AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0095220


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095220 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095220 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095220 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0095220 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0095220 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0095220 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0095220 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
Msa0095220 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0095220 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 1_2:-79039311 Msa0095220:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 1_2:+79039049 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 1_2:+79039345 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 1_2:-79039394 Msa0095220:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 1_2:-79039446 Msa0095220:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 1_2:-79039353 Msa0095220:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 1_2:+79039346 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 1_2:-79038991 Msa0095220:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 1_2:+79039278 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 1_2:+79039043 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 1_2:+79039388 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 1_2:-79039437 Msa0095220:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 1_2:+79039060 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 1_2:-79038990 Msa0095220:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 1_2:-79039462 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 1_2:-79039332 Msa0095220:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 1_2:+79039283 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 1_2:+79039284 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 1_2:-79039333 Msa0095220:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 1_2:-79039349 Msa0095220:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 1_2:+79039282 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 1_2:+79038982 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 1_2:-79039455 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 1_2:-79039354 Msa0095220:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 1_2:+79039350 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 1_2:+79039349 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 1_2:-79038989 Msa0095220:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr1_2:79039184-79039203 Msa0095220:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr1_2:79039374-79039393 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr1_2:79039375-79039394 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr1_2:79039133-79039152 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr1_2:79039187-79039206 Msa0095220:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr1_2:79039288-79039307 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr1_2:79038991-79039010 Msa0095220:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr1_2:79039000-79039019 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr1_2:79039110-79039129 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr1_2:79039134-79039153 Msa0095220:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr1_2:79039160-79039179 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr1_2:79039239-79039258 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr1_2:79039074-79039093 Msa0095220:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr1_2:79039105-79039124 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr1_2:79039106-79039125 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr1_2:79039116-79039135 Msa0095220:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr1_2:79039146-79039165 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr1_2:79039234-79039253 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr1_2:79039234-79039253 Msa0095220:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr1_2:79039240-79039259 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr1_2:79039238-79039257 Msa0095220:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr1_2:79039328-79039347 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr1_2:79039339-79039358 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr1_2:79039345-79039364 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr1_2:79039031-79039050 Msa0095220:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr1_2:79039042-79039061 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr1_2:79039043-79039062 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr1_2:79039104-79039123 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr1_2:79039151-79039170 Msa0095220:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr1_2:79039215-79039234 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr1_2:79039222-79039241 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr1_2:79039278-79039297 Msa0095220:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr1_2:79039284-79039303 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr1_2:79039285-79039304 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr1_2:79039406-79039425 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr1_2:79039032-79039051 Msa0095220:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr1_2:79039052-79039071 Msa0095220:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr1_2:79039053-79039072 Msa0095220:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr1_2:79039207-79039226 Msa0095220:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr1_2:79039277-79039296 Msa0095220:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr1_2:79039394-79039413 Msa0095220:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr1_2:79039395-79039414 Msa0095220:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr1_2:79039396-79039415 Msa0095220:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr1_2:79039038-79039057 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr1_2:79039248-79039267 Msa0095220:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr1_2:79038939-79038958 Msa0095220:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr1_2:79039039-79039058 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr1_2:79039036-79039055 Msa0095220:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr1_2:79039256-79039275 Msa0095220:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr1_2:79038948-79038967 Msa0095220:CDS 60.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 79038937 79039470 79038937 ID=Msa0095220;Name=Msa0095220
chr1_2 mRNA 79038937 79039470 79038937 ID=Msa0095220-mRNA-1;Parent=Msa0095220;Name=Msa0095220-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr1_2 exon 79039293 79039470 79039293 ID=Msa0095220-mRNA-1:exon:28081;Parent=Msa0095220-mRNA-1
chr1_2 exon 79038937 79039087 79038937 ID=Msa0095220-mRNA-1:exon:28080;Parent=Msa0095220-mRNA-1
chr1_2 five_prime_UTR 79039454 79039470 79039454 ID=Msa0095220-mRNA-1:five_prime_utr;Parent=Msa0095220-mRNA-1
chr1_2 CDS 79039293 79039453 79039293 ID=Msa0095220-mRNA-1:cds;Parent=Msa0095220-mRNA-1
chr1_2 CDS 79038937 79039087 79038937 ID=Msa0095220-mRNA-1:cds;Parent=Msa0095220-mRNA-1
Gene Sequence

>Msa0095220

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0095220

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN