AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0872870


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0872870 MtrunA17_Chr6g0454071 95.556 90 4 0 3 92 866 955 4.76e-54 180
Msa0872870 MtrunA17_Chr7g0218421 80.374 107 21 0 3 109 870 976 6.84e-52 174
Msa0872870 MtrunA17_Chr3g0137071 52.174 92 44 0 3 94 879 970 8.51e-27 103
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0872870 AT5G15450.1 75.532 94 23 0 3 96 863 956 2.86e-45 156
Msa0872870 AT2G25140.1 50.000 96 42 2 3 98 870 959 6.59e-24 95.1
Msa0872870 AT5G51070.1 37.143 70 44 0 1 70 848 917 1.77e-11 59.7

Find 28 sgRNAs with CRISPR-Local

Find 34 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCATTTCAAATACTATTTCT+AGG 0.203814 6_1:+8469605 None:intergenic
ATCCAACTTCTTGGAAGTTT+AGG 0.235052 6_1:-8470076 Msa0872870:CDS
TATTCTTCGAGGAGAATTTA+AGG 0.278524 6_1:-8469978 Msa0872870:CDS
TCCAACTTCTTGGAAGTTTA+GGG 0.290774 6_1:-8470075 Msa0872870:CDS
GAACCTGCTATCCAACTTCT+TGG 0.317322 6_1:-8470085 Msa0872870:CDS
AACTTGGCATGGAAGATAAA+AGG 0.330056 6_1:+8469792 None:intergenic
ATCGTTCTGTTATTATAGAT+TGG 0.336034 6_1:-8469749 Msa0872870:three_prime_UTR
ACCCTAAACTTCCAAGAAGT+TGG 0.420686 6_1:+8470074 None:intergenic
GTTATTATAGATTGGAACTC+TGG 0.429182 6_1:-8469741 Msa0872870:three_prime_UTR
TCTCAAAATTCGTGTAAACT+TGG 0.442353 6_1:+8469776 None:intergenic
CTTCCAAGAAGTTGGATAGC+AGG 0.453391 6_1:+8470082 None:intergenic
TCGAGGAGAATTTAAGGAAG+AGG 0.483569 6_1:-8469972 Msa0872870:CDS
TGTTGAATCACTCGCTTCAC+CGG 0.489454 6_1:+8470028 None:intergenic
GGATAGCAGGTTCTGTTACT+CGG 0.501544 6_1:+8470095 None:intergenic
ACCGGTCTAGCACCATAGCT+TGG 0.505665 6_1:+8470046 None:intergenic
TTGCTGAGGACGTTGACCAT+TGG 0.509376 6_1:+8469913 None:intergenic
AATCTACTGCTAAAGACAGC+AGG 0.516797 6_1:-8469856 Msa0872870:CDS
CTTGCAAAGGGTATTCTTCG+AGG 0.524988 6_1:-8469989 Msa0872870:CDS
AAATTTCTTCATATAATCTG+TGG 0.530253 6_1:+8469824 None:intergenic
TCCAAGCTATGGTGCTAGAC+CGG 0.530798 6_1:-8470047 Msa0872870:CDS
GTGGAAAATGAACTTGCAAA+GGG 0.543223 6_1:-8470001 Msa0872870:CDS
TGTGGAAAATGAACTTGCAA+AGG 0.545576 6_1:-8470002 Msa0872870:CDS
GCGAGTGATTCAACAAAATG+TGG 0.563340 6_1:-8470020 Msa0872870:CDS
AAATTCGTGTAAACTTGGCA+TGG 0.589380 6_1:+8469781 None:intergenic
TTAGGGTACGATCCAAGCTA+TGG 0.593819 6_1:-8470058 Msa0872870:CDS
ATCTACTGCTAAAGACAGCA+GGG 0.595696 6_1:-8469855 Msa0872870:CDS
GAAGTCACAATACTCGCCAA+TGG 0.657171 6_1:-8469929 Msa0872870:CDS
AGTATATGCAAGCTATACAC+AGG 0.666070 6_1:+8469717 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! GTTTATATTTTACTTTATAT+TGG - chr6_1:8470034-8470053 Msa0872870:CDS 10.0%
!! AAATTTCTTCATATAATCTG+TGG + chr6_1:8469899-8469918 None:intergenic 20.0%
!!! TCATTTCAAATACTATTTCT+AGG + chr6_1:8470118-8470137 None:intergenic 20.0%
! ATCGTTCTGTTATTATAGAT+TGG - chr6_1:8469971-8469990 Msa0872870:CDS 25.0%
TATTCTTCGAGGAGAATTTA+AGG - chr6_1:8469742-8469761 Msa0872870:three_prime_UTR 30.0%
TCTCAAAATTCGTGTAAACT+TGG + chr6_1:8469947-8469966 None:intergenic 30.0%
GTTATTATAGATTGGAACTC+TGG - chr6_1:8469979-8469998 Msa0872870:CDS 30.0%
! TTACTCGGATTTTCATCTTG+CGG + chr6_1:8469613-8469632 None:intergenic 35.0%
ATCCAACTTCTTGGAAGTTT+AGG - chr6_1:8469644-8469663 Msa0872870:three_prime_UTR 35.0%
TCCAACTTCTTGGAAGTTTA+GGG - chr6_1:8469645-8469664 Msa0872870:three_prime_UTR 35.0%
TGTGGAAAATGAACTTGCAA+AGG - chr6_1:8469718-8469737 Msa0872870:three_prime_UTR 35.0%
GTGGAAAATGAACTTGCAAA+GGG - chr6_1:8469719-8469738 Msa0872870:three_prime_UTR 35.0%
!!! CTAAAAACTAGCTTTTGCTG+AGG + chr6_1:8469824-8469843 None:intergenic 35.0%
!!! CTCAGCAAAAGCTAGTTTTT+AGG - chr6_1:8469822-8469841 Msa0872870:exon 35.0%
!!! AGCAAAAGCTAGTTTTTAGG+AGG - chr6_1:8469825-8469844 Msa0872870:exon 35.0%
!!! GCAAAAGCTAGTTTTTAGGA+GGG - chr6_1:8469826-8469845 Msa0872870:exon 35.0%
AACTTGGCATGGAAGATAAA+AGG + chr6_1:8469931-8469950 None:intergenic 35.0%
AAATTCGTGTAAACTTGGCA+TGG + chr6_1:8469942-8469961 None:intergenic 35.0%
AGTATATGCAAGCTATACAC+AGG + chr6_1:8470006-8470025 None:intergenic 35.0%
ACCCTAAACTTCCAAGAAGT+TGG + chr6_1:8469649-8469668 None:intergenic 40.0%
GCGAGTGATTCAACAAAATG+TGG - chr6_1:8469700-8469719 Msa0872870:three_prime_UTR 40.0%
TCGAGGAGAATTTAAGGAAG+AGG - chr6_1:8469748-8469767 Msa0872870:three_prime_UTR 40.0%
AATCTACTGCTAAAGACAGC+AGG - chr6_1:8469864-8469883 Msa0872870:CDS 40.0%
ATCTACTGCTAAAGACAGCA+GGG - chr6_1:8469865-8469884 Msa0872870:CDS 40.0%
GGATAGCAGGTTCTGTTACT+CGG + chr6_1:8469628-8469647 None:intergenic 45.0%
GAACCTGCTATCCAACTTCT+TGG - chr6_1:8469635-8469654 Msa0872870:three_prime_UTR 45.0%
CTTCCAAGAAGTTGGATAGC+AGG + chr6_1:8469641-8469660 None:intergenic 45.0%
TTAGGGTACGATCCAAGCTA+TGG - chr6_1:8469662-8469681 Msa0872870:three_prime_UTR 45.0%
TGTTGAATCACTCGCTTCAC+CGG + chr6_1:8469695-8469714 None:intergenic 45.0%
!! CTTGCAAAGGGTATTCTTCG+AGG - chr6_1:8469731-8469750 Msa0872870:three_prime_UTR 45.0%
GAAGTCACAATACTCGCCAA+TGG - chr6_1:8469791-8469810 Msa0872870:three_prime_UTR 45.0%
! TCCAAGCTATGGTGCTAGAC+CGG - chr6_1:8469673-8469692 Msa0872870:three_prime_UTR 50.0%
TTGCTGAGGACGTTGACCAT+TGG + chr6_1:8469810-8469829 None:intergenic 50.0%
ACCGGTCTAGCACCATAGCT+TGG + chr6_1:8469677-8469696 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr6_1 gene 8469565 8470177 8469565 ID=Msa0872870;Name=Msa0872870
chr6_1 mRNA 8469565 8470177 8469565 ID=Msa0872870-mRNA-1;Parent=Msa0872870;Name=Msa0872870-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|0|0.5|1|1|1|2|267|111
chr6_1 exon 8469565 8470161 8469565 ID=Msa0872870-mRNA-1:exon:2611;Parent=Msa0872870-mRNA-1
chr6_1 exon 8470172 8470177 8470172 ID=Msa0872870-mRNA-1:exon:2610;Parent=Msa0872870-mRNA-1
chr6_1 CDS 8470172 8470177 8470172 ID=Msa0872870-mRNA-1:cds;Parent=Msa0872870-mRNA-1
chr6_1 CDS 8469832 8470161 8469832 ID=Msa0872870-mRNA-1:cds;Parent=Msa0872870-mRNA-1
chr6_1 three_prime_UTR 8469565 8469831 8469565 ID=Msa0872870-mRNA-1:three_prime_utr;Parent=Msa0872870-mRNA-1
Gene Sequence

>Msa0872870

ATGTTTTTGGAGCGCGTGCAGAAGAGAATTGCTGACCGCAAGATGAAAATCCGAGTAACAGAACCTGCTATCCAACTTCTTGGAAGTTTAGGGTACGATCCAAGCTATGGTGCTAGACCGGTGAAGCGAGTGATTCAACAAAATGTGGAAAATGAACTTGCAAAGGGTATTCTTCGAGGAGAATTTAAGGAAGAGGACACAATTTTAGTCGACACAGAAGTCACAATACTCGCCAATGGTCAACGTCCTCAGCAAAAGCTAGTTTTTAGGAGGGTTGAAGCTGATTCAGAATCTACTGCTAAAGACAGCAGGGAAAGTTTTCCACAGATTATATGA

Protein sequence

>Msa0872870

MFLERVQKRIADRKMKIRVTEPAIQLLGSLGYDPSYGARPVKRVIQQNVENELAKGILRGEFKEEDTILVDTEVTILANGQRPQQKLVFRRVEADSESTAKDSRESFPQII*