710:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:-70371568 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:+70371923 Msa0268710:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:-70371636 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:-70371871 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:-70371526 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:+70371477 Msa0268710:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:-70371854 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:+70371924 Msa0268710:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:+70371452 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:+70371582 Msa0268710:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:-70371631 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:-70371630 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:+70371581 Msa0268710:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:+70371565 Msa0268710:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:-70371632 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:-70371932 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:+70371459 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:+70371560 Msa0268710:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:-70371564 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:-70371565 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:+70371925 Msa0268710:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr2_2:70371713-70371732 Msa0268710:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr2_2:70371903-70371922 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr2_2:70371904-70371923 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr2_2:70371662-70371681 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr2_2:70371716-70371735 Msa0268710:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr2_2:70371817-70371836 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr2_2:70371520-70371539 Msa0268710:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr2_2:70371529-70371548 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr2_2:70371639-70371658 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr2_2:70371663-70371682 Msa0268710:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr2_2:70371689-70371708 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr2_2:70371768-70371787 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr2_2:70371603-70371622 Msa0268710:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr2_2:70371634-70371653 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr2_2:70371635-70371654 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr2_2:70371645-70371664 Msa0268710:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr2_2:70371675-70371694 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr2_2:70371763-70371782 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr2_2:70371763-70371782 Msa0268710:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr2_2:70371769-70371788 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr2_2:70371767-70371786 Msa0268710:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr2_2:70371857-70371876 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr2_2:70371868-70371887 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr2_2:70371874-70371893 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr2_2:70371560-70371579 Msa0268710:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr2_2:70371571-70371590 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr2_2:70371572-70371591 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr2_2:70371633-70371652 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr2_2:70371680-70371699 Msa0268710:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr2_2:70371744-70371763 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr2_2:70371751-70371770 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr2_2:70371807-70371826 Msa0268710:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr2_2:70371813-70371832 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr2_2:70371814-70371833 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr2_2:70371935-70371954 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr2_2:70371561-70371580 Msa0268710:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr2_2:70371581-70371600 Msa0268710:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr2_2:70371582-70371601 Msa0268710:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr2_2:70371736-70371755 Msa0268710:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr2_2:70371806-70371825 Msa0268710:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr2_2:70371923-70371942 Msa0268710:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr2_2:70371924-70371943 Msa0268710:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr2_2:70371925-70371944 Msa0268710:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr2_2:70371567-70371586 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr2_2:70371777-70371796 Msa0268710:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr2_2:70371468-70371487 Msa0268710:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr2_2:70371568-70371587 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr2_2:70371565-70371584 Msa0268710:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr2_2:70371785-70371804 Msa0268710:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr2_2:70371477-70371496 Msa0268710:exon 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70371466 70371999 70371466 ID=Msa0268710;Name=Msa0268710
chr2_2 mRNA 70371466 70371999 70371466 ID=Msa0268710-mRNA-1;Parent=Msa0268710;Name=Msa0268710-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70371466 70371643 70371466 ID=Msa0268710-mRNA-1:exon:22602;Parent=Msa0268710-mRNA-1
chr2_2 exon 70371849 70371999 70371849 ID=Msa0268710-mRNA-1:exon:22603;Parent=Msa0268710-mRNA-1
chr2_2 five_prime_UTR 70371466 70371482 70371466 ID=Msa0268710-mRNA-1:five_prime_utr;Parent=Msa0268710-mRNA-1
chr2_2 CDS 70371483 70371643 70371483 ID=Msa0268710-mRNA-1:cds;Parent=Msa0268710-mRNA-1
chr2_2 CDS 70371849 70371999 70371849 ID=Msa0268710-mRNA-1:cds;Parent=Msa0268710-mRNA-1
Gene Sequence

>Msa0268710

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268710

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN