AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG032193

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG032193 MtrunA17_Chr5g0421971 91.860 172 14 0 3 174 1 172 9.32e-117 328
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG032193 AT5G05330.1 42.515 167 76 5 2 159 32 187 2.44e-30 110
MsaG032193 AT5G05330.3 38.922 167 74 6 2 159 32 179 1.28e-22 90.1
MsaG032193 AT5G05330.2 37.121 132 65 4 37 159 2 124 1.72e-16 72.8

Find 40 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATCCTGTTTCAAAGCTTCT+TGG 0.215238 6:+46893933 None:intergenic
GGAGAAGAAGAGTTAGAAAA+AGG 0.281580 6:-46896029 MsaT032193.1:CDS
GTGAGGAATGTTACATAAAA+AGG 0.291799 6:+46895700 None:intergenic
CCTCATGCTCGTGCTCTTGA+TGG 0.300970 6:-46895994 MsaT032193.1:CDS
TTCATCAAATGTTGAATGTT+TGG 0.319797 6:+46895747 None:intergenic
ATATATATACCATTTGAAAA+AGG 0.336282 6:+46895966 None:intergenic
AATGTTTGGCCGAGTTCGCC+TGG 0.350229 6:+46895761 None:intergenic
TGTTTCTCATGCTAGAGAAT+TGG 0.360591 6:-46893966 MsaT032193.1:CDS
ATTATAATATTGAACTTGAT+AGG 0.361065 6:-46894173 MsaT032193.1:CDS
CTTCTCCGTGCCATCAGCAT+TGG 0.388133 6:+46896045 None:intergenic
ATTCAATTCAAAAGGTTACT+TGG 0.396107 6:-46895792 MsaT032193.1:CDS
GGATGCTGATGGGATCATTA+AGG 0.400417 6:-46893915 MsaT032193.1:intron
ACTGGTTGAGATTCTTGATA+AGG 0.406697 6:-46893108 MsaT032193.1:intron
ATATTGAACTTGATAGGATA+GGG 0.419391 6:-46894167 MsaT032193.1:CDS
CCAACAAGATTCAATTCAAA+AGG 0.430763 6:-46895800 MsaT032193.1:CDS
AGATTCTCTAAAGATCATTT+CGG 0.433090 6:+46892982 None:intergenic
AATATTGAACTTGATAGGAT+AGG 0.444990 6:-46894168 MsaT032193.1:CDS
ATAGGATAGGGTTTGAAAAG+TGG 0.454750 6:-46894155 MsaT032193.1:CDS
ACACCAAGAAGCTTTGAAAC+AGG 0.456775 6:-46893936 MsaT032193.1:CDS
GGTTACTTGGAATCGTTCCC+AGG 0.456873 6:-46895779 MsaT032193.1:CDS
AAAAGGCGATAAGGCGAAAT+GGG 0.467083 6:+46895717 None:intergenic
GAATCGTTCCCAGGCGAACT+CGG 0.512839 6:-46895770 MsaT032193.1:CDS
TCTCTAGCATGAGAAACAAA+TGG 0.535184 6:+46893971 None:intergenic
TATCAGGGAAAGCTTCATGA+AGG 0.540658 6:-46894211 MsaT032193.1:intron
GGCGATAAGGCGAAATGGGT+TGG 0.554242 6:+46895721 None:intergenic
ATGTTTGGCCGAGTTCGCCT+GGG 0.560956 6:+46895762 None:intergenic
ATCAACCAATGCTGATGGCA+CGG 0.570517 6:-46896050 None:intergenic
AAGAGCACGAGCATGAGGTA+TGG 0.582268 6:+46895999 None:intergenic
CTTTGAAACAGGATGCTGAT+GGG 0.589300 6:-46893925 MsaT032193.1:CDS
CTTCATGAAGGGTCAAGACG+TGG 0.592712 6:-46894199 MsaT032193.1:CDS
ACAATAATGCATATCAGCCA+AGG 0.611858 6:+46895827 None:intergenic
GATCAATCAACCAATGCTGA+TGG 0.613091 6:-46896055 None:intergenic
GCTTTGAAACAGGATGCTGA+TGG 0.615619 6:-46893926 MsaT032193.1:CDS
CCATCAAGAGCACGAGCATG+AGG 0.616092 6:+46895994 None:intergenic
ATCAGGGAAAGCTTCATGAA+GGG 0.616747 6:-46894210 MsaT032193.1:intron
GTATGGAGCAGATTCACCAC+TGG 0.653372 6:-46893126 MsaT032193.1:CDS
GTGTATGTAGTGAAACATGT+GGG 0.656930 6:-46895866 MsaT032193.1:intron
TTATCAAGAATCTCAACCAG+TGG 0.666090 6:+46893110 None:intergenic
GATCTTTAGAGAATCTTCAG+CGG 0.684407 6:-46892975 MsaT032193.1:CDS
TGTGTATGTAGTGAAACATG+TGG 0.688569 6:-46895867 MsaT032193.1:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr6 gene 46892958 46896064 46892958 ID=MsaG032193
Chr6 mRNA 46892958 46896064 46892958 ID=MsaT032193.1;Parent=MsaG032193
Chr6 exon 46892958 46893005 46892958 ID=MsaT032193.1.exon6;Parent=MsaT032193.1
Chr6 CDS 46892958 46893005 46892958 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Chr6 exon 46893109 46893153 46893109 ID=MsaT032193.1.exon5;Parent=MsaT032193.1
Chr6 CDS 46893109 46893153 46893109 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Chr6 exon 46893916 46894002 46893916 ID=MsaT032193.1.exon4;Parent=MsaT032193.1
Chr6 CDS 46893916 46894002 46893916 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Chr6 exon 46894137 46894227 46894137 ID=MsaT032193.1.exon3;Parent=MsaT032193.1
Chr6 CDS 46894137 46894227 46894137 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Chr6 exon 46895714 46895878 46895714 ID=MsaT032193.1.exon2;Parent=MsaT032193.1
Chr6 CDS 46895714 46895878 46895714 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Chr6 exon 46895976 46896064 46895976 ID=MsaT032193.1.exon1;Parent=MsaT032193.1
Chr6 CDS 46895976 46896064 46895976 ID=cds.MsaT032193.1;Parent=MsaT032193.1
Gene Sequence

>MsaT032193.1

ATGCTGATGGCACGGAGAAGAAGAGTTAGAAAAAGGGTTAGTGCCATACCTCATGCTCGTGCTCTTGATGGAAGTGCCTTTTTCAAATGTGAAACATGTGGGTTTTCTGTTGCTATTGCCTTGGCTGATATGCATTATTGTGACTCCAACAAGATTCAATTCAAAAGGTTACTTGGAATCGTTCCCAGGCGAACTCGGCCAAACATTCAACATTTGATGAAGAGCCAACCCATTTCGCCTTATCGCCTTTTTATGGAAAGCTTCATGAAGGGTCAAGACGTGGAAAATTATAATATTGAACTTGATAGGATAGGGTTTGAAAAGTGGAAAAATATGTCGAAGGAGGAGAAGCAACCATTTGTTTCTCATGCTAGAGAATTGGACAATAAACACCAAGAAGCTTTGAAACAGGATGCTGATGGGATCATTAAGATAAAGTATGGAGCAGATTCACCACTGGTTGAGATTCTTGATAAGACCGAAATGATCTTTAGAGAATCTTCAGCGGATCACTCAAAAGAATAA
Protein sequence

>MsaT032193.1

MLMARRRRVRKRVSAIPHARALDGSAFFKCETCGFSVAIALADMHYCDSNKIQFKRLLGIVPRRTRPNIQHLMKSQPISPYRLFMESFMKGQDVENYNIELDRIGFEKWKNMSKEEKQPFVSHARELDNKHQEALKQDADGIIKIKYGADSPLVEILDKTEMIFRESSADHSKE*