AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1176980


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1176980 MtrunA17_Chr8g0347791 98.630 146 2 0 1 146 1 146 2.56e-101 286
Msa1176980 MtrunA17_Chr3g0077491 83.333 150 21 1 1 146 1 150 1.84e-77 226
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1176980 AT2G04520.1 87.671 146 17 1 1 146 1 145 8.62e-85 245
Msa1176980 AT5G35680.1 86.986 146 18 1 1 146 1 145 8.00e-80 232
Msa1176980 AT5G35680.2 86.986 146 18 1 1 146 1 145 8.00e-80 232
Msa1176980 AT5G35680.3 93.277 119 8 0 1 119 1 119 6.65e-78 228

Find 47 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGTTGGGTTGCGTGATTATC+AGG 0.308178 8_1:+9338894 Msa1176980:CDS
TCATTAAGCCTCACACCTTC+AGG 0.319525 8_1:-9338988 None:intergenic
CCTCCCTTTCCCTTGTTCTT+CGG 0.331257 8_1:-9338664 None:intergenic
GCTGGGGATATTATTCTTGT+TGG 0.331915 8_1:+9338877 Msa1176980:CDS
CTGGGGATATTATTCTTGTT+GGG 0.363705 8_1:+9338878 Msa1176980:CDS
GGAATTGGCGGTGGGATTGA+TGG 0.364077 8_1:+9339012 Msa1176980:CDS
GAGGATATTGATAAGATTTG+AGG 0.399236 8_1:+9339081 Msa1176980:CDS
GAAAGATGCACAAGAAGGTT+TGG 0.408452 8_1:+9338848 Msa1176980:CDS
CTTTCCCTTGTTCTTCGGCA+TGG 0.425552 8_1:-9338659 None:intergenic
GAATTGGCGGTGGGATTGAT+GGG 0.426333 8_1:+9339013 Msa1176980:CDS
GTGAGGCTTAATGAAGGAAT+TGG 0.445642 8_1:+9338997 Msa1176980:CDS
AAGAAGGTTTGGATTGCTGC+TGG 0.450047 8_1:+9338859 Msa1176980:CDS
TTATATTGAGTTTGAGGATG+AGG 0.463979 8_1:+9339062 Msa1176980:CDS
GCACAGGTTCTTCGTATGCT+TGG 0.465282 8_1:+9338766 Msa1176980:CDS
GGGGATGATGATGAGGGTGA+TGG 0.471229 8_1:+9339033 Msa1176980:CDS
GGGATGATGATGAGGGTGAT+GGG 0.477444 8_1:+9339034 Msa1176980:CDS
TTCAACAATCTCGCCTCATC+CGG 0.477469 8_1:-9338949 None:intergenic
AGGATATTGATAAGATTTGA+GGG 0.478420 8_1:+9339082 Msa1176980:CDS
GAATGATTATATTGAGTTTG+AGG 0.491210 8_1:+9339056 Msa1176980:CDS
GAAGGTTTGGATTGCTGCTG+GGG 0.517248 8_1:+9338861 Msa1176980:CDS
GCGTGATTATCAGGATGATA+AGG 0.518535 8_1:+9338903 Msa1176980:CDS
AGAAGGTTTGGATTGCTGCT+GGG 0.519846 8_1:+9338860 Msa1176980:CDS
CTTAATGAAGGAATTGGCGG+TGG 0.526665 8_1:+9339003 Msa1176980:CDS
CCTTCTTGTGCATCTTTCCA+CGG 0.526928 8_1:-9338843 None:intergenic
GGATGAGGCGAGATTGTTGA+AGG 0.537010 8_1:+9338951 Msa1176980:CDS
ATGCCGAAGAACAAGGGAAA+GGG 0.538255 8_1:+9338661 Msa1176980:CDS
GATTGATGGGGATGATGATG+AGG 0.545936 8_1:+9339026 Msa1176980:CDS
TTCAACCATGCCGAAGAACA+AGG 0.546102 8_1:+9338654 None:intergenic
GTTCTTCGTATGCTTGGAAA+CGG 0.546331 8_1:+9338772 Msa1176980:CDS
CTTGAAGTATATGCCGGATG+AGG 0.557673 8_1:+9338936 Msa1176980:CDS
ATTGATGGGGATGATGATGA+GGG 0.568262 8_1:+9339027 Msa1176980:CDS
CTTTGTTCCATCGATACACA+TGG 0.573074 8_1:-9338806 None:intergenic
GGAGGAAAGAATCGCAAGAG+AGG 0.578624 8_1:+9338682 Msa1176980:CDS
CCGTGGAAAGATGCACAAGA+AGG 0.600822 8_1:+9338843 Msa1176980:CDS
CATGCCGAAGAACAAGGGAA+AGG 0.602323 8_1:+9338660 None:intergenic
AAGCGTCTCTGTCATATCCG+TGG 0.616715 8_1:+9338826 Msa1176980:CDS
GCGTATAGCGAGCTTCCTGA+AGG 0.618073 8_1:+9338973 Msa1176980:CDS
GAAGGTGTGAGGCTTAATGA+AGG 0.621479 8_1:+9338991 Msa1176980:CDS
AATTGGCGGTGGGATTGATG+GGG 0.623047 8_1:+9339014 Msa1176980:CDS
TGTGAAGCCATGTGTATCGA+TGG 0.627821 8_1:+9338799 Msa1176980:CDS
CCGAAGAACAAGGGAAAGGG+AGG 0.634335 8_1:+9338664 Msa1176980:CDS
TCAACCATGCCGAAGAACAA+GGG 0.635918 8_1:+9338655 None:intergenic
GCGAGCTTCCTGAAGGTGTG+AGG 0.643888 8_1:+9338980 Msa1176980:CDS
TTAATGAAGGAATTGGCGGT+GGG 0.646610 8_1:+9339004 Msa1176980:CDS
AGATGGTCAAGAATACGCAC+AGG 0.647023 8_1:+9338750 Msa1176980:CDS
TGTGATCTTGAAGTATATGC+CGG 0.651550 8_1:+9338930 Msa1176980:CDS
AGGCTTAATGAAGGAATTGG+CGG 0.656842 8_1:+9339000 Msa1176980:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! GAATGATTATATTGAGTTTG+AGG + chr8_1:9339056-9339075 Msa1176980:CDS 25.0%
TTATATTGAGTTTGAGGATG+AGG + chr8_1:9339062-9339081 Msa1176980:CDS 30.0%
CTGGGGATATTATTCTTGTT+GGG + chr8_1:9338878-9338897 Msa1176980:CDS 35.0%
TGTGATCTTGAAGTATATGC+CGG + chr8_1:9338930-9338949 Msa1176980:CDS 35.0%
!! AAAGCGTGAGCTTGTTTTCA+AGG + chr8_1:9338726-9338745 Msa1176980:CDS 40.0%
!! GAGCTTGTTTTCAAGGAAGA+TGG + chr8_1:9338733-9338752 Msa1176980:CDS 40.0%
GTTCTTCGTATGCTTGGAAA+CGG + chr8_1:9338772-9338791 Msa1176980:CDS 40.0%
CTTTGTTCCATCGATACACA+TGG - chr8_1:9338809-9338828 None:intergenic 40.0%
GAAAGATGCACAAGAAGGTT+TGG + chr8_1:9338848-9338867 Msa1176980:CDS 40.0%
GCTGGGGATATTATTCTTGT+TGG + chr8_1:9338877-9338896 Msa1176980:CDS 40.0%
GCGTGATTATCAGGATGATA+AGG + chr8_1:9338903-9338922 Msa1176980:CDS 40.0%
GTGAGGCTTAATGAAGGAAT+TGG + chr8_1:9338997-9339016 Msa1176980:CDS 40.0%
AGGCTTAATGAAGGAATTGG+CGG + chr8_1:9339000-9339019 Msa1176980:CDS 40.0%
TTAATGAAGGAATTGGCGGT+GGG + chr8_1:9339004-9339023 Msa1176980:CDS 40.0%
! ATTGATGGGGATGATGATGA+GGG + chr8_1:9339027-9339046 Msa1176980:CDS 40.0%
ATGCCGAAGAACAAGGGAAA+GGG + chr8_1:9338661-9338680 Msa1176980:CDS 45.0%
AGATGGTCAAGAATACGCAC+AGG + chr8_1:9338750-9338769 Msa1176980:CDS 45.0%
TGTGAAGCCATGTGTATCGA+TGG + chr8_1:9338799-9338818 Msa1176980:CDS 45.0%
CCTTCTTGTGCATCTTTCCA+CGG - chr8_1:9338846-9338865 None:intergenic 45.0%
AAGAAGGTTTGGATTGCTGC+TGG + chr8_1:9338859-9338878 Msa1176980:CDS 45.0%
AGAAGGTTTGGATTGCTGCT+GGG + chr8_1:9338860-9338879 Msa1176980:CDS 45.0%
! TGTTGGGTTGCGTGATTATC+AGG + chr8_1:9338894-9338913 Msa1176980:CDS 45.0%
CTTGAAGTATATGCCGGATG+AGG + chr8_1:9338936-9338955 Msa1176980:CDS 45.0%
TTCAACAATCTCGCCTCATC+CGG - chr8_1:9338952-9338971 None:intergenic 45.0%
TCATTAAGCCTCACACCTTC+AGG - chr8_1:9338991-9339010 None:intergenic 45.0%
! GAAGGTGTGAGGCTTAATGA+AGG + chr8_1:9338991-9339010 Msa1176980:CDS 45.0%
CTTAATGAAGGAATTGGCGG+TGG + chr8_1:9339003-9339022 Msa1176980:CDS 45.0%
! GATTGATGGGGATGATGATG+AGG + chr8_1:9339026-9339045 Msa1176980:CDS 45.0%
CCTCCCTTTCCCTTGTTCTT+CGG - chr8_1:9338667-9338686 None:intergenic 50.0%
GGAGGAAAGAATCGCAAGAG+AGG + chr8_1:9338682-9338701 Msa1176980:CDS 50.0%
GCACAGGTTCTTCGTATGCT+TGG + chr8_1:9338766-9338785 Msa1176980:CDS 50.0%
AAGCGTCTCTGTCATATCCG+TGG + chr8_1:9338826-9338845 Msa1176980:CDS 50.0%
CCGTGGAAAGATGCACAAGA+AGG + chr8_1:9338843-9338862 Msa1176980:CDS 50.0%
GAAGGTTTGGATTGCTGCTG+GGG + chr8_1:9338861-9338880 Msa1176980:CDS 50.0%
GGATGAGGCGAGATTGTTGA+AGG + chr8_1:9338951-9338970 Msa1176980:CDS 50.0%
GAATTGGCGGTGGGATTGAT+GGG + chr8_1:9339013-9339032 Msa1176980:CDS 50.0%
AATTGGCGGTGGGATTGATG+GGG + chr8_1:9339014-9339033 Msa1176980:CDS 50.0%
! GGGATGATGATGAGGGTGAT+GGG + chr8_1:9339034-9339053 Msa1176980:CDS 50.0%
CCGAAGAACAAGGGAAAGGG+AGG + chr8_1:9338664-9338683 Msa1176980:CDS 55.0%
GCGTATAGCGAGCTTCCTGA+AGG + chr8_1:9338973-9338992 Msa1176980:CDS 55.0%
GGAATTGGCGGTGGGATTGA+TGG + chr8_1:9339012-9339031 Msa1176980:CDS 55.0%
! GGGGATGATGATGAGGGTGA+TGG + chr8_1:9339033-9339052 Msa1176980:CDS 55.0%
! GCGAGCTTCCTGAAGGTGTG+AGG + chr8_1:9338980-9338999 Msa1176980:CDS 60.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 9338661 9339101 9338661 ID=Msa1176980;Name=Msa1176980
chr8_1 mRNA 9338661 9339101 9338661 ID=Msa1176980-mRNA-1;Parent=Msa1176980;Name=Msa1176980-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|146
chr8_1 exon 9338661 9339101 9338661 ID=Msa1176980-mRNA-1:exon:3117;Parent=Msa1176980-mRNA-1
chr8_1 CDS 9338661 9339101 9338661 ID=Msa1176980-mRNA-1:cds;Parent=Msa1176980-mRNA-1
Gene Sequence

>Msa1176980

ATGCCGAAGAACAAGGGAAAGGGAGGAAAGAATCGCAAGAGAGGAAAGAACGAAGCAGATGACGAAAAGCGTGAGCTTGTTTTCAAGGAAGATGGTCAAGAATACGCACAGGTTCTTCGTATGCTTGGAAACGGTCGTTGTGAAGCCATGTGTATCGATGGAACAAAGCGTCTCTGTCATATCCGTGGAAAGATGCACAAGAAGGTTTGGATTGCTGCTGGGGATATTATTCTTGTTGGGTTGCGTGATTATCAGGATGATAAGGCTGATGTGATCTTGAAGTATATGCCGGATGAGGCGAGATTGTTGAAGGCGTATAGCGAGCTTCCTGAAGGTGTGAGGCTTAATGAAGGAATTGGCGGTGGGATTGATGGGGATGATGATGAGGGTGATGGGAATGATTATATTGAGTTTGAGGATGAGGATATTGATAAGATTTGA

Protein sequence

>Msa1176980

MPKNKGKGGKNRKRGKNEADDEKRELVFKEDGQEYAQVLRMLGNGRCEAMCIDGTKRLCHIRGKMHKKVWIAAGDIILVGLRDYQDDKADVILKYMPDEARLLKAYSELPEGVRLNEGIGGGIDGDDDEGDGNDYIEFEDEDIDKI*