AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1029260


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1029260 MtrunA17_Chr7g0249681 100.000 36 0 0 71 106 6 41 8.61e-19 80.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1029260 AT5G16270.1 100.000 36 0 0 71 106 6 41 1.29e-18 79.7

Find 19 sgRNAs with CRISPR-Local

Find 124 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CACGAGGACCATTTCCATTT+TGG 0.140981 7_1:+62685745 None:intergenic
TGTGGTCGCAATTTCCATTT+TGG 0.250565 7_1:+62685721 None:intergenic
AATGGTCCTCGTGACCAAAA+TGG 0.328047 7_1:-62685759 Msa1029260:CDS
AATGGTCCTCGTGACCAAAA+TGG 0.358354 7_1:-62685735 Msa1029260:CDS
ATTAATTAGACTTCATATAA+TGG 0.390508 7_1:-62685777 Msa1029260:intron
TATCAGCCACCTGATTCTTT+CGG 0.397326 7_1:+62684934 None:intergenic
AAGGTCCACTTGGGACTATA+TGG 0.411921 7_1:-62684983 Msa1029260:CDS
GAGGAAGCTCCGAAAGAATC+AGG 0.413394 7_1:-62684943 Msa1029260:CDS
CAGGTGGCTGATACGGATAT+TGG 0.425599 7_1:-62684924 Msa1029260:CDS
TTGTAAACGATCCATGCATA+TGG 0.426395 7_1:-62685824 None:intergenic
CCTCGTGACCAAAATGGAAA+TGG 0.464929 7_1:-62685753 Msa1029260:CDS
AAAGAATCAGGTGGCTGATA+CGG 0.490347 7_1:-62684931 Msa1029260:CDS
ACGGATATTGGCGTCTCTGT+AGG 0.533498 7_1:-62684912 None:intergenic
TTGGCGAAGAAAGGTCCACT+TGG 0.565886 7_1:-62684993 Msa1029260:CDS
TGGCGAAGAAAGGTCCACTT+GGG 0.594047 7_1:-62684992 Msa1029260:CDS
AAAAGAAATACATACTAATG+TGG 0.603225 7_1:-62685679 Msa1029260:CDS
GGATAGCTGCACATTTAGAG+AGG 0.646542 7_1:-62684962 Msa1029260:CDS
GCTATCCATATAGTCCCAAG+TGG 0.665780 7_1:+62684978 None:intergenic
GAAGCTCCGAAAGAATCAGG+TGG 0.714446 7_1:-62684940 Msa1029260:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATTAATTAGACTTCATATAA+TGG - chr7_1:62684948-62684967 Msa1029260:CDS 15.0%
!! AATTTGAAAGAAATTAAGAA+TGG + chr7_1:62685284-62685303 None:intergenic 15.0%
!! ATTAATTAGACTTCATATAA+TGG - chr7_1:62684948-62684967 Msa1029260:CDS 15.0%
!! AATTTGAAAGAAATTAAGAA+TGG + chr7_1:62685284-62685303 None:intergenic 15.0%
!! AAAAGAAATACATACTAATG+TGG - chr7_1:62685046-62685065 Msa1029260:intron 20.0%
!!! GTAAATAGGAAATTTTTTGA+GGG + chr7_1:62685336-62685355 None:intergenic 20.0%
!!! AGTAAATAGGAAATTTTTTG+AGG + chr7_1:62685337-62685356 None:intergenic 20.0%
!! AAAAGAAATACATACTAATG+TGG - chr7_1:62685046-62685065 Msa1029260:intron 20.0%
!!! GTAAATAGGAAATTTTTTGA+GGG + chr7_1:62685336-62685355 None:intergenic 20.0%
!!! AGTAAATAGGAAATTTTTTG+AGG + chr7_1:62685337-62685356 None:intergenic 20.0%
! AAAGAAAAACATGAAACAAG+TGG - chr7_1:62685091-62685110 Msa1029260:intron 25.0%
!!! GAAATTTTTTGAGGGAAAAT+CGG + chr7_1:62685328-62685347 None:intergenic 25.0%
!! AGAATTAAGCTTTTAGTAAC+AGG + chr7_1:62685485-62685504 None:intergenic 25.0%
!!! ATTTTGGAGAAAGTGAAATT+AGG - chr7_1:62685561-62685580 Msa1029260:intron 25.0%
!!! TTTTGGAGAAAGTGAAATTA+GGG - chr7_1:62685562-62685581 Msa1029260:intron 25.0%
!!! GCTATGATTTGTGTATTTTT+AGG - chr7_1:62685611-62685630 Msa1029260:intron 25.0%
!!! TGGGAAAAAGTGATTTTTTT+AGG - chr7_1:62685683-62685702 Msa1029260:CDS 25.0%
!! GTTTTACTCTCAGTTTATTT+TGG - chr7_1:62685713-62685732 Msa1029260:CDS 25.0%
! AAAGAAAAACATGAAACAAG+TGG - chr7_1:62685091-62685110 Msa1029260:intron 25.0%
!!! GAAATTTTTTGAGGGAAAAT+CGG + chr7_1:62685328-62685347 None:intergenic 25.0%
!! AGAATTAAGCTTTTAGTAAC+AGG + chr7_1:62685485-62685504 None:intergenic 25.0%
!!! ATTTTGGAGAAAGTGAAATT+AGG - chr7_1:62685561-62685580 Msa1029260:intron 25.0%
!!! TTTTGGAGAAAGTGAAATTA+GGG - chr7_1:62685562-62685581 Msa1029260:intron 25.0%
!!! GCTATGATTTGTGTATTTTT+AGG - chr7_1:62685611-62685630 Msa1029260:intron 25.0%
!!! TGGGAAAAAGTGATTTTTTT+AGG - chr7_1:62685683-62685702 Msa1029260:CDS 25.0%
!! GTTTTACTCTCAGTTTATTT+TGG - chr7_1:62685713-62685732 Msa1029260:CDS 25.0%
AAATTAAGAATGGTTGTGTG+AGG + chr7_1:62685274-62685293 None:intergenic 30.0%
!! ATTGGGAAAGAATTTGTTGA+GGG + chr7_1:62685367-62685386 None:intergenic 30.0%
!! AATTGGGAAAGAATTTGTTG+AGG + chr7_1:62685368-62685387 None:intergenic 30.0%
TGAAATTAGGGTTTGTAAAG+AGG - chr7_1:62685574-62685593 Msa1029260:intron 30.0%
GAAATTAGGGTTTGTAAAGA+GGG - chr7_1:62685575-62685594 Msa1029260:intron 30.0%
!!! TTTTTAGGTGTGTTTGTAGA+TGG - chr7_1:62685626-62685645 Msa1029260:intron 30.0%
!! TTTTAGGTGTGTTTGTAGAT+GGG - chr7_1:62685627-62685646 Msa1029260:intron 30.0%
ATTGAGATTTAAGCTGTGTT+CGG - chr7_1:62685651-62685670 Msa1029260:intron 30.0%
AAATTAAGAATGGTTGTGTG+AGG + chr7_1:62685274-62685293 None:intergenic 30.0%
!! ATTGGGAAAGAATTTGTTGA+GGG + chr7_1:62685367-62685386 None:intergenic 30.0%
!! AATTGGGAAAGAATTTGTTG+AGG + chr7_1:62685368-62685387 None:intergenic 30.0%
TGAAATTAGGGTTTGTAAAG+AGG - chr7_1:62685574-62685593 Msa1029260:intron 30.0%
GAAATTAGGGTTTGTAAAGA+GGG - chr7_1:62685575-62685594 Msa1029260:intron 30.0%
!!! TTTTTAGGTGTGTTTGTAGA+TGG - chr7_1:62685626-62685645 Msa1029260:intron 30.0%
!! TTTTAGGTGTGTTTGTAGAT+GGG - chr7_1:62685627-62685646 Msa1029260:intron 30.0%
ATTGAGATTTAAGCTGTGTT+CGG - chr7_1:62685651-62685670 Msa1029260:intron 30.0%
!!! CTTGTGCTACACTTTTTTTG+TGG + chr7_1:62685025-62685044 None:intergenic 35.0%
TCGTGAAGCATATTAGTGTT+TGG + chr7_1:62685182-62685201 None:intergenic 35.0%
!! TTGGGAAAGAATTTGTTGAG+GGG + chr7_1:62685366-62685385 None:intergenic 35.0%
GAGTTTCTGATTTCTCTGTT+AGG - chr7_1:62685508-62685527 Msa1029260:intron 35.0%
!!! CTGTTAGGTTTTGAGCTATT+TGG - chr7_1:62685523-62685542 Msa1029260:intron 35.0%
!!! GTTTTGAGCTATTTGGTGTT+TGG - chr7_1:62685530-62685549 Msa1029260:intron 35.0%
!!! GTGTTTGGTTTGGTTGATTT+TGG - chr7_1:62685545-62685564 Msa1029260:intron 35.0%
! TAAAGAGGGTTTTTACGAAG+TGG - chr7_1:62685589-62685608 Msa1029260:intron 35.0%
TTTAGGTGTGTTTGTAGATG+GGG - chr7_1:62685628-62685647 Msa1029260:intron 35.0%
!!! CAGTTTATTTTGGCGAAGAA+AGG - chr7_1:62685723-62685742 Msa1029260:CDS 35.0%
!!! CTTGTGCTACACTTTTTTTG+TGG + chr7_1:62685025-62685044 None:intergenic 35.0%
TCGTGAAGCATATTAGTGTT+TGG + chr7_1:62685182-62685201 None:intergenic 35.0%
!! TTGGGAAAGAATTTGTTGAG+GGG + chr7_1:62685366-62685385 None:intergenic 35.0%
GAGTTTCTGATTTCTCTGTT+AGG - chr7_1:62685508-62685527 Msa1029260:intron 35.0%
!!! CTGTTAGGTTTTGAGCTATT+TGG - chr7_1:62685523-62685542 Msa1029260:intron 35.0%
!!! GTTTTGAGCTATTTGGTGTT+TGG - chr7_1:62685530-62685549 Msa1029260:intron 35.0%
!!! GTGTTTGGTTTGGTTGATTT+TGG - chr7_1:62685545-62685564 Msa1029260:intron 35.0%
! TAAAGAGGGTTTTTACGAAG+TGG - chr7_1:62685589-62685608 Msa1029260:intron 35.0%
TTTAGGTGTGTTTGTAGATG+GGG - chr7_1:62685628-62685647 Msa1029260:intron 35.0%
!!! CAGTTTATTTTGGCGAAGAA+AGG - chr7_1:62685723-62685742 Msa1029260:CDS 35.0%
!! CAATTTCCATTTTGGTCACG+AGG + chr7_1:62684999-62685018 None:intergenic 40.0%
! TGTGGTCGCAATTTCCATTT+TGG + chr7_1:62685007-62685026 None:intergenic 40.0%
TGAGGGGAAAACGAGTAAAT+AGG + chr7_1:62685350-62685369 None:intergenic 40.0%
! GAAACCCTAATTTGCAGCTA+GGG + chr7_1:62685395-62685414 None:intergenic 40.0%
! AGAAACCCTAATTTGCAGCT+AGG + chr7_1:62685396-62685415 None:intergenic 40.0%
!! GAGCTATTTGGTGTTTGGTT+TGG - chr7_1:62685535-62685554 Msa1029260:intron 40.0%
!!! CTGTGTTCGGTGTTGATTTT+GGG - chr7_1:62685664-62685683 Msa1029260:intron 40.0%
TATCAGCCACCTGATTCTTT+CGG + chr7_1:62685794-62685813 None:intergenic 40.0%
AAAGAATCAGGTGGCTGATA+CGG - chr7_1:62685794-62685813 Msa1029260:intron 40.0%
!! CAATTTCCATTTTGGTCACG+AGG + chr7_1:62684999-62685018 None:intergenic 40.0%
! TGTGGTCGCAATTTCCATTT+TGG + chr7_1:62685007-62685026 None:intergenic 40.0%
TGAGGGGAAAACGAGTAAAT+AGG + chr7_1:62685350-62685369 None:intergenic 40.0%
! GAAACCCTAATTTGCAGCTA+GGG + chr7_1:62685395-62685414 None:intergenic 40.0%
! AGAAACCCTAATTTGCAGCT+AGG + chr7_1:62685396-62685415 None:intergenic 40.0%
!! GAGCTATTTGGTGTTTGGTT+TGG - chr7_1:62685535-62685554 Msa1029260:intron 40.0%
!!! CTGTGTTCGGTGTTGATTTT+GGG - chr7_1:62685664-62685683 Msa1029260:intron 40.0%
TATCAGCCACCTGATTCTTT+CGG + chr7_1:62685794-62685813 None:intergenic 40.0%
AAAGAATCAGGTGGCTGATA+CGG - chr7_1:62685794-62685813 Msa1029260:intron 40.0%
AATGGTCCTCGTGACCAAAA+TGG - chr7_1:62684966-62684985 Msa1029260:CDS 45.0%
!! CCATTTCCATTTTGGTCACG+AGG + chr7_1:62684975-62684994 None:intergenic 45.0%
CCTCGTGACCAAAATGGAAA+TGG - chr7_1:62684972-62684991 Msa1029260:CDS 45.0%
! CACGAGGACCATTTCCATTT+TGG + chr7_1:62684983-62685002 None:intergenic 45.0%
AATGGTCCTCGTGACCAAAA+TGG - chr7_1:62684966-62684985 Msa1029260:CDS 45.0%
TGTCGTGTCAGTGTCTGATT+GGG + chr7_1:62685154-62685173 None:intergenic 45.0%
TTGTCGTGTCAGTGTCTGAT+TGG + chr7_1:62685155-62685174 None:intergenic 45.0%
TTGCAGCTAGGGTGAGAATT+GGG + chr7_1:62685384-62685403 None:intergenic 45.0%
TTTGCAGCTAGGGTGAGAAT+TGG + chr7_1:62685385-62685404 None:intergenic 45.0%
TCTCACCCTAGCTGCAAATT+AGG - chr7_1:62685387-62685406 Msa1029260:intron 45.0%
CTCACCCTAGCTGCAAATTA+GGG - chr7_1:62685388-62685407 Msa1029260:intron 45.0%
!!! GCTGTGTTCGGTGTTGATTT+TGG - chr7_1:62685663-62685682 Msa1029260:intron 45.0%
AAGGTCCACTTGGGACTATA+TGG - chr7_1:62685742-62685761 Msa1029260:CDS 45.0%
GCTATCCATATAGTCCCAAG+TGG + chr7_1:62685750-62685769 None:intergenic 45.0%
GGATAGCTGCACATTTAGAG+AGG - chr7_1:62685763-62685782 Msa1029260:CDS 45.0%
AATGGTCCTCGTGACCAAAA+TGG - chr7_1:62684966-62684985 Msa1029260:CDS 45.0%
!! CCATTTCCATTTTGGTCACG+AGG + chr7_1:62684975-62684994 None:intergenic 45.0%
CCTCGTGACCAAAATGGAAA+TGG - chr7_1:62684972-62684991 Msa1029260:CDS 45.0%
! CACGAGGACCATTTCCATTT+TGG + chr7_1:62684983-62685002 None:intergenic 45.0%
AATGGTCCTCGTGACCAAAA+TGG - chr7_1:62684966-62684985 Msa1029260:CDS 45.0%
TGTCGTGTCAGTGTCTGATT+GGG + chr7_1:62685154-62685173 None:intergenic 45.0%
TTGTCGTGTCAGTGTCTGAT+TGG + chr7_1:62685155-62685174 None:intergenic 45.0%
TTGCAGCTAGGGTGAGAATT+GGG + chr7_1:62685384-62685403 None:intergenic 45.0%
TTTGCAGCTAGGGTGAGAAT+TGG + chr7_1:62685385-62685404 None:intergenic 45.0%
TCTCACCCTAGCTGCAAATT+AGG - chr7_1:62685387-62685406 Msa1029260:intron 45.0%
CTCACCCTAGCTGCAAATTA+GGG - chr7_1:62685388-62685407 Msa1029260:intron 45.0%
!!! GCTGTGTTCGGTGTTGATTT+TGG - chr7_1:62685663-62685682 Msa1029260:intron 45.0%
AAGGTCCACTTGGGACTATA+TGG - chr7_1:62685742-62685761 Msa1029260:CDS 45.0%
GCTATCCATATAGTCCCAAG+TGG + chr7_1:62685750-62685769 None:intergenic 45.0%
GGATAGCTGCACATTTAGAG+AGG - chr7_1:62685763-62685782 Msa1029260:CDS 45.0%
! AGCGCGATCGAGATTTGGTT+TGG + chr7_1:62685251-62685270 None:intergenic 50.0%
TTGGCGAAGAAAGGTCCACT+TGG - chr7_1:62685732-62685751 Msa1029260:CDS 50.0%
TGGCGAAGAAAGGTCCACTT+GGG - chr7_1:62685733-62685752 Msa1029260:CDS 50.0%
GAGGAAGCTCCGAAAGAATC+AGG - chr7_1:62685782-62685801 Msa1029260:intron 50.0%
GAAGCTCCGAAAGAATCAGG+TGG - chr7_1:62685785-62685804 Msa1029260:intron 50.0%
CAGGTGGCTGATACGGATAT+TGG - chr7_1:62685801-62685820 Msa1029260:intron 50.0%
! AGCGCGATCGAGATTTGGTT+TGG + chr7_1:62685251-62685270 None:intergenic 50.0%
TTGGCGAAGAAAGGTCCACT+TGG - chr7_1:62685732-62685751 Msa1029260:CDS 50.0%
TGGCGAAGAAAGGTCCACTT+GGG - chr7_1:62685733-62685752 Msa1029260:CDS 50.0%
GAGGAAGCTCCGAAAGAATC+AGG - chr7_1:62685782-62685801 Msa1029260:intron 50.0%
GAAGCTCCGAAAGAATCAGG+TGG - chr7_1:62685785-62685804 Msa1029260:intron 50.0%
CAGGTGGCTGATACGGATAT+TGG - chr7_1:62685801-62685820 Msa1029260:intron 50.0%
! TGAGGAGCGCGATCGAGATT+TGG + chr7_1:62685256-62685275 None:intergenic 55.0%
! TGAGGAGCGCGATCGAGATT+TGG + chr7_1:62685256-62685275 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 62684914 62685833 62684914 ID=Msa1029260;Name=Msa1029260
chr7_1 mRNA 62684914 62685833 62684914 ID=Msa1029260-mRNA-1;Parent=Msa1029260;Name=Msa1029260-mRNA-1;_AED=0.50;_eAED=0.79;_QI=0|0|0|0.5|0.33|0.25|4|0|106
chr7_1 exon 62685825 62685833 62685825 ID=Msa1029260-mRNA-1:exon:13454;Parent=Msa1029260-mRNA-1
chr7_1 exon 62685670 62685790 62685670 ID=Msa1029260-mRNA-1:exon:13453;Parent=Msa1029260-mRNA-1
chr7_1 exon 62685242 62685321 62685242 ID=Msa1029260-mRNA-1:exon:13452;Parent=Msa1029260-mRNA-1
chr7_1 exon 62684914 62685021 62684914 ID=Msa1029260-mRNA-1:exon:13451;Parent=Msa1029260-mRNA-1
chr7_1 CDS 62685825 62685833 62685825 ID=Msa1029260-mRNA-1:cds;Parent=Msa1029260-mRNA-1
chr7_1 CDS 62685670 62685790 62685670 ID=Msa1029260-mRNA-1:cds;Parent=Msa1029260-mRNA-1
chr7_1 CDS 62685242 62685321 62685242 ID=Msa1029260-mRNA-1:cds;Parent=Msa1029260-mRNA-1
chr7_1 CDS 62684914 62685021 62684914 ID=Msa1029260-mRNA-1:cds;Parent=Msa1029260-mRNA-1
Gene Sequence

>Msa1029260

ATGCATATGACTTCATATAATGGTCCTCGTGACCAAAATGGAAATGGTCCTCGTGACCAAAATGGAAATTGCGACCACAAAAAAAGTGTAGCACAAGAAAAAGAAATACATACTAATGTGGAAAGTGAAACTTCAAATTTACACTCGTCACATTTTCGCTTCGTTTTTCTTCGATCTTCAGCTTCACCTGTTACTAAAAGCTTAATTCTCTTTATTTTGGCGAAGAAAGGTCCACTTGGGACTATATGGATAGCTGCACATTTAGAGAGGAAGCTCCGAAAGAATCAGGTGGCTGATACGGATATTGGCGTCTCTGTA

Protein sequence

>Msa1029260

MHMTSYNGPRDQNGNGPRDQNGNCDHKKSVAQEKEIHTNVESETSNLHSSHFRFVFLRSSASPVTKSLILFILAKKGPLGTIWIAAHLERKLRKNQVADTDIGVSV