AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1419810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419810 MtrunA17_Chr4g0068031 74.227 97 19 2 5 95 16 112 7.67e-32 108
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1419810 AT5G49300.1 45.238 84 36 2 15 95 32 108 4.03e-13 61.2
Msa1419810 AT3G06740.1 45.122 82 33 3 15 93 37 109 2.75e-12 58.9
Msa1419810 AT4G16141.1 61.702 47 15 1 18 61 36 82 1.19e-11 58.2

Find 27 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAGAGATTATTGAATTTA+AGG 0.060866 tig0024730:+22292 Msa1419810:CDS
AAGAAGAAGAGAGCAATATT+AGG 0.216353 tig0024730:+22177 Msa1419810:CDS
AACAGAGCTAGTAAAGTTTA+TGG 0.220023 tig0024730:-21942 Msa1419810:intergenic
ACCACGACATTGAGGAGTTT+TGG 0.295427 tig0024730:-22014 Msa1419810:intergenic
TCTCTTCTTCTTCCTGCTCC+TGG 0.356990 tig0024730:-22166 Msa1419810:intergenic
AGAAGAAGAGAGCAATATTA+GGG 0.387155 tig0024730:+22178 Msa1419810:CDS
AACGAAGAAGGAACAAGAAA+GGG 0.398579 tig0024730:+22216 Msa1419810:CDS
GCGGCGCAGGAAGCAAAGTT+GGG 0.416991 tig0024730:+22253 Msa1419810:CDS
GGCGGCGCAGGAAGCAAAGT+TGG 0.432286 tig0024730:+22252 Msa1419810:CDS
ATGCTTGCCGGACCAGGAGC+AGG 0.441262 tig0024730:+22154 Msa1419810:CDS
TCTTCTTCCTGCTCCTGGTC+CGG 0.461348 tig0024730:-22161 Msa1419810:intergenic
AGTCACTATGCAATGCTTGC+CGG 0.470918 tig0024730:+22142 Msa1419810:intron
CAACGAAGAAGGAACAAGAA+AGG 0.479363 tig0024730:+22215 Msa1419810:CDS
AATAAGAGTAACGGCGGCGC+AGG 0.488121 tig0024730:+22240 Msa1419810:CDS
TATGCAATGCTTGCCGGACC+AGG 0.510626 tig0024730:+22148 Msa1419810:CDS
AGCAAAGAAAACAACGAAGA+AGG 0.512688 tig0024730:+22204 Msa1419810:CDS
AAGAAAACCTGTGCTGGTTG+CGG 0.513917 tig0024730:+21986 Msa1419810:CDS
GGACGTTCCGCAACCAGCAC+AGG 0.525995 tig0024730:-21993 Msa1419810:intergenic
AATCCAAAGAAAACCTGTGC+TGG 0.535791 tig0024730:+21980 Msa1419810:CDS
TTTGGACCACCACGACATTG+AGG 0.595285 tig0024730:-22022 Msa1419810:intergenic
TCAATGTCGTGGTGGTCCAA+AGG 0.602676 tig0024730:+22024 Msa1419810:CDS
TCCAAAACTCCTCAATGTCG+TGG 0.628200 tig0024730:+22013 Msa1419810:CDS
ACGAAGAAGGAACAAGAAAG+GGG 0.636309 tig0024730:+22217 Msa1419810:CDS
CGGCGCAGGAAGCAAAGTTG+GGG 0.652494 tig0024730:+22254 Msa1419810:CDS
AGAAAGGGGAATAAGAGTAA+CGG 0.665248 tig0024730:+22231 Msa1419810:CDS
AAAACTCCTCAATGTCGTGG+TGG 0.684546 tig0024730:+22016 Msa1419810:CDS
AAGGGGAATAAGAGTAACGG+CGG 0.727683 tig0024730:+22234 Msa1419810:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCAGAGATTATTGAATTTA+AGG + tig0024730:22292-22311 Msa1419810:CDS 20.0%
AACAGAGCTAGTAAAGTTTA+TGG - tig0024730:21945-21964 None:intergenic 30.0%
TGATTAGCGTTAATTACCTT+TGG - tig0024730:22043-22062 Msa1419810:intergenic 30.0%
AAGAAGAAGAGAGCAATATT+AGG + tig0024730:22177-22196 Msa1419810:CDS 30.0%
AGAAGAAGAGAGCAATATTA+GGG + tig0024730:22178-22197 Msa1419810:CDS 30.0%
AGCAAAGAAAACAACGAAGA+AGG + tig0024730:22204-22223 Msa1419810:CDS 35.0%
AACGAAGAAGGAACAAGAAA+GGG + tig0024730:22216-22235 Msa1419810:CDS 35.0%
AGAAAGGGGAATAAGAGTAA+CGG + tig0024730:22231-22250 Msa1419810:CDS 35.0%
AATCCAAAGAAAACCTGTGC+TGG + tig0024730:21980-21999 Msa1419810:CDS 40.0%
CAACGAAGAAGGAACAAGAA+AGG + tig0024730:22215-22234 Msa1419810:CDS 40.0%
ACGAAGAAGGAACAAGAAAG+GGG + tig0024730:22217-22236 Msa1419810:CDS 40.0%
! CAACCAGCACAGGTTTTCTT+TGG - tig0024730:21986-22005 Msa1419810:intergenic 45.0%
!! AAGAAAACCTGTGCTGGTTG+CGG + tig0024730:21986-22005 Msa1419810:CDS 45.0%
TCCAAAACTCCTCAATGTCG+TGG + tig0024730:22013-22032 Msa1419810:CDS 45.0%
! ACCACGACATTGAGGAGTTT+TGG - tig0024730:22017-22036 Msa1419810:intergenic 45.0%
AAAACTCCTCAATGTCGTGG+TGG + tig0024730:22016-22035 Msa1419810:CDS 45.0%
AGTCACTATGCAATGCTTGC+CGG + tig0024730:22142-22161 Msa1419810:intron 45.0%
AAGGGGAATAAGAGTAACGG+CGG + tig0024730:22234-22253 Msa1419810:CDS 45.0%
TTTGGACCACCACGACATTG+AGG - tig0024730:22025-22044 Msa1419810:intergenic 50.0%
TCAATGTCGTGGTGGTCCAA+AGG + tig0024730:22024-22043 Msa1419810:CDS 50.0%
TCTCTTCTTCTTCCTGCTCC+TGG - tig0024730:22169-22188 Msa1419810:intergenic 50.0%
TATGCAATGCTTGCCGGACC+AGG + tig0024730:22148-22167 Msa1419810:CDS 55.0%
TCTTCTTCCTGCTCCTGGTC+CGG - tig0024730:22164-22183 Msa1419810:intergenic 55.0%
AATAAGAGTAACGGCGGCGC+AGG + tig0024730:22240-22259 Msa1419810:CDS 55.0%
GCGGCGCAGGAAGCAAAGTT+GGG + tig0024730:22253-22272 Msa1419810:CDS 60.0%
CGGCGCAGGAAGCAAAGTTG+GGG + tig0024730:22254-22273 Msa1419810:CDS 60.0%
GGACGTTCCGCAACCAGCAC+AGG - tig0024730:21996-22015 Msa1419810:intergenic 65.0%
ATGCTTGCCGGACCAGGAGC+AGG + tig0024730:22154-22173 Msa1419810:CDS 65.0%
GGCGGCGCAGGAAGCAAAGT+TGG + tig0024730:22252-22271 Msa1419810:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0024730 gene 21935 22320 21935 ID=Msa1419810;Name=Msa1419810
tig0024730 mRNA 21935 22320 21935 ID=Msa1419810-mRNA-1;Parent=Msa1419810;Name=Msa1419810-mRNA-1;_AED=0.15;_eAED=0.15;_QI=0|0|0|1|1|1|2|0|95
tig0024730 exon 21935 22045 21935 ID=Msa1419810-mRNA-1:exon:1080;Parent=Msa1419810-mRNA-1
tig0024730 exon 22144 22320 22144 ID=Msa1419810-mRNA-1:exon:1081;Parent=Msa1419810-mRNA-1
tig0024730 CDS 21935 22045 21935 ID=Msa1419810-mRNA-1:cds;Parent=Msa1419810-mRNA-1
tig0024730 CDS 22144 22320 22144 ID=Msa1419810-mRNA-1:cds;Parent=Msa1419810-mRNA-1
Gene Sequence

>Msa1419810

TTGCATGCCATAAACTTTACTAGCTCTGTTTCATCAGATAACAACAATCCAAAGAAAACCTGTGCTGGTTGCGGAACGTCCAAAACTCCTCAATGTCGTGGTGGTCCAAAGTCACTATGCAATGCTTGCCGGACCAGGAGCAGGAAGAAGAAGAGAGCAATATTAGGGATAAGCAAAGAAAACAACGAAGAAGGAACAAGAAAGGGGAATAAGAGTAACGGCGGCGCAGGAAGCAAAGTTGGGGATAATATGAACATGAATCAGAGATTATTGAATTTAAGGAAATAA
Protein sequence

>Msa1419810

LHAINFTSSVSSDNNNPKKTCAGCGTSKTPQCRGGPKSLCNACRTRSRKKKRAILGISKENNEEGTRKGNKSNGGAGSKVGDNMNMNQRLLNLRK*