AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0582880


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0582880 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582880 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582880 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0582880 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0582880 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0582880 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0582880 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
Msa0582880 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0582880 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:+1267403 Msa0582880:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 4_2:-1267665 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 4_2:-1267369 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 4_2:+1267320 Msa0582880:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 4_2:+1267268 Msa0582880:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 4_2:+1267361 Msa0582880:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 4_2:-1267368 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 4_2:+1267723 Msa0582880:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 4_2:-1267436 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 4_2:-1267671 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 4_2:-1267326 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 4_2:+1267277 Msa0582880:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 4_2:-1267654 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 4_2:+1267724 Msa0582880:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 4_2:+1267252 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 4_2:+1267382 Msa0582880:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 4_2:-1267431 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 4_2:-1267430 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 4_2:+1267381 Msa0582880:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 4_2:+1267365 Msa0582880:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 4_2:-1267432 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 4_2:-1267732 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 4_2:+1267259 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 4_2:+1267360 Msa0582880:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 4_2:-1267364 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 4_2:-1267365 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 4_2:+1267725 Msa0582880:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG + chr4_2:1267513-1267532 Msa0582880:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG - chr4_2:1267703-1267722 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG - chr4_2:1267704-1267723 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG - chr4_2:1267462-1267481 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG + chr4_2:1267516-1267535 Msa0582880:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG - chr4_2:1267617-1267636 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG + chr4_2:1267320-1267339 Msa0582880:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG - chr4_2:1267329-1267348 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG - chr4_2:1267439-1267458 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG + chr4_2:1267463-1267482 Msa0582880:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG - chr4_2:1267489-1267508 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG - chr4_2:1267568-1267587 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG + chr4_2:1267403-1267422 Msa0582880:CDS 35.0%
TGTAAAATACTCGTTTGGAC+GGG - chr4_2:1267434-1267453 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG - chr4_2:1267435-1267454 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG + chr4_2:1267445-1267464 Msa0582880:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG - chr4_2:1267475-1267494 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG - chr4_2:1267563-1267582 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG + chr4_2:1267563-1267582 Msa0582880:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG - chr4_2:1267569-1267588 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG + chr4_2:1267567-1267586 Msa0582880:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG - chr4_2:1267657-1267676 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG - chr4_2:1267668-1267687 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG - chr4_2:1267674-1267693 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG + chr4_2:1267360-1267379 Msa0582880:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG - chr4_2:1267371-1267390 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG - chr4_2:1267372-1267391 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG - chr4_2:1267433-1267452 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG + chr4_2:1267480-1267499 Msa0582880:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG - chr4_2:1267544-1267563 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG - chr4_2:1267551-1267570 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG + chr4_2:1267607-1267626 Msa0582880:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG - chr4_2:1267613-1267632 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG - chr4_2:1267614-1267633 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG - chr4_2:1267735-1267754 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG + chr4_2:1267361-1267380 Msa0582880:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG + chr4_2:1267381-1267400 Msa0582880:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG + chr4_2:1267382-1267401 Msa0582880:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG + chr4_2:1267536-1267555 Msa0582880:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG + chr4_2:1267606-1267625 Msa0582880:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG + chr4_2:1267723-1267742 Msa0582880:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG + chr4_2:1267724-1267743 Msa0582880:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG + chr4_2:1267725-1267744 Msa0582880:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG - chr4_2:1267367-1267386 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG + chr4_2:1267577-1267596 Msa0582880:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG + chr4_2:1267268-1267287 Msa0582880:exon 55.0%
CCAACCCGCAATGAATAGGG+AGG - chr4_2:1267368-1267387 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG + chr4_2:1267365-1267384 Msa0582880:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG + chr4_2:1267585-1267604 Msa0582880:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG + chr4_2:1267277-1267296 Msa0582880:exon 60.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 1267266 1267799 1267266 ID=Msa0582880;Name=Msa0582880
chr4_2 mRNA 1267266 1267799 1267266 ID=Msa0582880-mRNA-1;Parent=Msa0582880;Name=Msa0582880-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr4_2 exon 1267266 1267443 1267266 ID=Msa0582880-mRNA-1:exon:294;Parent=Msa0582880-mRNA-1
chr4_2 exon 1267649 1267799 1267649 ID=Msa0582880-mRNA-1:exon:295;Parent=Msa0582880-mRNA-1
chr4_2 five_prime_UTR 1267266 1267282 1267266 ID=Msa0582880-mRNA-1:five_prime_utr;Parent=Msa0582880-mRNA-1
chr4_2 CDS 1267283 1267443 1267283 ID=Msa0582880-mRNA-1:cds;Parent=Msa0582880-mRNA-1
chr4_2 CDS 1267649 1267799 1267649 ID=Msa0582880-mRNA-1:cds;Parent=Msa0582880-mRNA-1
Gene Sequence

>Msa0582880

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0582880

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN