AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0983690


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0983690 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0983690 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0983690 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0983690 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0983690 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0983690 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0983690 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
Msa0983690 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0983690 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_4:+26790163 Msa0983690:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 6_4:-26790425 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 6_4:-26790129 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 6_4:+26790080 Msa0983690:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 6_4:+26790028 Msa0983690:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 6_4:+26790121 Msa0983690:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 6_4:-26790128 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 6_4:+26790483 Msa0983690:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 6_4:-26790196 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 6_4:-26790431 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 6_4:-26790086 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 6_4:+26790037 Msa0983690:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 6_4:-26790414 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 6_4:+26790484 Msa0983690:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 6_4:+26790012 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 6_4:+26790142 Msa0983690:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 6_4:-26790191 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 6_4:-26790190 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 6_4:+26790141 Msa0983690:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 6_4:+26790125 Msa0983690:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 6_4:-26790192 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 6_4:-26790492 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 6_4:+26790019 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 6_4:+26790120 Msa0983690:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 6_4:-26790124 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 6_4:-26790125 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 6_4:+26790485 Msa0983690:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr6_4:26790273-26790292 Msa0983690:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr6_4:26790463-26790482 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr6_4:26790464-26790483 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr6_4:26790222-26790241 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr6_4:26790276-26790295 Msa0983690:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr6_4:26790377-26790396 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr6_4:26790080-26790099 Msa0983690:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr6_4:26790089-26790108 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr6_4:26790199-26790218 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr6_4:26790223-26790242 Msa0983690:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr6_4:26790249-26790268 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr6_4:26790328-26790347 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr6_4:26790163-26790182 Msa0983690:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr6_4:26790194-26790213 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr6_4:26790195-26790214 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr6_4:26790205-26790224 Msa0983690:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr6_4:26790235-26790254 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr6_4:26790323-26790342 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr6_4:26790323-26790342 Msa0983690:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr6_4:26790329-26790348 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr6_4:26790327-26790346 Msa0983690:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr6_4:26790417-26790436 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr6_4:26790428-26790447 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr6_4:26790434-26790453 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr6_4:26790120-26790139 Msa0983690:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr6_4:26790131-26790150 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr6_4:26790132-26790151 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr6_4:26790193-26790212 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr6_4:26790240-26790259 Msa0983690:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr6_4:26790304-26790323 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr6_4:26790311-26790330 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr6_4:26790367-26790386 Msa0983690:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr6_4:26790373-26790392 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr6_4:26790374-26790393 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr6_4:26790495-26790514 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr6_4:26790121-26790140 Msa0983690:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr6_4:26790141-26790160 Msa0983690:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr6_4:26790142-26790161 Msa0983690:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr6_4:26790296-26790315 Msa0983690:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr6_4:26790366-26790385 Msa0983690:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr6_4:26790483-26790502 Msa0983690:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr6_4:26790484-26790503 Msa0983690:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr6_4:26790485-26790504 Msa0983690:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr6_4:26790127-26790146 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr6_4:26790337-26790356 Msa0983690:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr6_4:26790028-26790047 Msa0983690:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr6_4:26790128-26790147 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr6_4:26790125-26790144 Msa0983690:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr6_4:26790345-26790364 Msa0983690:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr6_4:26790037-26790056 Msa0983690:exon 60.0%
Chromosome Type Strat End Strand Name
chr6_4 gene 26790026 26790559 26790026 ID=Msa0983690;Name=Msa0983690
chr6_4 mRNA 26790026 26790559 26790026 ID=Msa0983690-mRNA-1;Parent=Msa0983690;Name=Msa0983690-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr6_4 exon 26790026 26790203 26790026 ID=Msa0983690-mRNA-1:exon:7588;Parent=Msa0983690-mRNA-1
chr6_4 exon 26790409 26790559 26790409 ID=Msa0983690-mRNA-1:exon:7589;Parent=Msa0983690-mRNA-1
chr6_4 five_prime_UTR 26790026 26790042 26790026 ID=Msa0983690-mRNA-1:five_prime_utr;Parent=Msa0983690-mRNA-1
chr6_4 CDS 26790043 26790203 26790043 ID=Msa0983690-mRNA-1:cds;Parent=Msa0983690-mRNA-1
chr6_4 CDS 26790409 26790559 26790409 ID=Msa0983690-mRNA-1:cds;Parent=Msa0983690-mRNA-1
Gene Sequence

>Msa0983690

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0983690

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN