AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1339190


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1339190 MtrunA17_Chr4g0035601 82.162 185 20 5 1 181 1 176 4.26e-85 248
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1339190 AT4G34630.1 54.217 83 34 2 99 179 117 197 2.54e-19 81.6

Find 34 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGATGATTCTTTCATTTCT+TGG 0.184142 tig0003042:-48015 Msa1339190:CDS
GAGACAGAGGATGAGGAAAT+TGG 0.199364 tig0003042:-47786 Msa1339190:CDS
CGATGGGTTATTCGTTCAAT+TGG 0.268599 tig0003042:+47968 None:intergenic
AGACAGAGGATGAGGAAATT+GGG 0.300950 tig0003042:-47785 Msa1339190:CDS
TGGGATATAGGGAACAAGTT+AGG 0.321052 tig0003042:-47809 Msa1339190:CDS
TGGTCAAATTCTTCTATAAT+CGG 0.322860 tig0003042:-47995 Msa1339190:CDS
GAGCTTGTACCATGGGATAT+AGG 0.333576 tig0003042:-47821 Msa1339190:CDS
AGCTTGTACCATGGGATATA+GGG 0.370332 tig0003042:-47820 Msa1339190:CDS
ATGCTGATTCTCTTCTTCAA+TGG 0.381531 tig0003042:-48111 Msa1339190:CDS
TCATGAATTGAACTTGTTCA+AGG 0.391947 tig0003042:+48143 None:intergenic
TGCTGATTCTCTTCTTCAAT+GGG 0.397374 tig0003042:-48110 Msa1339190:CDS
AGATGATGGTGATGATGATT+TGG 0.404444 tig0003042:-47849 Msa1339190:CDS
GGGATATAGGGAACAAGTTA+GGG 0.447825 tig0003042:-47808 Msa1339190:CDS
GGATGAGGAAATTGGGGAAA+AGG 0.455028 tig0003042:-47778 Msa1339190:CDS
CTTCACTTTCATCATCATCA+TGG 0.456100 tig0003042:+47882 None:intergenic
GATGAGGAAATTGGGGAAAA+GGG 0.462244 tig0003042:-47777 Msa1339190:CDS
GATGGGTTATTCGTTCAATT+GGG 0.466090 tig0003042:+47969 None:intergenic
GTGAGGCCTGGCTGTGTTCG+TGG 0.506555 tig0003042:-47710 Msa1339190:CDS
TGTTCGTGGCAAACATGGCA+TGG 0.512051 tig0003042:-47696 Msa1339190:CDS
GACAGAGGATGAGGAAATTG+GGG 0.528458 tig0003042:-47784 Msa1339190:CDS
AGTTAGGGAGACAGAGGATG+AGG 0.528796 tig0003042:-47793 Msa1339190:CDS
CTGGGTCATCGAGATGAATA+CGG 0.538229 tig0003042:+47945 None:intergenic
GGCTGTGTTCGTGGCAAACA+TGG 0.545203 tig0003042:-47701 Msa1339190:CDS
TGTTTGCCACGAACACAGCC+AGG 0.561152 tig0003042:+47704 None:intergenic
CATCGAGATGAATACGGCGA+TGG 0.565334 tig0003042:+47951 None:intergenic
GGATGATGAGCTTGTACCAT+GGG 0.574358 tig0003042:-47828 Msa1339190:CDS
GTTCTTCACTGTAGCCAACA+TGG 0.585726 tig0003042:+47912 None:intergenic
ATCGAGATGAATACGGCGAT+GGG 0.587715 tig0003042:+47952 None:intergenic
AACTTGTTCCCTATATCCCA+TGG 0.592792 tig0003042:+47812 None:intergenic
GAAGAAGATGATGAAGATGA+TGG 0.597886 tig0003042:-47863 Msa1339190:CDS
GGAACAAGTTAGGGAGACAG+AGG 0.614922 tig0003042:-47799 Msa1339190:CDS
CCAGTTGAAAATCACCATGT+TGG 0.626221 tig0003042:-47926 Msa1339190:CDS
GTTCGTGGCAAACATGGCAT+GGG 0.629055 tig0003042:-47695 Msa1339190:CDS
TGGATGATGAGCTTGTACCA+TGG 0.630254 tig0003042:-47829 Msa1339190:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATGATGATTCTTTCATTTCT+TGG - tig0003042:47860-47879 Msa1339190:CDS 25.0%
! TGGTCAAATTCTTCTATAAT+CGG - tig0003042:47880-47899 Msa1339190:CDS 25.0%
! CAAAAATGAATAATTCGAAG+AGG - tig0003042:48127-48146 Msa1339190:CDS 25.0%
! ATGATGATGATGATGAAGTT+TGG + tig0003042:47687-47706 None:intergenic 30.0%
! TCATGAATTGAACTTGTTCA+AGG + tig0003042:47735-47754 None:intergenic 30.0%
AGAAGAAGAAGAAGAAGAAA+GGG - tig0003042:47822-47841 Msa1339190:CDS 30.0%
!! ATGCTGATTCTCTTCTTCAA+TGG - tig0003042:47764-47783 Msa1339190:CDS 35.0%
!! TGCTGATTCTCTTCTTCAAT+GGG - tig0003042:47765-47784 Msa1339190:CDS 35.0%
CAGAAGAAGAAGAAGAAGAA+AGG - tig0003042:47821-47840 Msa1339190:CDS 35.0%
!! GATGGGTTATTCGTTCAATT+GGG + tig0003042:47909-47928 None:intergenic 35.0%
! CAACATGGTGATTTTCAACT+GGG + tig0003042:47951-47970 None:intergenic 35.0%
CTTCACTTTCATCATCATCA+TGG + tig0003042:47996-48015 None:intergenic 35.0%
GAAGAAGATGATGAAGATGA+TGG - tig0003042:48012-48031 Msa1339190:CDS 35.0%
! AGATGATGGTGATGATGATT+TGG - tig0003042:48026-48045 Msa1339190:CDS 35.0%
!! CGATGGGTTATTCGTTCAAT+TGG + tig0003042:47910-47929 None:intergenic 40.0%
! CCAACATGGTGATTTTCAAC+TGG + tig0003042:47952-47971 None:intergenic 40.0%
CCAGTTGAAAATCACCATGT+TGG - tig0003042:47949-47968 Msa1339190:CDS 40.0%
AGCTTGTACCATGGGATATA+GGG - tig0003042:48055-48074 Msa1339190:CDS 40.0%
! AACTTGTTCCCTATATCCCA+TGG + tig0003042:48066-48085 None:intergenic 40.0%
TGGGATATAGGGAACAAGTT+AGG - tig0003042:48066-48085 Msa1339190:CDS 40.0%
GGGATATAGGGAACAAGTTA+GGG - tig0003042:48067-48086 Msa1339190:CDS 40.0%
AGACAGAGGATGAGGAAATT+GGG - tig0003042:48090-48109 Msa1339190:CDS 40.0%
GATGAGGAAATTGGGGAAAA+GGG - tig0003042:48098-48117 Msa1339190:CDS 40.0%
AGGCCTCACAAAAAGAATAG+GGG + tig0003042:48154-48173 None:intergenic 40.0%
CAGGCCTCACAAAAAGAATA+GGG + tig0003042:48155-48174 None:intergenic 40.0%
ATCGAGATGAATACGGCGAT+GGG + tig0003042:47926-47945 None:intergenic 45.0%
CTGGGTCATCGAGATGAATA+CGG + tig0003042:47933-47952 None:intergenic 45.0%
GTTCTTCACTGTAGCCAACA+TGG + tig0003042:47966-47985 None:intergenic 45.0%
TGGATGATGAGCTTGTACCA+TGG - tig0003042:48046-48065 Msa1339190:CDS 45.0%
GGATGATGAGCTTGTACCAT+GGG - tig0003042:48047-48066 Msa1339190:CDS 45.0%
GAGCTTGTACCATGGGATAT+AGG - tig0003042:48054-48073 Msa1339190:CDS 45.0%
GAGACAGAGGATGAGGAAAT+TGG - tig0003042:48089-48108 Msa1339190:CDS 45.0%
GACAGAGGATGAGGAAATTG+GGG - tig0003042:48091-48110 Msa1339190:CDS 45.0%
GGATGAGGAAATTGGGGAAA+AGG - tig0003042:48097-48116 Msa1339190:CDS 45.0%
! GGTCCCCTATTCTTTTTGTG+AGG - tig0003042:48148-48167 Msa1339190:CDS 45.0%
CCAGGCCTCACAAAAAGAAT+AGG + tig0003042:48156-48175 None:intergenic 45.0%
! CCTATTCTTTTTGTGAGGCC+TGG - tig0003042:48153-48172 Msa1339190:CDS 45.0%
CATCGAGATGAATACGGCGA+TGG + tig0003042:47927-47946 None:intergenic 50.0%
GGAACAAGTTAGGGAGACAG+AGG - tig0003042:48076-48095 Msa1339190:CDS 50.0%
AGTTAGGGAGACAGAGGATG+AGG - tig0003042:48082-48101 Msa1339190:CDS 50.0%
TGTTCGTGGCAAACATGGCA+TGG - tig0003042:48179-48198 Msa1339190:CDS 50.0%
GTTCGTGGCAAACATGGCAT+GGG - tig0003042:48180-48199 Msa1339190:CDS 50.0%
TGTTTGCCACGAACACAGCC+AGG + tig0003042:48174-48193 None:intergenic 55.0%
GGCTGTGTTCGTGGCAAACA+TGG - tig0003042:48174-48193 Msa1339190:CDS 55.0%
GTGAGGCCTGGCTGTGTTCG+TGG - tig0003042:48165-48184 Msa1339190:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0003042 gene 47676 48221 47676 ID=Msa1339190;Name=Msa1339190
tig0003042 mRNA 47676 48221 47676 ID=Msa1339190-mRNA-1;Parent=Msa1339190;Name=Msa1339190-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|181
tig0003042 exon 47676 48221 47676 ID=Msa1339190-mRNA-1:exon:1996;Parent=Msa1339190-mRNA-1
tig0003042 CDS 47676 48221 47676 ID=Msa1339190-mRNA-1:cds;Parent=Msa1339190-mRNA-1
Gene Sequence

>Msa1339190

ATGGAAAACCAAACTTCATCATCATCATCATCATCATCATCGATGCAGTTTCTCATCCTTGAACAAGTTCAATTCATGAAAGTGAATGATGCTGATTCTCTTCTTCAATGGGAACTTGTCGATGTTGTTGACGCTGAAGAACAATCAGAAGAAGAAGAAGAAGAAAGGGTTGATGTTGACGATGATGATGATTCTTTCATTTCTTGGTCAAATTCTTCTATAATCGGTGACCCAATTGAACGAATAACCCATCGCCGTATTCATCTCGATGACCCAGTTGAAAATCACCATGTTGGCTACAGTGAAGAACAAGTTAGCCATGATGATGATGAAAGTGAAGAAGATGATGAAGATGATGGTGATGATGATTTGGATGATGAGCTTGTACCATGGGATATAGGGAACAAGTTAGGGAGACAGAGGATGAGGAAATTGGGGAAAAGGGTTTCTTCAAAAATGAATAATTCGAAGAGGTCCCCTATTCTTTTTGTGAGGCCTGGCTGTGTTCGTGGCAAACATGGCATGGGTCTTAAACACTGTTTTTAG

Protein sequence

>Msa1339190

MENQTSSSSSSSSSMQFLILEQVQFMKVNDADSLLQWELVDVVDAEEQSEEEEEERVDVDDDDDSFISWSNSSIIGDPIERITHRRIHLDDPVENHHVGYSEEQVSHDDDESEEDDEDDGDDDLDDELVPWDIGNKLGRQRMRKLGKRVSSKMNNSKRSPILFVRPGCVRGKHGMGLKHCF*