AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0268870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0268870 MtrunA17_CPg0492821 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268870 MtrunA17_Chr4g0016851 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268870 MtrunA17_Chr4g0015751 70.732 82 24 0 1 82 1 82 6.38e-34 112
Msa0268870 MtrunA17_Chr4g0017011 98.148 54 1 0 1 54 1 54 2.07e-33 111
Msa0268870 MtrunA17_Chr5g0423051 96.296 54 2 0 1 54 1 54 3.52e-32 107
Msa0268870 MtrunA17_Chr4g0016841 61.538 91 21 2 14 104 9 85 4.52e-31 105
Msa0268870 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
Msa0268870 ATCG00580.1 70.732 82 24 0 1 82 1 82 1.19e-34 114
Msa0268870 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:-70427679 Msa0268870:CDS
GTAGCTCTATAATTCGGATT+AGG 0.338134 2_2:+70427417 None:intergenic
ATAACCAACCCGCAATGAAT+AGG 0.348030 2_2:+70427713 None:intergenic
TTATTACCAGTATTCGATAC+TGG 0.348418 2_2:-70427762 Msa0268870:CDS
TATGTGGAGCTCGGCATGTC+TGG 0.349487 2_2:-70427814 Msa0268870:exon
ATACCCTCCCTATTCATTGC+GGG 0.391873 2_2:-70427721 Msa0268870:CDS
TAACCAACCCGCAATGAATA+GGG 0.406851 2_2:+70427714 None:intergenic
TGAATCGTACCAGTCTCTAC+TGG 0.410190 2_2:-70427359 Msa0268870:CDS
CTTTCTGTAAAATACTCGTT+TGG 0.412027 2_2:+70427646 None:intergenic
TGTGTCGTAGCTCTATAATT+CGG 0.415726 2_2:+70427411 None:intergenic
AATAATCCAGTATCGAATAC+TGG 0.423687 2_2:+70427756 None:intergenic
CTCGGCATGTCTGGAAGCAC+AGG 0.508926 2_2:-70427805 Msa0268870:exon
ATTCGGATTAGGTTTATCGT+TGG 0.512045 2_2:+70427428 None:intergenic
GAATCGTACCAGTCTCTACT+GGG 0.515213 2_2:-70427358 Msa0268870:CDS
TTTGACTGTATAAGAATATG+TGG 0.517465 2_2:-70427830 None:intergenic
GGTTGGTTATTTGTCAGCAC+GGG 0.523918 2_2:-70427700 Msa0268870:CDS
TGTAAAATACTCGTTTGGAC+GGG 0.525534 2_2:+70427651 None:intergenic
GTAAAATACTCGTTTGGACG+GGG 0.531710 2_2:+70427652 None:intergenic
GGGTTGGTTATTTGTCAGCA+CGG 0.532372 2_2:-70427701 Msa0268870:CDS
CCTCCCTATTCATTGCGGGT+TGG 0.536548 2_2:-70427717 Msa0268870:CDS
CTGTAAAATACTCGTTTGGA+CGG 0.550313 2_2:+70427650 None:intergenic
TAATAAACCCCAGTAGAGAC+TGG 0.572062 2_2:+70427350 None:intergenic
GTATAAGAATATGTGGAGCT+CGG 0.584815 2_2:-70427823 None:intergenic
TATACCCTCCCTATTCATTG+CGG 0.586067 2_2:-70427722 Msa0268870:CDS
CAACCCGCAATGAATAGGGA+GGG 0.665638 2_2:+70427718 None:intergenic
CCAACCCGCAATGAATAGGG+AGG 0.678708 2_2:+70427717 None:intergenic
AATCGTACCAGTCTCTACTG+GGG 0.711157 2_2:-70427357 Msa0268870:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGAATTTAGTAGATCTTTTT+AGG - chr2_2:70427552-70427571 Msa0268870:intron 20.0%
!!! ATTCAACATTTTGTTCATTT+GGG + chr2_2:70427742-70427761 None:intergenic 20.0%
!!! AATTCAACATTTTGTTCATT+TGG + chr2_2:70427743-70427762 None:intergenic 20.0%
! TTATTAATGGAATTCCTTGT+CGG + chr2_2:70427501-70427520 None:intergenic 25.0%
!!! ATTTAGTAGATCTTTTTAGG+AGG - chr2_2:70427555-70427574 Msa0268870:intron 25.0%
! TATTGATCCCAAAAAAAAGA+CGG + chr2_2:70427656-70427675 None:intergenic 25.0%
TTATTACCAGTATTCGATAC+TGG - chr2_2:70427359-70427378 Msa0268870:CDS 30.0%
! AATAATCCAGTATCGAATAC+TGG + chr2_2:70427368-70427387 None:intergenic 30.0%
CTTTCTGTAAAATACTCGTT+TGG + chr2_2:70427478-70427497 None:intergenic 30.0%
CAAGGAATTCCATTAATAAC+TGG - chr2_2:70427502-70427521 Msa0268870:intron 30.0%
GTTGTTCCAAAGAATCAAAA+CGG + chr2_2:70427528-70427547 None:intergenic 30.0%
AACCATCGTACTGTAAAAAT+GGG + chr2_2:70427607-70427626 None:intergenic 30.0%
! GGTTTAGCTTACGATGTATT+TGG - chr2_2:70427442-70427461 Msa0268870:intron 35.0%
TGTAAAATACTCGTTTGGAC+GGG + chr2_2:70427473-70427492 None:intergenic 35.0%
CTGTAAAATACTCGTTTGGA+CGG + chr2_2:70427474-70427493 None:intergenic 35.0%
! TATTTTACAGAAAGCCGACA+AGG - chr2_2:70427484-70427503 Msa0268870:intron 35.0%
TCAAAACGGCCAGTTATTAA+TGG + chr2_2:70427514-70427533 None:intergenic 35.0%
TCGTACTGTAAAAATGGGAT+AGG + chr2_2:70427602-70427621 None:intergenic 35.0%
!! ATCCCATTTTTACAGTACGA+TGG - chr2_2:70427602-70427621 Msa0268870:intron 35.0%
CAACCATCGTACTGTAAAAA+TGG + chr2_2:70427608-70427627 None:intergenic 35.0%
! CATTTTTACAGTACGATGGT+TGG - chr2_2:70427606-70427625 Msa0268870:intron 35.0%
! ATTCGGATTAGGTTTATCGT+TGG + chr2_2:70427696-70427715 None:intergenic 35.0%
! GTAGCTCTATAATTCGGATT+AGG + chr2_2:70427707-70427726 None:intergenic 35.0%
! TGTGTCGTAGCTCTATAATT+CGG + chr2_2:70427713-70427732 None:intergenic 35.0%
TATACCCTCCCTATTCATTG+CGG - chr2_2:70427399-70427418 Msa0268870:CDS 40.0%
TAACCAACCCGCAATGAATA+GGG + chr2_2:70427410-70427429 None:intergenic 40.0%
ATAACCAACCCGCAATGAAT+AGG + chr2_2:70427411-70427430 None:intergenic 40.0%
GTAAAATACTCGTTTGGACG+GGG + chr2_2:70427472-70427491 None:intergenic 40.0%
!!! AACTGGCCGTTTTGATTCTT+TGG - chr2_2:70427519-70427538 Msa0268870:intron 40.0%
TAGGTCCTATCTATGGTCAT+TGG + chr2_2:70427583-70427602 None:intergenic 40.0%
AATGGGATAGGTCCTATCTA+TGG + chr2_2:70427590-70427609 None:intergenic 40.0%
!!! GTACCCACCGTCTTTTTTTT+GGG - chr2_2:70427646-70427665 Msa0268870:intron 40.0%
GATCCCAAAAAAAAGACGGT+GGG + chr2_2:70427652-70427671 None:intergenic 40.0%
TGATCCCAAAAAAAAGACGG+TGG + chr2_2:70427653-70427672 None:intergenic 40.0%
TAATAAACCCCAGTAGAGAC+TGG + chr2_2:70427774-70427793 None:intergenic 40.0%
ATACCCTCCCTATTCATTGC+GGG - chr2_2:70427400-70427419 Msa0268870:CDS 45.0%
!! GGGTTGGTTATTTGTCAGCA+CGG - chr2_2:70427420-70427439 Msa0268870:CDS 45.0%
! GGTTGGTTATTTGTCAGCAC+GGG - chr2_2:70427421-70427440 Msa0268870:CDS 45.0%
AGGCTCCAATGACCATAGAT+AGG - chr2_2:70427575-70427594 Msa0268870:intron 45.0%
!!! GGTACCCACCGTCTTTTTTT+TGG - chr2_2:70427645-70427664 Msa0268870:intron 45.0%
TGAATCGTACCAGTCTCTAC+TGG - chr2_2:70427762-70427781 Msa0268870:CDS 45.0%
GAATCGTACCAGTCTCTACT+GGG - chr2_2:70427763-70427782 Msa0268870:CDS 45.0%
AATCGTACCAGTCTCTACTG+GGG - chr2_2:70427764-70427783 Msa0268870:CDS 45.0%
CAACCCGCAATGAATAGGGA+GGG + chr2_2:70427406-70427425 None:intergenic 50.0%
! GTACGATGGTTGGCTGTTCA+CGG - chr2_2:70427616-70427635 Msa0268870:intron 50.0%
TATGTGGAGCTCGGCATGTC+TGG - chr2_2:70427307-70427326 Msa0268870:CDS 55.0%
CCAACCCGCAATGAATAGGG+AGG + chr2_2:70427407-70427426 None:intergenic 55.0%
CCTCCCTATTCATTGCGGGT+TGG - chr2_2:70427404-70427423 Msa0268870:CDS 55.0%
!! GTTGGCTGTTCACGGACTAG+CGG - chr2_2:70427624-70427643 Msa0268870:intron 55.0%
! CTCGGCATGTCTGGAAGCAC+AGG - chr2_2:70427316-70427335 Msa0268870:CDS 60.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 70427305 70427838 70427305 ID=Msa0268870;Name=Msa0268870
chr2_2 mRNA 70427305 70427838 70427305 ID=Msa0268870-mRNA-1;Parent=Msa0268870;Name=Msa0268870-mRNA-1;_AED=0.22;_eAED=0.22;_QI=17|0|0|1|0|0|2|0|104
chr2_2 exon 70427661 70427838 70427661 ID=Msa0268870-mRNA-1:exon:22691;Parent=Msa0268870-mRNA-1
chr2_2 exon 70427305 70427455 70427305 ID=Msa0268870-mRNA-1:exon:22690;Parent=Msa0268870-mRNA-1
chr2_2 five_prime_UTR 70427822 70427838 70427822 ID=Msa0268870-mRNA-1:five_prime_utr;Parent=Msa0268870-mRNA-1
chr2_2 CDS 70427661 70427821 70427661 ID=Msa0268870-mRNA-1:cds;Parent=Msa0268870-mRNA-1
chr2_2 CDS 70427305 70427455 70427305 ID=Msa0268870-mRNA-1:cds;Parent=Msa0268870-mRNA-1
Gene Sequence

>Msa0268870

ATGTCTGGAAGCACAGGAGAACGTTCTTTTGCTGATATTATTACCAGTATTCGATACTGGATTATTCATAGCATTACTATACCCTCCCTATTCATTGCGGGTTGGTTATTTGTCAGCACGGGTTTAGCTTACGATGTATTTGGAAGTCCCCGTCCAAACGATTCATCCAACGATAAACCTAATCCGAATTATAGAGCTACGACACAATCAAACCCAAATGAACAAAATGTTGAATTGAATCGTACCAGTCTCTACTGGGGTTTATTACTCATTTTTGTACTTGCTGTTTTATTTTCAAATTATTTCTTCAAT

Protein sequence

>Msa0268870

MSGSTGERSFADIITSIRYWIIHSITIPSLFIAGWLFVSTGLAYDVFGSPRPNDSSNDKPNPNYRATTQSNPNEQNVELNRTSLYWGLLLIFVLAVLFSNYFFN