AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0013450

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0013450 MtrunA17_Chr1g0162931 77.966 59 13 0 1 59 1 59 3.18e-29 104
Msa0013450 MtrunA17_Chr1g0210911 65.574 61 18 1 2 59 3 63 1.84e-23 89.7
Msa0013450 MtrunA17_Chr2g0288601 54.902 51 23 0 9 59 62 112 6.12e-17 68.9
Msa0013450 MtrunA17_Chr2g0320231 53.704 54 25 0 5 58 84 137 8.64e-16 69.3
Msa0013450 MtrunA17_Chr8g0379121 51.852 54 26 0 6 59 99 152 2.17e-15 68.2
Msa0013450 MtrunA17_Chr2g0283951 51.852 54 26 0 6 59 77 130 1.25e-14 65.9
Msa0013450 MtrunA17_Chr7g0243081 45.614 57 31 0 3 59 56 112 4.01e-14 64.7
Msa0013450 MtrunA17_Chr3g0095611 48.980 49 25 0 10 58 11 59 3.88e-12 58.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0013450 AT1G14600.1 51.562 64 26 1 1 59 1 64 5.22e-16 69.3
Msa0013450 AT2G02060.2 56.000 50 22 0 10 59 21 70 2.23e-15 67.8
Msa0013450 AT2G02060.1 56.000 50 22 0 10 59 21 70 2.23e-15 67.8
Msa0013450 AT2G40260.1 53.846 52 24 0 8 59 72 123 7.23e-14 64.3
Msa0013450 AT2G38300.1 56.000 50 22 0 10 59 46 95 3.31e-13 62.4
Msa0013450 AT4G04605.1 49.020 51 26 0 9 59 5 55 1.11e-12 60.1
Msa0013450 AT2G42660.1 50.000 50 25 0 10 59 42 91 2.10e-12 59.7

Find 17 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCATTCTTTCAAATCCAAA+AGG 0.369949 1_1:-20806850 None:intergenic
GTTTATGCCATTGAAACTCT+TGG 0.378805 1_1:+20806961 Msa0013450:CDS
ACAAAGCAACGATGAAGTTC+AGG 0.401903 1_1:-20806940 None:intergenic
CAAAGGTTCCTCGTTTAAGA+TGG 0.432536 1_1:+20806914 Msa0013450:CDS
ATGACCACCAAGAGTTTCAA+TGG 0.434104 1_1:-20806968 None:intergenic
TTCCTCGGTATGCACATGTC+AGG 0.442104 1_1:+20807108 Msa0013450:CDS
TCATTCTTTCAAATCCAAAA+GGG 0.518435 1_1:-20806849 None:intergenic
ATGAGTAGTTGTGGAAGGGA+AGG 0.528216 1_1:+20806868 Msa0013450:CDS
AAAGAATGAGTAGTTGTGGA+AGG 0.546541 1_1:+20806863 Msa0013450:exon
TTTGAAAGAATGAGTAGTTG+TGG 0.567741 1_1:+20806859 Msa0013450:exon
GGTCATACTGATTATGCAGT+AGG 0.571456 1_1:-20807144 None:intergenic
AAGAATGAGTAGTTGTGGAA+GGG 0.598417 1_1:+20806864 Msa0013450:exon
GAGACAATATGTAAGATCAA+AGG 0.602756 1_1:+20806897 Msa0013450:CDS
TATGCCATTGAAACTCTTGG+TGG 0.619663 1_1:+20806964 Msa0013450:CDS
GCTAAATAGAGGTAATTCCG+AGG 0.689396 1_1:+20807079 Msa0013450:intron
TTCCTGACATGTGCATACCG+AGG 0.711764 1_1:-20807110 None:intergenic
TCAGGTGTCCATCTTAAACG+AGG 0.752182 1_1:-20806922 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCATTCTTTCAAATCCAAAA+GGG - chr1_1:20806852-20806871 None:intergenic 25.0%
! TTATTCACTACAAGAAATGA+TGG + chr1_1:20807017-20807036 Msa0013450:intron 25.0%
CTCATTCTTTCAAATCCAAA+AGG - chr1_1:20806853-20806872 None:intergenic 30.0%
TTTGAAAGAATGAGTAGTTG+TGG + chr1_1:20806859-20806878 Msa0013450:exon 30.0%
GAGACAATATGTAAGATCAA+AGG + chr1_1:20806897-20806916 Msa0013450:CDS 30.0%
!!! GTGTTTTGAGGGTTTTTTTG+AGG + chr1_1:20806825-20806844 Msa0013450:five_prime_UTR 35.0%
AAAGAATGAGTAGTTGTGGA+AGG + chr1_1:20806863-20806882 Msa0013450:exon 35.0%
AAGAATGAGTAGTTGTGGAA+GGG + chr1_1:20806864-20806883 Msa0013450:exon 35.0%
GTTTATGCCATTGAAACTCT+TGG + chr1_1:20806961-20806980 Msa0013450:CDS 35.0%
!!! GGTTTTTTTGAGGACCCTTT+TGG + chr1_1:20806835-20806854 Msa0013450:five_prime_UTR 40.0%
CAAAGGTTCCTCGTTTAAGA+TGG + chr1_1:20806914-20806933 Msa0013450:CDS 40.0%
ACAAAGCAACGATGAAGTTC+AGG - chr1_1:20806943-20806962 None:intergenic 40.0%
TATGCCATTGAAACTCTTGG+TGG + chr1_1:20806964-20806983 Msa0013450:CDS 40.0%
ATGACCACCAAGAGTTTCAA+TGG - chr1_1:20806971-20806990 None:intergenic 40.0%
ATTCCGACCAAAAAATTCCG+AGG + chr1_1:20807042-20807061 Msa0013450:intron 40.0%
!!! GTTCCTCGGAATTTTTTGGT+CGG - chr1_1:20807048-20807067 None:intergenic 40.0%
!!! GATGGTTCCTCGGAATTTTT+TGG - chr1_1:20807052-20807071 None:intergenic 40.0%
CTCTATTTAGCGAGAAACGA+TGG - chr1_1:20807070-20807089 None:intergenic 40.0%
CATCGTTTCTCGCTAAATAG+AGG + chr1_1:20807068-20807087 Msa0013450:intron 40.0%
GCTAAATAGAGGTAATTCCG+AGG + chr1_1:20807079-20807098 Msa0013450:intron 40.0%
!! ATTCCGAGGAACTTTTTCCT+CGG + chr1_1:20807093-20807112 Msa0013450:CDS 40.0%
ATACCGAGGAAAAAGTTCCT+CGG - chr1_1:20807099-20807118 None:intergenic 40.0%
ATGAGTAGTTGTGGAAGGGA+AGG + chr1_1:20806868-20806887 Msa0013450:CDS 45.0%
TCAGGTGTCCATCTTAAACG+AGG - chr1_1:20806925-20806944 None:intergenic 45.0%
AGCGAGAAACGATGGTTCCT+CGG - chr1_1:20807062-20807081 None:intergenic 50.0%
TTCCTCGGTATGCACATGTC+AGG + chr1_1:20807108-20807127 Msa0013450:CDS 50.0%
TTCCTGACATGTGCATACCG+AGG - chr1_1:20807113-20807132 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr1_1 gene 20806819 20807155 20806819 ID=Msa0013450;Name=Msa0013450
chr1_1 mRNA 20806819 20807155 20806819 ID=Msa0013450-mRNA-1;Parent=Msa0013450;Name=Msa0013450-mRNA-1;_AED=0.28;_eAED=0.28;_QI=49|0|0.5|0.5|1|1|2|0|64
chr1_1 exon 20806819 20806994 20806819 ID=Msa0013450-mRNA-1:exon:7435;Parent=Msa0013450-mRNA-1
chr1_1 exon 20807088 20807155 20807088 ID=Msa0013450-mRNA-1:exon:7436;Parent=Msa0013450-mRNA-1
chr1_1 five_prime_UTR 20806819 20806867 20806819 ID=Msa0013450-mRNA-1:five_prime_utr;Parent=Msa0013450-mRNA-1
chr1_1 CDS 20806868 20806994 20806868 ID=Msa0013450-mRNA-1:cds;Parent=Msa0013450-mRNA-1
chr1_1 CDS 20807088 20807155 20807088 ID=Msa0013450-mRNA-1:cds;Parent=Msa0013450-mRNA-1
Gene Sequence

>Msa0013450

ATGAGTAGTTGTGGAAGGGAAGGTGTTGTGAGACAATATGTAAGATCAAAGGTTCCTCGTTTAAGATGGACACCTGAACTTCATCGTTGCTTTGTTTATGCCATTGAAACTCTTGGTGGTCATCAAAAGGTAATTCCGAGGAACTTTTTCCTCGGTATGCACATGTCAGGAATCTCTGCTCTTCCTACTGCATAA
Protein sequence

>Msa0013450

MSSCGREGVVRQYVRSKVPRLRWTPELHRCFVYAIETLGGHQKVIPRNFFLGMHMSGISALPTA*