AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268520


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268520 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268520 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268520 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268520 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268520 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268520 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268520 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
Msa0268520 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268520 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:+70291487 Msa0268520:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:-70291749 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:-70291453 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:+70291404 Msa0268520:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:+70291352 Msa0268520:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:+70291445 Msa0268520:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:-70291452 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:+70291807 Msa0268520:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:-70291520 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:-70291755 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:-70291410 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:+70291361 Msa0268520:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:-70291738 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:+70291808 Msa0268520:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:+70291336 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:+70291466 Msa0268520:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:-70291515 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:-70291514 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:+70291465 Msa0268520:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:+70291449 Msa0268520:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:-70291516 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:-70291816 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:+70291343 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:+70291444 Msa0268520:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:-70291448 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:-70291449 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:+70291809 Msa0268520:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr2_2:70291597-70291616 Msa0268520:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr2_2:70291787-70291806 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr2_2:70291788-70291807 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr2_2:70291546-70291565 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr2_2:70291600-70291619 Msa0268520:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr2_2:70291701-70291720 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr2_2:70291404-70291423 Msa0268520:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr2_2:70291413-70291432 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr2_2:70291523-70291542 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr2_2:70291547-70291566 Msa0268520:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr2_2:70291573-70291592 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr2_2:70291652-70291671 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr2_2:70291487-70291506 Msa0268520:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr2_2:70291518-70291537 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr2_2:70291519-70291538 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr2_2:70291529-70291548 Msa0268520:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr2_2:70291559-70291578 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr2_2:70291647-70291666 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr2_2:70291647-70291666 Msa0268520:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr2_2:70291653-70291672 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr2_2:70291651-70291670 Msa0268520:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr2_2:70291741-70291760 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr2_2:70291752-70291771 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr2_2:70291758-70291777 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr2_2:70291444-70291463 Msa0268520:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr2_2:70291455-70291474 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr2_2:70291456-70291475 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr2_2:70291517-70291536 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr2_2:70291564-70291583 Msa0268520:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr2_2:70291628-70291647 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr2_2:70291635-70291654 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr2_2:70291691-70291710 Msa0268520:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr2_2:70291697-70291716 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr2_2:70291698-70291717 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr2_2:70291819-70291838 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr2_2:70291445-70291464 Msa0268520:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr2_2:70291465-70291484 Msa0268520:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr2_2:70291466-70291485 Msa0268520:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr2_2:70291620-70291639 Msa0268520:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr2_2:70291690-70291709 Msa0268520:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr2_2:70291807-70291826 Msa0268520:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr2_2:70291808-70291827 Msa0268520:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr2_2:70291809-70291828 Msa0268520:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr2_2:70291451-70291470 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr2_2:70291661-70291680 Msa0268520:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr2_2:70291352-70291371 Msa0268520:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr2_2:70291452-70291471 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr2_2:70291449-70291468 Msa0268520:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr2_2:70291669-70291688 Msa0268520:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr2_2:70291361-70291380 Msa0268520:exon 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70291350 70291883 70291350 ID=Msa0268520;Name=Msa0268520
chr2_2 mRNA 70291350 70291883 70291350 ID=Msa0268520-mRNA-1;Parent=Msa0268520;Name=Msa0268520-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70291350 70291527 70291350 ID=Msa0268520-mRNA-1:exon:22600;Parent=Msa0268520-mRNA-1
chr2_2 exon 70291733 70291883 70291733 ID=Msa0268520-mRNA-1:exon:22601;Parent=Msa0268520-mRNA-1
chr2_2 five_prime_UTR 70291350 70291366 70291350 ID=Msa0268520-mRNA-1:five_prime_utr;Parent=Msa0268520-mRNA-1
chr2_2 CDS 70291367 70291527 70291367 ID=Msa0268520-mRNA-1:cds;Parent=Msa0268520-mRNA-1
chr2_2 CDS 70291733 70291883 70291733 ID=Msa0268520-mRNA-1:cds;Parent=Msa0268520-mRNA-1
Gene Sequence

>Msa0268520

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268520

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN