AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1355040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1355040 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1355040 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1355040 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1355040 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1355040 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1355040 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1355040 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
Msa1355040 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1355040 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 tig0014543:+696906 Msa1355040:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0014543:-697168 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0014543:-696872 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0014543:+696823 Msa1355040:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0014543:+696771 Msa1355040:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0014543:+696864 Msa1355040:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0014543:-696871 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0014543:+697226 Msa1355040:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0014543:-696939 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0014543:-697174 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0014543:-696829 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0014543:+696780 Msa1355040:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0014543:-697157 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0014543:+697227 Msa1355040:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0014543:+696755 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0014543:+696885 Msa1355040:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0014543:-696934 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0014543:-696933 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0014543:+696884 Msa1355040:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0014543:+696868 Msa1355040:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0014543:-696935 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0014543:-697235 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0014543:+696762 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0014543:+696863 Msa1355040:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0014543:-696867 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0014543:-696868 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0014543:+697228 Msa1355040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + tig0014543:697016-697035 Msa1355040:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - tig0014543:697206-697225 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - tig0014543:697207-697226 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - tig0014543:696965-696984 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + tig0014543:697019-697038 Msa1355040:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - tig0014543:697120-697139 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + tig0014543:696823-696842 Msa1355040:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - tig0014543:696832-696851 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - tig0014543:696942-696961 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + tig0014543:696966-696985 Msa1355040:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - tig0014543:696992-697011 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - tig0014543:697071-697090 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + tig0014543:696906-696925 Msa1355040:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - tig0014543:696937-696956 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - tig0014543:696938-696957 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + tig0014543:696948-696967 Msa1355040:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - tig0014543:696978-696997 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - tig0014543:697066-697085 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + tig0014543:697066-697085 Msa1355040:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - tig0014543:697072-697091 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + tig0014543:697070-697089 Msa1355040:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - tig0014543:697160-697179 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - tig0014543:697171-697190 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - tig0014543:697177-697196 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + tig0014543:696863-696882 Msa1355040:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - tig0014543:696874-696893 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - tig0014543:696875-696894 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - tig0014543:696936-696955 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + tig0014543:696983-697002 Msa1355040:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - tig0014543:697047-697066 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - tig0014543:697054-697073 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + tig0014543:697110-697129 Msa1355040:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - tig0014543:697116-697135 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - tig0014543:697117-697136 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - tig0014543:697238-697257 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + tig0014543:696864-696883 Msa1355040:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + tig0014543:696884-696903 Msa1355040:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + tig0014543:696885-696904 Msa1355040:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + tig0014543:697039-697058 Msa1355040:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + tig0014543:697109-697128 Msa1355040:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + tig0014543:697226-697245 Msa1355040:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + tig0014543:697227-697246 Msa1355040:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + tig0014543:697228-697247 Msa1355040:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - tig0014543:696870-696889 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + tig0014543:697080-697099 Msa1355040:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + tig0014543:696771-696790 Msa1355040:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - tig0014543:696871-696890 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + tig0014543:696868-696887 Msa1355040:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + tig0014543:697088-697107 Msa1355040:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + tig0014543:696780-696799 Msa1355040:exon 60.0%
Chromosome Type Strat End Strand Name
tig0014543 gene 696769 697302 696769 ID=Msa1355040;Name=Msa1355040
tig0014543 mRNA 696769 697302 696769 ID=Msa1355040-mRNA-1;Parent=Msa1355040;Name=Msa1355040-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0014543 exon 696769 696946 696769 ID=Msa1355040-mRNA-1:exon:9318;Parent=Msa1355040-mRNA-1
tig0014543 exon 697152 697302 697152 ID=Msa1355040-mRNA-1:exon:9319;Parent=Msa1355040-mRNA-1
tig0014543 five_prime_UTR 696769 696785 696769 ID=Msa1355040-mRNA-1:five_prime_utr;Parent=Msa1355040-mRNA-1
tig0014543 CDS 696786 696946 696786 ID=Msa1355040-mRNA-1:cds;Parent=Msa1355040-mRNA-1
tig0014543 CDS 697152 697302 697152 ID=Msa1355040-mRNA-1:cds;Parent=Msa1355040-mRNA-1
Gene Sequence

>Msa1355040

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1355040

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN