AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1380560


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1380560 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1380560 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1380560 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa1380560 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa1380560 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa1380560 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa1380560 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
Msa1380560 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa1380560 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 tig0020386:+8762 Msa1380560:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 tig0020386:-9024 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 tig0020386:-8728 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 tig0020386:+8679 Msa1380560:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 tig0020386:+8627 Msa1380560:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 tig0020386:+8720 Msa1380560:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 tig0020386:-8727 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 tig0020386:+9082 Msa1380560:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 tig0020386:-8795 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 tig0020386:-9030 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 tig0020386:-8685 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 tig0020386:+8636 Msa1380560:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 tig0020386:-9013 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 tig0020386:+9083 Msa1380560:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 tig0020386:+8611 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 tig0020386:+8741 Msa1380560:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 tig0020386:-8790 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 tig0020386:-8789 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 tig0020386:+8740 Msa1380560:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 tig0020386:+8724 Msa1380560:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 tig0020386:-8791 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 tig0020386:-9091 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 tig0020386:+8618 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 tig0020386:+8719 Msa1380560:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 tig0020386:-8723 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 tig0020386:-8724 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 tig0020386:+9084 Msa1380560:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + tig0020386:8872-8891 Msa1380560:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - tig0020386:9062-9081 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - tig0020386:9063-9082 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - tig0020386:8821-8840 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + tig0020386:8875-8894 Msa1380560:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - tig0020386:8976-8995 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + tig0020386:8679-8698 Msa1380560:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - tig0020386:8688-8707 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - tig0020386:8798-8817 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + tig0020386:8822-8841 Msa1380560:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - tig0020386:8848-8867 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - tig0020386:8927-8946 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + tig0020386:8762-8781 Msa1380560:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - tig0020386:8793-8812 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - tig0020386:8794-8813 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + tig0020386:8804-8823 Msa1380560:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - tig0020386:8834-8853 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - tig0020386:8922-8941 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + tig0020386:8922-8941 Msa1380560:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - tig0020386:8928-8947 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + tig0020386:8926-8945 Msa1380560:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - tig0020386:9016-9035 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - tig0020386:9027-9046 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - tig0020386:9033-9052 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + tig0020386:8719-8738 Msa1380560:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - tig0020386:8730-8749 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - tig0020386:8731-8750 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - tig0020386:8792-8811 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + tig0020386:8839-8858 Msa1380560:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - tig0020386:8903-8922 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - tig0020386:8910-8929 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + tig0020386:8966-8985 Msa1380560:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - tig0020386:8972-8991 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - tig0020386:8973-8992 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - tig0020386:9094-9113 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + tig0020386:8720-8739 Msa1380560:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + tig0020386:8740-8759 Msa1380560:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + tig0020386:8741-8760 Msa1380560:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + tig0020386:8895-8914 Msa1380560:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + tig0020386:8965-8984 Msa1380560:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + tig0020386:9082-9101 Msa1380560:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + tig0020386:9083-9102 Msa1380560:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + tig0020386:9084-9103 Msa1380560:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - tig0020386:8726-8745 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + tig0020386:8936-8955 Msa1380560:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + tig0020386:8627-8646 Msa1380560:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - tig0020386:8727-8746 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + tig0020386:8724-8743 Msa1380560:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + tig0020386:8944-8963 Msa1380560:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + tig0020386:8636-8655 Msa1380560:exon 60.0%
Chromosome Type Strat End Strand Name
tig0020386 gene 8625 9158 8625 ID=Msa1380560;Name=Msa1380560
tig0020386 mRNA 8625 9158 8625 ID=Msa1380560-mRNA-1;Parent=Msa1380560;Name=Msa1380560-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
tig0020386 exon 8625 8802 8625 ID=Msa1380560-mRNA-1:exon:7200;Parent=Msa1380560-mRNA-1
tig0020386 exon 9008 9158 9008 ID=Msa1380560-mRNA-1:exon:7201;Parent=Msa1380560-mRNA-1
tig0020386 five_prime_UTR 8625 8641 8625 ID=Msa1380560-mRNA-1:five_prime_utr;Parent=Msa1380560-mRNA-1
tig0020386 CDS 8642 8802 8642 ID=Msa1380560-mRNA-1:cds;Parent=Msa1380560-mRNA-1
tig0020386 CDS 9008 9158 9008 ID=Msa1380560-mRNA-1:cds;Parent=Msa1380560-mRNA-1
Gene Sequence

>Msa1380560

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa1380560

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN