AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0931180


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0931180 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931180 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931180 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0931180 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0931180 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0931180 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0931180 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
Msa0931180 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0931180 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:+80371383 Msa0931180:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 6_2:-80371645 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 6_2:-80371349 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 6_2:+80371300 Msa0931180:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 6_2:+80371248 Msa0931180:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 6_2:+80371341 Msa0931180:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 6_2:-80371348 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 6_2:+80371703 Msa0931180:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 6_2:-80371416 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 6_2:-80371651 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 6_2:-80371306 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 6_2:+80371257 Msa0931180:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 6_2:-80371634 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 6_2:+80371704 Msa0931180:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 6_2:+80371232 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 6_2:+80371362 Msa0931180:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 6_2:-80371411 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 6_2:-80371410 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 6_2:+80371361 Msa0931180:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 6_2:+80371345 Msa0931180:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 6_2:-80371412 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 6_2:-80371712 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 6_2:+80371239 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 6_2:+80371340 Msa0931180:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 6_2:-80371344 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 6_2:-80371345 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 6_2:+80371705 Msa0931180:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr6_2:80371493-80371512 Msa0931180:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr6_2:80371683-80371702 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr6_2:80371684-80371703 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr6_2:80371442-80371461 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr6_2:80371496-80371515 Msa0931180:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr6_2:80371597-80371616 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr6_2:80371300-80371319 Msa0931180:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr6_2:80371309-80371328 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr6_2:80371419-80371438 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr6_2:80371443-80371462 Msa0931180:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr6_2:80371469-80371488 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr6_2:80371548-80371567 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr6_2:80371383-80371402 Msa0931180:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr6_2:80371414-80371433 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr6_2:80371415-80371434 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr6_2:80371425-80371444 Msa0931180:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr6_2:80371455-80371474 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr6_2:80371543-80371562 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr6_2:80371543-80371562 Msa0931180:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr6_2:80371549-80371568 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr6_2:80371547-80371566 Msa0931180:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr6_2:80371637-80371656 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr6_2:80371648-80371667 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr6_2:80371654-80371673 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr6_2:80371340-80371359 Msa0931180:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr6_2:80371351-80371370 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr6_2:80371352-80371371 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr6_2:80371413-80371432 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr6_2:80371460-80371479 Msa0931180:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr6_2:80371524-80371543 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr6_2:80371531-80371550 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr6_2:80371587-80371606 Msa0931180:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr6_2:80371593-80371612 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr6_2:80371594-80371613 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr6_2:80371715-80371734 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr6_2:80371341-80371360 Msa0931180:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr6_2:80371361-80371380 Msa0931180:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr6_2:80371362-80371381 Msa0931180:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr6_2:80371516-80371535 Msa0931180:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr6_2:80371586-80371605 Msa0931180:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr6_2:80371703-80371722 Msa0931180:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr6_2:80371704-80371723 Msa0931180:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr6_2:80371705-80371724 Msa0931180:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr6_2:80371347-80371366 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr6_2:80371557-80371576 Msa0931180:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr6_2:80371248-80371267 Msa0931180:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr6_2:80371348-80371367 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr6_2:80371345-80371364 Msa0931180:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr6_2:80371565-80371584 Msa0931180:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr6_2:80371257-80371276 Msa0931180:exon 60.0%
Chromosome Type Strat End Strand Name
chr6_2 gene 80371246 80371779 80371246 ID=Msa0931180;Name=Msa0931180
chr6_2 mRNA 80371246 80371779 80371246 ID=Msa0931180-mRNA-1;Parent=Msa0931180;Name=Msa0931180-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr6_2 exon 80371246 80371423 80371246 ID=Msa0931180-mRNA-1:exon:14069;Parent=Msa0931180-mRNA-1
chr6_2 exon 80371629 80371779 80371629 ID=Msa0931180-mRNA-1:exon:14070;Parent=Msa0931180-mRNA-1
chr6_2 five_prime_UTR 80371246 80371262 80371246 ID=Msa0931180-mRNA-1:five_prime_utr;Parent=Msa0931180-mRNA-1
chr6_2 CDS 80371263 80371423 80371263 ID=Msa0931180-mRNA-1:cds;Parent=Msa0931180-mRNA-1
chr6_2 CDS 80371629 80371779 80371629 ID=Msa0931180-mRNA-1:cds;Parent=Msa0931180-mRNA-1
Gene Sequence

>Msa0931180

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0931180

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN