AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0269080


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0269080 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0269080 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0269080 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0269080 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0269080 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0269080 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0269080 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
Msa0269080 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0269080 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 2_2:-70503660 Msa0269080:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:+70503398 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:+70503694 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:-70503743 Msa0269080:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:-70503795 Msa0269080:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:-70503702 Msa0269080:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:+70503695 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:-70503340 Msa0269080:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:+70503627 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:+70503392 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:+70503737 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:-70503786 Msa0269080:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:+70503409 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:-70503339 Msa0269080:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:-70503811 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:-70503681 Msa0269080:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:+70503632 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:+70503633 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:-70503682 Msa0269080:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:-70503698 Msa0269080:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:+70503631 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:+70503331 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:-70503804 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:-70503703 Msa0269080:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:+70503699 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:+70503698 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:-70503338 Msa0269080:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr2_2:70503533-70503552 Msa0269080:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr2_2:70503723-70503742 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr2_2:70503724-70503743 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr2_2:70503482-70503501 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr2_2:70503536-70503555 Msa0269080:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr2_2:70503637-70503656 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr2_2:70503340-70503359 Msa0269080:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr2_2:70503349-70503368 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr2_2:70503459-70503478 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr2_2:70503483-70503502 Msa0269080:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr2_2:70503509-70503528 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr2_2:70503588-70503607 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr2_2:70503423-70503442 Msa0269080:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr2_2:70503454-70503473 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr2_2:70503455-70503474 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr2_2:70503465-70503484 Msa0269080:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr2_2:70503495-70503514 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr2_2:70503583-70503602 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr2_2:70503583-70503602 Msa0269080:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr2_2:70503589-70503608 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr2_2:70503587-70503606 Msa0269080:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr2_2:70503677-70503696 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr2_2:70503688-70503707 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr2_2:70503694-70503713 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr2_2:70503380-70503399 Msa0269080:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr2_2:70503391-70503410 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr2_2:70503392-70503411 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr2_2:70503453-70503472 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr2_2:70503500-70503519 Msa0269080:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr2_2:70503564-70503583 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr2_2:70503571-70503590 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr2_2:70503627-70503646 Msa0269080:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr2_2:70503633-70503652 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr2_2:70503634-70503653 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr2_2:70503755-70503774 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr2_2:70503381-70503400 Msa0269080:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr2_2:70503401-70503420 Msa0269080:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr2_2:70503402-70503421 Msa0269080:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr2_2:70503556-70503575 Msa0269080:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr2_2:70503626-70503645 Msa0269080:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr2_2:70503743-70503762 Msa0269080:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr2_2:70503744-70503763 Msa0269080:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr2_2:70503745-70503764 Msa0269080:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr2_2:70503387-70503406 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr2_2:70503597-70503616 Msa0269080:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr2_2:70503288-70503307 Msa0269080:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr2_2:70503388-70503407 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr2_2:70503385-70503404 Msa0269080:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr2_2:70503605-70503624 Msa0269080:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr2_2:70503297-70503316 Msa0269080:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70503286 70503819 70503286 ID=Msa0269080;Name=Msa0269080
chr2_2 mRNA 70503286 70503819 70503286 ID=Msa0269080-mRNA-1;Parent=Msa0269080;Name=Msa0269080-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70503642 70503819 70503642 ID=Msa0269080-mRNA-1:exon:22770;Parent=Msa0269080-mRNA-1
chr2_2 exon 70503286 70503436 70503286 ID=Msa0269080-mRNA-1:exon:22769;Parent=Msa0269080-mRNA-1
chr2_2 five_prime_UTR 70503803 70503819 70503803 ID=Msa0269080-mRNA-1:five_prime_utr;Parent=Msa0269080-mRNA-1
chr2_2 CDS 70503642 70503802 70503642 ID=Msa0269080-mRNA-1:cds;Parent=Msa0269080-mRNA-1
chr2_2 CDS 70503286 70503436 70503286 ID=Msa0269080-mRNA-1:cds;Parent=Msa0269080-mRNA-1
Gene Sequence

>Msa0269080

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0269080

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN