AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0931170


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931170 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931170 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931170 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931170 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0931170 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0931170 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0931170 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
Msa0931170 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0931170 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 6_2:-80370333 Msa0931170:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 6_2:+80370071 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 6_2:+80370367 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 6_2:-80370416 Msa0931170:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 6_2:-80370468 Msa0931170:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 6_2:-80370375 Msa0931170:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 6_2:+80370368 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 6_2:-80370013 Msa0931170:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 6_2:+80370300 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 6_2:+80370065 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 6_2:+80370410 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 6_2:-80370459 Msa0931170:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 6_2:+80370082 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 6_2:-80370012 Msa0931170:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 6_2:-80370484 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 6_2:-80370354 Msa0931170:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 6_2:+80370305 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 6_2:+80370306 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 6_2:-80370355 Msa0931170:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 6_2:-80370371 Msa0931170:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 6_2:+80370304 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 6_2:+80370004 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 6_2:-80370477 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 6_2:-80370376 Msa0931170:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 6_2:+80370372 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 6_2:+80370371 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 6_2:-80370011 Msa0931170:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr6_2:80370206-80370225 Msa0931170:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr6_2:80370396-80370415 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr6_2:80370397-80370416 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr6_2:80370155-80370174 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr6_2:80370209-80370228 Msa0931170:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr6_2:80370310-80370329 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr6_2:80370013-80370032 Msa0931170:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr6_2:80370022-80370041 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr6_2:80370132-80370151 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr6_2:80370156-80370175 Msa0931170:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr6_2:80370182-80370201 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr6_2:80370261-80370280 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr6_2:80370096-80370115 Msa0931170:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr6_2:80370127-80370146 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr6_2:80370128-80370147 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr6_2:80370138-80370157 Msa0931170:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr6_2:80370168-80370187 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr6_2:80370256-80370275 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr6_2:80370256-80370275 Msa0931170:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr6_2:80370262-80370281 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr6_2:80370260-80370279 Msa0931170:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr6_2:80370350-80370369 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr6_2:80370361-80370380 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr6_2:80370367-80370386 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr6_2:80370053-80370072 Msa0931170:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr6_2:80370064-80370083 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr6_2:80370065-80370084 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr6_2:80370126-80370145 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr6_2:80370173-80370192 Msa0931170:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr6_2:80370237-80370256 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr6_2:80370244-80370263 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr6_2:80370300-80370319 Msa0931170:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr6_2:80370306-80370325 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr6_2:80370307-80370326 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr6_2:80370428-80370447 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr6_2:80370054-80370073 Msa0931170:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr6_2:80370074-80370093 Msa0931170:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr6_2:80370075-80370094 Msa0931170:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr6_2:80370229-80370248 Msa0931170:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr6_2:80370299-80370318 Msa0931170:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr6_2:80370416-80370435 Msa0931170:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr6_2:80370417-80370436 Msa0931170:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr6_2:80370418-80370437 Msa0931170:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr6_2:80370060-80370079 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr6_2:80370270-80370289 Msa0931170:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr6_2:80369961-80369980 Msa0931170:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr6_2:80370061-80370080 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr6_2:80370058-80370077 Msa0931170:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr6_2:80370278-80370297 Msa0931170:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr6_2:80369970-80369989 Msa0931170:CDS 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 80369959 80370492 80369959 ID=Msa0931170;Name=Msa0931170
chr6_2 mRNA 80369959 80370492 80369959 ID=Msa0931170-mRNA-1;Parent=Msa0931170;Name=Msa0931170-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr6_2 exon 80370315 80370492 80370315 ID=Msa0931170-mRNA-1:exon:14072;Parent=Msa0931170-mRNA-1
chr6_2 exon 80369959 80370109 80369959 ID=Msa0931170-mRNA-1:exon:14071;Parent=Msa0931170-mRNA-1
chr6_2 five_prime_UTR 80370476 80370492 80370476 ID=Msa0931170-mRNA-1:five_prime_utr;Parent=Msa0931170-mRNA-1
chr6_2 CDS 80370315 80370475 80370315 ID=Msa0931170-mRNA-1:cds;Parent=Msa0931170-mRNA-1
chr6_2 CDS 80369959 80370109 80369959 ID=Msa0931170-mRNA-1:cds;Parent=Msa0931170-mRNA-1
Gene Sequence

>Msa0931170

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0931170

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN