AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0484780


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0484780 MtrunA17_Chr5g0422001 77.419 62 11 1 85 146 74 132 9.67e-22 89.4
Msa0484780 MtrunA17_Chr5g0421951 76.667 60 11 1 87 146 79 135 1.95e-20 85.9
Msa0484780 MtrunA17_Chr6g0461801 67.742 62 12 1 85 146 77 130 2.42e-18 79.0
Msa0484780 MtrunA17_Chr6g0458841 55.882 68 29 1 62 129 14 80 2.79e-16 70.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 25 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTTCAGCGAGTTTGCGTATA+AGG 0.233166 3_4:-2288060 Msa0484780:CDS
ATGAACAAGAGTCTATAAAA+TGG 0.316589 3_4:-2287772 Msa0484780:CDS
TGAGAGTCTTTGGAAATCTT+AGG 0.320912 3_4:+2287674 None:intergenic
AAGAGGATTCTTGTCGTATT+AGG 0.324958 3_4:-2287820 Msa0484780:CDS
AGATGAACAAGAGTCTAAAA+TGG 0.348101 3_4:+2287386 None:intergenic
TTCAGCGAGTTTGCGTATAA+GGG 0.425403 3_4:-2288059 Msa0484780:CDS
TCTCAAGGCTGAGAGATGTA+TGG 0.456033 3_4:-2287597 Msa0484780:CDS
CATCTCTCAGCCTTGAGAAA+AGG 0.461884 3_4:-2287554 Msa0484780:intron
CATCTCTCAGCCTTGAGAAA+AGG 0.462783 3_4:+2287602 None:intergenic
AGAAAACTTGAAAGTGGAAG+AGG 0.478875 3_4:-2287837 Msa0484780:CDS
ATTTGAAGAAAACTTGAAAG+TGG 0.485844 3_4:-2287843 Msa0484780:CDS
TTGGAAATCTTAGGAGGAAG+AGG 0.490870 3_4:-2287473 Msa0484780:intron
TTGGAAATCTTAGGAGGAAG+AGG 0.490870 3_4:+2287683 None:intergenic
TAGAAAGAGTGAAGTTGAGG+AGG 0.525784 3_4:-2288027 Msa0484780:CDS
GATGTATGGAGGCTAACAAA+AGG 0.531871 3_4:-2287583 Msa0484780:CDS
TTAGAACAAACATGGTAGGA+AGG 0.551792 3_4:-2287909 Msa0484780:intron
GGATTCTTGTCGTATTAGGA+AGG 0.559347 3_4:-2287816 Msa0484780:CDS
TCTTAGAAAGAGTGAAGTTG+AGG 0.569104 3_4:-2288030 Msa0484780:CDS
ACATGAAGGAACTGTTGAAG+AGG 0.590429 3_4:+2287442 None:intergenic
ACATGAAGGAACTGTTGAAG+AGG 0.590429 3_4:-2287714 Msa0484780:CDS
TTATACGCAAACTCGCTGAA+AGG 0.605794 3_4:+2288062 None:intergenic
GAGTCTTTGGAAATCTTAGG+AGG 0.609374 3_4:+2287677 None:intergenic
CAAGGCTGAGAGATGTATGG+AGG 0.661627 3_4:-2287594 Msa0484780:CDS
GCTAAGAAGAGTGAACATGA+AGG 0.682669 3_4:-2287728 Msa0484780:CDS
GCTAACAAGAGTGAACATGA+AGG 0.705514 3_4:+2287428 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAAAGGTTTAGTTTTTCTTT+TGG + chr3_4:2287936-2287955 None:intergenic 20.0%
!!! AAAAGGTTTAGTTTTTCTTT+CGG - chr3_4:2287936-2287955 Msa0484780:intron 20.0%
!!! TGTTCTAAAAATAAGGAGAT+AGG + chr3_4:2287552-2287571 None:intergenic 25.0%
!!! CCATGTTTGTTCTAAAAATA+AGG + chr3_4:2287559-2287578 None:intergenic 25.0%
!!! CCTTATTTTTAGAACAAACA+TGG - chr3_4:2287556-2287575 Msa0484780:CDS 25.0%
!!! ATTTTTAGAACAAACATGGT+AGG - chr3_4:2287560-2287579 Msa0484780:CDS 25.0%
! ATTTGAAGAAAACTTGAAAG+TGG - chr3_4:2287630-2287649 Msa0484780:CDS 25.0%
! ATGAACAAGAGTCTATAAAA+TGG - chr3_4:2287701-2287720 Msa0484780:CDS 25.0%
!! GTTTTTCTTTTGGATTTACT+AGG + chr3_4:2287847-2287866 None:intergenic 25.0%
!! AAAAACTAAACCTTTTCTCA+AGG - chr3_4:2287861-2287880 Msa0484780:CDS 25.0%
!! AAAAACTAAACCTTTTCTCA+AGG + chr3_4:2287861-2287880 None:intergenic 25.0%
!!! TAGTCTTTTTTGAGAGTCTT+TGG + chr3_4:2287981-2288000 None:intergenic 30.0%
! GTTTTTCTTTCGGATTTACT+AGG - chr3_4:2287946-2287965 Msa0484780:intron 30.0%
!!! TAGTCTTTTTTGAGAGTCTT+TGG - chr3_4:2287981-2288000 Msa0484780:intron 30.0%
TCTTAGAAAGAGTGAAGTTG+AGG - chr3_4:2287443-2287462 Msa0484780:CDS 35.0%
TTAGAACAAACATGGTAGGA+AGG - chr3_4:2287564-2287583 Msa0484780:CDS 35.0%
AGAAAACTTGAAAGTGGAAG+AGG - chr3_4:2287636-2287655 Msa0484780:CDS 35.0%
AAGAGGATTCTTGTCGTATT+AGG - chr3_4:2287653-2287672 Msa0484780:CDS 35.0%
! TGAGAGTCTTTGGAAATCTT+AGG + chr3_4:2287991-2288010 None:intergenic 35.0%
! TGAGAGTCTTTGGAAATCTT+AGG - chr3_4:2287991-2288010 Msa0484780:intron 35.0%
TTATACGCAAACTCGCTGAA+AGG + chr3_4:2287414-2287433 None:intergenic 40.0%
TTTCAGCGAGTTTGCGTATA+AGG - chr3_4:2287413-2287432 Msa0484780:CDS 40.0%
TTCAGCGAGTTTGCGTATAA+GGG - chr3_4:2287414-2287433 Msa0484780:CDS 40.0%
TAGAAAGAGTGAAGTTGAGG+AGG - chr3_4:2287446-2287465 Msa0484780:CDS 40.0%
! GTGAAGTTGAGGAGGATTTT+TGG - chr3_4:2287454-2287473 Msa0484780:CDS 40.0%
!!! GATTTTTGGTCGTACTAGGA+AGG - chr3_4:2287468-2287487 Msa0484780:intron 40.0%
AGTCGAACCAAAGTGTAAAG+TGG - chr3_4:2287510-2287529 Msa0484780:intron 40.0%
GGATTCTTGTCGTATTAGGA+AGG - chr3_4:2287657-2287676 Msa0484780:CDS 40.0%
GCTAAGAAGAGTGAACATGA+AGG - chr3_4:2287745-2287764 Msa0484780:CDS 40.0%
ACATGAAGGAACTGTTGAAG+AGG - chr3_4:2287759-2287778 Msa0484780:CDS 40.0%
TTGGAAATCTTAGGAGGAAG+AGG + chr3_4:2288000-2288019 None:intergenic 40.0%
! GAGTCTTTGGAAATCTTAGG+AGG + chr3_4:2287994-2288013 None:intergenic 40.0%
GATGTATGGAGGCTAACAAA+AGG - chr3_4:2287890-2287909 Msa0484780:CDS 40.0%
! GAGTCTTTGGAAATCTTAGG+AGG - chr3_4:2287994-2288013 Msa0484780:intron 40.0%
TTGGAAATCTTAGGAGGAAG+AGG - chr3_4:2288000-2288019 Msa0484780:intron 40.0%
ACATGAAGGAACTGTTGAAG+AGG + chr3_4:2287759-2287778 None:intergenic 40.0%
GCTAACAAGAGTGAACATGA+AGG + chr3_4:2288048-2288067 None:intergenic 40.0%
!!! GGAGGATTTTTGGTCGTACT+AGG - chr3_4:2287464-2287483 Msa0484780:intron 45.0%
CGATGCTCCACTTTACACTT+TGG + chr3_4:2287520-2287539 None:intergenic 45.0%
CATCTCTCAGCCTTGAGAAA+AGG + chr3_4:2287919-2287938 None:intergenic 45.0%
TCTCAAGGCTGAGAGATGTA+TGG - chr3_4:2287876-2287895 Msa0484780:CDS 45.0%
CATCTCTCAGCCTTGAGAAA+AGG - chr3_4:2287919-2287938 Msa0484780:intron 45.0%
CAAGGCTGAGAGATGTATGG+AGG - chr3_4:2287879-2287898 Msa0484780:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 2287400 2288095 2287400 ID=Msa0484780;Name=Msa0484780
chr3_4 mRNA 2287400 2288095 2287400 ID=Msa0484780-mRNA-1;Parent=Msa0484780;Name=Msa0484780-mRNA-1;_AED=0.20;_eAED=0.24;_QI=0|0|0|0.66|1|1|3|0|181
chr3_4 exon 2288006 2288095 2288006 ID=Msa0484780-mRNA-1:exon:789;Parent=Msa0484780-mRNA-1
chr3_4 exon 2287555 2287927 2287555 ID=Msa0484780-mRNA-1:exon:788;Parent=Msa0484780-mRNA-1
chr3_4 exon 2287400 2287482 2287400 ID=Msa0484780-mRNA-1:exon:787;Parent=Msa0484780-mRNA-1
chr3_4 CDS 2288006 2288095 2288006 ID=Msa0484780-mRNA-1:cds;Parent=Msa0484780-mRNA-1
chr3_4 CDS 2287555 2287927 2287555 ID=Msa0484780-mRNA-1:cds;Parent=Msa0484780-mRNA-1
chr3_4 CDS 2287400 2287482 2287400 ID=Msa0484780-mRNA-1:cds;Parent=Msa0484780-mRNA-1
Gene Sequence

>Msa0484780

ATGTGGACAATCCTTTCAGCGAGTTTGCGTATAAGGGAGATCATCTTAGAAAGAGTGAAGTTGAGGAGGATTTTTGGTCGTACTAGGAAGAACAAACATGGTAGGAAGGATTCTGATGATGTTTCTAGAGATTTTTTATGTCAGCACGAAACATTTGAAGAAAACTTGAAAGTGGAAGAGGATTCTTGTCGTATTAGGAAGGTTTCGAAATATTCTCAGAAAGATGAACAAGAGTCTATAAAATGGAGCATCAGTCTCAGAGAGTGTGCTAAGAAGAGTGAACATGAAGGAACTGTTGAAGAGGATTCATCTCCTCTTCCTCCTAAGATTTCCAAAGACTCTCAAAAAAGACTAAAAGTTGAAAAGCCTAGTAAATCCAAAAGAAAAACTAAACCTTTTCTCAAGGCTGAGAGATGTATGGAGGCTAACAAAAGGAAAATACATCTCTCAGCCTTGAGAAAAGGAGGAAGAGGAGATGAATCCTCTTCAACAGTTCCTTCATGTTCACTCTTGTTAGCACACTCTGAGACTGATGCTCCATTTTAG

Protein sequence

>Msa0484780

MWTILSASLRIREIILERVKLRRIFGRTRKNKHGRKDSDDVSRDFLCQHETFEENLKVEEDSCRIRKVSKYSQKDEQESIKWSISLRECAKKSEHEGTVEEDSSPLPPKISKDSQKRLKVEKPSKSKRKTKPFLKAERCMEANKRKIHLSALRKGGRGDESSSTVPSCSLLLAHSETDAPF*