AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0931000


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931000 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931000 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931000 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931000 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0931000 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0931000 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0931000 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
Msa0931000 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0931000 ATCG00560.1 97.297 37 1 0 68 104 2 38 3.75e-19 73.9

Find 25 sgRNAs with CRISPR-Local

Find 48 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTTAGCTTACGATGTATT+TGG 0.244623 6_2:+80145593 Msa0931000:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 6_2:-80145855 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 6_2:-80145559 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 6_2:+80145510 Msa0931000:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 6_2:+80145458 Msa0931000:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 6_2:+80145551 Msa0931000:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 6_2:-80145558 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 6_2:+80145913 Msa0931000:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 6_2:-80145626 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 6_2:-80145861 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 6_2:-80145516 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 6_2:+80145467 Msa0931000:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 6_2:-80145844 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 6_2:+80145914 Msa0931000:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 6_2:+80145442 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 6_2:+80145572 Msa0931000:CDS
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 6_2:+80145571 Msa0931000:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 6_2:+80145555 Msa0931000:CDS
GTAAAATACTCGTTTGGACG+AGG 0.550593 6_2:-80145620 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 6_2:-80145922 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 6_2:+80145449 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 6_2:+80145550 Msa0931000:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 6_2:-80145554 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 6_2:-80145555 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 6_2:+80145915 Msa0931000:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr6_2:80145703-80145722 Msa0931000:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr6_2:80145893-80145912 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr6_2:80145894-80145913 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr6_2:80145652-80145671 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr6_2:80145706-80145725 Msa0931000:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr6_2:80145807-80145826 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr6_2:80145510-80145529 Msa0931000:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr6_2:80145519-80145538 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr6_2:80145629-80145648 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr6_2:80145653-80145672 Msa0931000:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr6_2:80145679-80145698 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr6_2:80145758-80145777 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr6_2:80145593-80145612 Msa0931000:CDS 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr6_2:80145635-80145654 Msa0931000:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr6_2:80145665-80145684 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr6_2:80145753-80145772 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr6_2:80145753-80145772 Msa0931000:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr6_2:80145759-80145778 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr6_2:80145757-80145776 Msa0931000:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr6_2:80145847-80145866 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr6_2:80145858-80145877 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr6_2:80145864-80145883 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr6_2:80145550-80145569 Msa0931000:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr6_2:80145561-80145580 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr6_2:80145562-80145581 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+AGG - chr6_2:80145623-80145642 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr6_2:80145670-80145689 Msa0931000:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr6_2:80145734-80145753 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr6_2:80145741-80145760 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr6_2:80145797-80145816 Msa0931000:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr6_2:80145803-80145822 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr6_2:80145804-80145823 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr6_2:80145925-80145944 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr6_2:80145551-80145570 Msa0931000:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr6_2:80145571-80145590 Msa0931000:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr6_2:80145572-80145591 Msa0931000:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr6_2:80145726-80145745 Msa0931000:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr6_2:80145796-80145815 Msa0931000:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr6_2:80145913-80145932 Msa0931000:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr6_2:80145914-80145933 Msa0931000:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr6_2:80145915-80145934 Msa0931000:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr6_2:80145557-80145576 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr6_2:80145767-80145786 Msa0931000:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr6_2:80145458-80145477 Msa0931000:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr6_2:80145558-80145577 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr6_2:80145555-80145574 Msa0931000:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr6_2:80145775-80145794 Msa0931000:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr6_2:80145467-80145486 Msa0931000:exon 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 80145456 80145989 80145456 ID=Msa0931000;Name=Msa0931000
chr6_2 mRNA 80145456 80145989 80145456 ID=Msa0931000-mRNA-1;Parent=Msa0931000;Name=Msa0931000-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr6_2 exon 80145456 80145633 80145456 ID=Msa0931000-mRNA-1:exon:14020;Parent=Msa0931000-mRNA-1
chr6_2 exon 80145839 80145989 80145839 ID=Msa0931000-mRNA-1:exon:14021;Parent=Msa0931000-mRNA-1
chr6_2 five_prime_UTR 80145456 80145472 80145456 ID=Msa0931000-mRNA-1:five_prime_utr;Parent=Msa0931000-mRNA-1
chr6_2 CDS 80145473 80145633 80145473 ID=Msa0931000-mRNA-1:cds;Parent=Msa0931000-mRNA-1
chr6_2 CDS 80145839 80145989 80145839 ID=Msa0931000-mRNA-1:cds;Parent=Msa0931000-mRNA-1
Gene Sequence

>Msa0931000

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCTCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0931000

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN