AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1086310


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1086310 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086310 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086310 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1086310 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1086310 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1086310 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1086310 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
Msa1086310 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1086310 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 7_2:-87312981 Msa1086310:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 7_2:+87312719 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 7_2:+87313015 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 7_2:-87313064 Msa1086310:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 7_2:-87313116 Msa1086310:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 7_2:-87313023 Msa1086310:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 7_2:+87313016 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 7_2:-87312661 Msa1086310:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 7_2:+87312948 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 7_2:+87312713 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 7_2:+87313058 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 7_2:-87313107 Msa1086310:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 7_2:+87312730 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 7_2:-87312660 Msa1086310:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 7_2:-87313132 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 7_2:-87313002 Msa1086310:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 7_2:+87312953 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 7_2:+87312954 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 7_2:-87313003 Msa1086310:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 7_2:-87313019 Msa1086310:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 7_2:+87312952 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 7_2:+87312652 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 7_2:-87313125 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 7_2:-87313024 Msa1086310:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 7_2:+87313020 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 7_2:+87313019 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 7_2:-87312659 Msa1086310:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr7_2:87312854-87312873 Msa1086310:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr7_2:87313044-87313063 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr7_2:87313045-87313064 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr7_2:87312803-87312822 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr7_2:87312857-87312876 Msa1086310:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr7_2:87312958-87312977 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr7_2:87312661-87312680 Msa1086310:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr7_2:87312670-87312689 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr7_2:87312780-87312799 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr7_2:87312804-87312823 Msa1086310:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr7_2:87312830-87312849 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr7_2:87312909-87312928 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr7_2:87312744-87312763 Msa1086310:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr7_2:87312775-87312794 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr7_2:87312776-87312795 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr7_2:87312786-87312805 Msa1086310:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr7_2:87312816-87312835 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr7_2:87312904-87312923 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr7_2:87312904-87312923 Msa1086310:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr7_2:87312910-87312929 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr7_2:87312908-87312927 Msa1086310:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr7_2:87312998-87313017 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr7_2:87313009-87313028 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr7_2:87313015-87313034 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr7_2:87312701-87312720 Msa1086310:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr7_2:87312712-87312731 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr7_2:87312713-87312732 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr7_2:87312774-87312793 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr7_2:87312821-87312840 Msa1086310:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr7_2:87312885-87312904 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr7_2:87312892-87312911 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr7_2:87312948-87312967 Msa1086310:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr7_2:87312954-87312973 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr7_2:87312955-87312974 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr7_2:87313076-87313095 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr7_2:87312702-87312721 Msa1086310:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr7_2:87312722-87312741 Msa1086310:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr7_2:87312723-87312742 Msa1086310:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr7_2:87312877-87312896 Msa1086310:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr7_2:87312947-87312966 Msa1086310:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr7_2:87313064-87313083 Msa1086310:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr7_2:87313065-87313084 Msa1086310:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr7_2:87313066-87313085 Msa1086310:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr7_2:87312708-87312727 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr7_2:87312918-87312937 Msa1086310:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr7_2:87312609-87312628 Msa1086310:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr7_2:87312709-87312728 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr7_2:87312706-87312725 Msa1086310:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr7_2:87312926-87312945 Msa1086310:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr7_2:87312618-87312637 Msa1086310:CDS 60.0%
Chromosome Type Strat End Strand Name
chr7_2 gene 87312607 87313140 87312607 ID=Msa1086310;Name=Msa1086310
chr7_2 mRNA 87312607 87313140 87312607 ID=Msa1086310-mRNA-1;Parent=Msa1086310;Name=Msa1086310-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr7_2 exon 87312963 87313140 87312963 ID=Msa1086310-mRNA-1:exon:23778;Parent=Msa1086310-mRNA-1
chr7_2 exon 87312607 87312757 87312607 ID=Msa1086310-mRNA-1:exon:23777;Parent=Msa1086310-mRNA-1
chr7_2 five_prime_UTR 87313124 87313140 87313124 ID=Msa1086310-mRNA-1:five_prime_utr;Parent=Msa1086310-mRNA-1
chr7_2 CDS 87312963 87313123 87312963 ID=Msa1086310-mRNA-1:cds;Parent=Msa1086310-mRNA-1
chr7_2 CDS 87312607 87312757 87312607 ID=Msa1086310-mRNA-1:cds;Parent=Msa1086310-mRNA-1
Gene Sequence

>Msa1086310

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1086310

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN