AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582600 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582600 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582600 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582600 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0582600 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0582600 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0582600 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
Msa0582600 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0582600 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 4_2:+1103991 Msa0582600:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 4_2:-1104253 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 4_2:-1103957 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 4_2:+1103908 Msa0582600:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 4_2:+1103856 Msa0582600:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 4_2:+1103949 Msa0582600:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 4_2:-1103956 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 4_2:+1104311 Msa0582600:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 4_2:-1104024 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 4_2:-1104259 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 4_2:-1103914 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 4_2:+1103865 Msa0582600:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 4_2:-1104242 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 4_2:+1104312 Msa0582600:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 4_2:+1103840 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 4_2:+1103970 Msa0582600:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 4_2:-1104019 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 4_2:-1104018 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 4_2:+1103969 Msa0582600:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 4_2:+1103953 Msa0582600:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 4_2:-1104020 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 4_2:-1104320 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 4_2:+1103847 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 4_2:+1103948 Msa0582600:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 4_2:-1103952 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 4_2:-1103953 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 4_2:+1104313 Msa0582600:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr4_2:1104101-1104120 Msa0582600:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr4_2:1104291-1104310 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr4_2:1104292-1104311 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr4_2:1104050-1104069 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr4_2:1104104-1104123 Msa0582600:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr4_2:1104205-1104224 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr4_2:1103908-1103927 Msa0582600:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr4_2:1103917-1103936 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr4_2:1104027-1104046 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr4_2:1104051-1104070 Msa0582600:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr4_2:1104077-1104096 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr4_2:1104156-1104175 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr4_2:1103991-1104010 Msa0582600:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr4_2:1104022-1104041 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr4_2:1104023-1104042 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr4_2:1104033-1104052 Msa0582600:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr4_2:1104063-1104082 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr4_2:1104151-1104170 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr4_2:1104151-1104170 Msa0582600:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr4_2:1104157-1104176 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr4_2:1104155-1104174 Msa0582600:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr4_2:1104245-1104264 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr4_2:1104256-1104275 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr4_2:1104262-1104281 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr4_2:1103948-1103967 Msa0582600:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr4_2:1103959-1103978 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr4_2:1103960-1103979 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr4_2:1104021-1104040 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr4_2:1104068-1104087 Msa0582600:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr4_2:1104132-1104151 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr4_2:1104139-1104158 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr4_2:1104195-1104214 Msa0582600:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr4_2:1104201-1104220 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr4_2:1104202-1104221 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr4_2:1104323-1104342 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr4_2:1103949-1103968 Msa0582600:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr4_2:1103969-1103988 Msa0582600:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr4_2:1103970-1103989 Msa0582600:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr4_2:1104124-1104143 Msa0582600:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr4_2:1104194-1104213 Msa0582600:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr4_2:1104311-1104330 Msa0582600:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr4_2:1104312-1104331 Msa0582600:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr4_2:1104313-1104332 Msa0582600:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr4_2:1103955-1103974 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr4_2:1104165-1104184 Msa0582600:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr4_2:1103856-1103875 Msa0582600:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr4_2:1103956-1103975 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr4_2:1103953-1103972 Msa0582600:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr4_2:1104173-1104192 Msa0582600:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr4_2:1103865-1103884 Msa0582600:exon 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1103854 1104387 1103854 ID=Msa0582600;Name=Msa0582600
chr4_2 mRNA 1103854 1104387 1103854 ID=Msa0582600-mRNA-1;Parent=Msa0582600;Name=Msa0582600-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr4_2 exon 1103854 1104031 1103854 ID=Msa0582600-mRNA-1:exon:259;Parent=Msa0582600-mRNA-1
chr4_2 exon 1104237 1104387 1104237 ID=Msa0582600-mRNA-1:exon:260;Parent=Msa0582600-mRNA-1
chr4_2 five_prime_UTR 1103854 1103870 1103854 ID=Msa0582600-mRNA-1:five_prime_utr;Parent=Msa0582600-mRNA-1
chr4_2 CDS 1103871 1104031 1103871 ID=Msa0582600-mRNA-1:cds;Parent=Msa0582600-mRNA-1
chr4_2 CDS 1104237 1104387 1104237 ID=Msa0582600-mRNA-1:cds;Parent=Msa0582600-mRNA-1
Gene Sequence

>Msa0582600

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0582600

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN