AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0393110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0393110 MtrunA17_Chr3g0078381 99.320 147 1 0 1 147 1 147 3.65e-104 293
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0393110 AT3G22480.1 70.667 150 39 3 1 147 1 148 5.50e-68 202
Msa0393110 AT3G22480.2 70.667 150 39 3 1 147 1 148 5.50e-68 202

Find 42 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CATTTCAAGTTCCGTTATTT+TGG 0.192430 3_2:-7085047 None:intergenic
GCAACTGCTTGTTCATTTAC+TGG 0.248625 3_2:-7084980 None:intergenic
TACTGGCTCCTTGCGATCTT+CGG 0.331035 3_2:-7084963 None:intergenic
CAAAATAACGGAACTTGAAA+TGG 0.346568 3_2:+7085048 Msa0393110:CDS
CGGCGTCTGCCTTCCTCATC+CGG 0.403003 3_2:-7085294 None:intergenic
AGACATTGGAAAAGAAGAAA+AGG 0.418775 3_2:+7085239 Msa0393110:CDS
GGAGTACTTGTGGGCTCTGC+GGG 0.418775 3_2:+7085358 Msa0393110:CDS
AGCAGGCAAGACCTCTTTGA+TGG 0.434394 3_2:-7085167 None:intergenic
TTCGATAGCATCGTCTAGAT+TGG 0.460560 3_2:-7085117 None:intergenic
TCTTAATGCCATTCAGCCGC+TGG 0.472683 3_2:+7085093 Msa0393110:CDS
GCCGAGGTGAACGATGAATC+TGG 0.481419 3_2:+7085313 Msa0393110:CDS
AGATTGGTCCAGCGGCTGAA+TGG 0.484859 3_2:-7085101 None:intergenic
TCTTTATTTCGCTGCACAGC+AGG 0.487561 3_2:-7085184 None:intergenic
TTGAGACTAAATATAAAATC+CGG 0.490885 3_2:+7085275 Msa0393110:CDS
TCTGCTCAAGGAGTACTTGT+GGG 0.492082 3_2:+7085349 Msa0393110:CDS
GACATTGGAAAAGAAGAAAA+GGG 0.500685 3_2:+7085240 Msa0393110:CDS
GTGTAGAATCATGGCTAGTA+AGG 0.508954 3_2:+7084940 None:intergenic
CCAAATTTACACCAAAATAA+CGG 0.527386 3_2:+7085036 Msa0393110:CDS
GAACGATGAATCTGGTAAGA+AGG 0.544140 3_2:+7085321 Msa0393110:CDS
TGCGAGGCTTAACGAGACAT+TGG 0.548123 3_2:+7085225 Msa0393110:CDS
AATGATCGGAGGGGTGCTTG+TGG 0.562981 3_2:+7085138 Msa0393110:CDS
AAGAAGGAAGGTTCTGCTCA+AGG 0.575142 3_2:+7085337 Msa0393110:CDS
GTACTTGTGGGCTCTGCGGG+TGG 0.579238 3_2:+7085361 Msa0393110:CDS
AGACGATGCTATCGAATGAT+CGG 0.583092 3_2:+7085124 Msa0393110:CDS
ATATAAAATCCGGATGAGGA+AGG 0.583660 3_2:+7085285 Msa0393110:CDS
TTCTGCTCAAGGAGTACTTG+TGG 0.584158 3_2:+7085348 Msa0393110:CDS
GCTGTGCAGCGAAATAAAGA+AGG 0.585102 3_2:+7085187 Msa0393110:CDS
GATGAATCTGGTAAGAAGGA+AGG 0.587326 3_2:+7085325 Msa0393110:CDS
CTAAATATAAAATCCGGATG+AGG 0.587775 3_2:+7085281 Msa0393110:CDS
TAGTAAGGCCGAAGATCGCA+AGG 0.597879 3_2:+7084955 Msa0393110:CDS
GGAAGTCAGCGAGCACTCGT+TGG 0.600111 3_2:+7085069 Msa0393110:CDS
AGGAGTACTTGTGGGCTCTG+CGG 0.607192 3_2:+7085357 Msa0393110:CDS
AAATAAAGAAGGACTTGAAG+AGG 0.608952 3_2:+7085198 Msa0393110:CDS
ACCAGATTCATCGTTCACCT+CGG 0.619609 3_2:-7085314 None:intergenic
CAAATATGTATGCAGCTATG+AGG 0.631644 3_2:+7085002 Msa0393110:CDS
CGATGCTATCGAATGATCGG+AGG 0.640428 3_2:+7085127 Msa0393110:CDS
GACTTGAAGAGGTTGTTGCG+AGG 0.642407 3_2:+7085209 Msa0393110:CDS
GATGCTATCGAATGATCGGA+GGG 0.647657 3_2:+7085128 Msa0393110:CDS
CATCGTCTAGATTGGTCCAG+CGG 0.650779 3_2:-7085109 None:intergenic
GATGAGGAAGGCAGACGCCG+AGG 0.652733 3_2:+7085297 Msa0393110:CDS
TGTGGAAAGAACCATCAAAG+AGG 0.689890 3_2:+7085156 Msa0393110:CDS
ATGCTATCGAATGATCGGAG+GGG 0.761886 3_2:+7085129 Msa0393110:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGAGACTAAATATAAAATC+CGG + chr3_2:7085275-7085294 Msa0393110:CDS 20.0%
! CCAAATTTACACCAAAATAA+CGG + chr3_2:7085036-7085055 Msa0393110:CDS 25.0%
!! TTTTGGTGTAAATTTGGTTG+AGG - chr3_2:7085033-7085052 None:intergenic 30.0%
!!! CCGTTATTTTGGTGTAAATT+TGG - chr3_2:7085039-7085058 None:intergenic 30.0%
!!! CATTTCAAGTTCCGTTATTT+TGG - chr3_2:7085050-7085069 None:intergenic 30.0%
! CAAAATAACGGAACTTGAAA+TGG + chr3_2:7085048-7085067 Msa0393110:CDS 30.0%
AAATAAAGAAGGACTTGAAG+AGG + chr3_2:7085198-7085217 Msa0393110:CDS 30.0%
AGACATTGGAAAAGAAGAAA+AGG + chr3_2:7085239-7085258 Msa0393110:CDS 30.0%
GACATTGGAAAAGAAGAAAA+GGG + chr3_2:7085240-7085259 Msa0393110:CDS 30.0%
CTAAATATAAAATCCGGATG+AGG + chr3_2:7085281-7085300 Msa0393110:CDS 30.0%
CAAATATGTATGCAGCTATG+AGG + chr3_2:7085002-7085021 Msa0393110:CDS 35.0%
ATATAAAATCCGGATGAGGA+AGG + chr3_2:7085285-7085304 Msa0393110:CDS 35.0%
GCAACTGCTTGTTCATTTAC+TGG - chr3_2:7084983-7085002 None:intergenic 40.0%
TTCGATAGCATCGTCTAGAT+TGG - chr3_2:7085120-7085139 None:intergenic 40.0%
AGACGATGCTATCGAATGAT+CGG + chr3_2:7085124-7085143 Msa0393110:CDS 40.0%
TGTGGAAAGAACCATCAAAG+AGG + chr3_2:7085156-7085175 Msa0393110:CDS 40.0%
GAACGATGAATCTGGTAAGA+AGG + chr3_2:7085321-7085340 Msa0393110:CDS 40.0%
GATGAATCTGGTAAGAAGGA+AGG + chr3_2:7085325-7085344 Msa0393110:CDS 40.0%
GATGCTATCGAATGATCGGA+GGG + chr3_2:7085128-7085147 Msa0393110:CDS 45.0%
ATGCTATCGAATGATCGGAG+GGG + chr3_2:7085129-7085148 Msa0393110:CDS 45.0%
! TCTTTATTTCGCTGCACAGC+AGG - chr3_2:7085187-7085206 None:intergenic 45.0%
GCTGTGCAGCGAAATAAAGA+AGG + chr3_2:7085187-7085206 Msa0393110:CDS 45.0%
ACCAGATTCATCGTTCACCT+CGG - chr3_2:7085317-7085336 None:intergenic 45.0%
AAGAAGGAAGGTTCTGCTCA+AGG + chr3_2:7085337-7085356 Msa0393110:CDS 45.0%
!! TTCTGCTCAAGGAGTACTTG+TGG + chr3_2:7085348-7085367 Msa0393110:CDS 45.0%
!! TCTGCTCAAGGAGTACTTGT+GGG + chr3_2:7085349-7085368 Msa0393110:CDS 45.0%
TAGTAAGGCCGAAGATCGCA+AGG + chr3_2:7084955-7084974 Msa0393110:CDS 50.0%
!! TACTGGCTCCTTGCGATCTT+CGG - chr3_2:7084966-7084985 None:intergenic 50.0%
TCTTAATGCCATTCAGCCGC+TGG + chr3_2:7085093-7085112 Msa0393110:CDS 50.0%
! CATCGTCTAGATTGGTCCAG+CGG - chr3_2:7085112-7085131 None:intergenic 50.0%
CGATGCTATCGAATGATCGG+AGG + chr3_2:7085127-7085146 Msa0393110:CDS 50.0%
AGCAGGCAAGACCTCTTTGA+TGG - chr3_2:7085170-7085189 None:intergenic 50.0%
GACTTGAAGAGGTTGTTGCG+AGG + chr3_2:7085209-7085228 Msa0393110:CDS 50.0%
TGCGAGGCTTAACGAGACAT+TGG + chr3_2:7085225-7085244 Msa0393110:CDS 50.0%
! AGATTGGTCCAGCGGCTGAA+TGG - chr3_2:7085104-7085123 None:intergenic 55.0%
!! AATGATCGGAGGGGTGCTTG+TGG + chr3_2:7085138-7085157 Msa0393110:CDS 55.0%
GCCGAGGTGAACGATGAATC+TGG + chr3_2:7085313-7085332 Msa0393110:CDS 55.0%
!! AGGAGTACTTGTGGGCTCTG+CGG + chr3_2:7085357-7085376 Msa0393110:CDS 55.0%
GGAAGTCAGCGAGCACTCGT+TGG + chr3_2:7085069-7085088 Msa0393110:CDS 60.0%
! GGAGTACTTGTGGGCTCTGC+GGG + chr3_2:7085358-7085377 Msa0393110:CDS 60.0%
CGGCGTCTGCCTTCCTCATC+CGG - chr3_2:7085297-7085316 None:intergenic 65.0%
GATGAGGAAGGCAGACGCCG+AGG + chr3_2:7085297-7085316 Msa0393110:CDS 65.0%
GTACTTGTGGGCTCTGCGGG+TGG + chr3_2:7085361-7085380 Msa0393110:CDS 65.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 7084950 7085393 7084950 ID=Msa0393110;Name=Msa0393110
chr3_2 mRNA 7084950 7085393 7084950 ID=Msa0393110-mRNA-1;Parent=Msa0393110;Name=Msa0393110-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|147
chr3_2 exon 7084950 7085393 7084950 ID=Msa0393110-mRNA-1:exon:1743;Parent=Msa0393110-mRNA-1
chr3_2 CDS 7084950 7085393 7084950 ID=Msa0393110-mRNA-1:cds;Parent=Msa0393110-mRNA-1
Gene Sequence

>Msa0393110

ATGGCTAGTAAGGCCGAAGATCGCAAGGAGCCAGTAAATGAACAAGCAGTTGCAAATATGTATGCAGCTATGAGGTCAGACCTCAACCAAATTTACACCAAAATAACGGAACTTGAAATGGAAGTCAGCGAGCACTCGTTGGTTCTTAATGCCATTCAGCCGCTGGACCAATCTAGACGATGCTATCGAATGATCGGAGGGGTGCTTGTGGAAAGAACCATCAAAGAGGTCTTGCCTGCTGTGCAGCGAAATAAAGAAGGACTTGAAGAGGTTGTTGCGAGGCTTAACGAGACATTGGAAAAGAAGAAAAGGGAAATTGCTGAGTTTGAGACTAAATATAAAATCCGGATGAGGAAGGCAGACGCCGAGGTGAACGATGAATCTGGTAAGAAGGAAGGTTCTGCTCAAGGAGTACTTGTGGGCTCTGCGGGTGGTAGCGAATGA
Protein sequence

>Msa0393110

MASKAEDRKEPVNEQAVANMYAAMRSDLNQIYTKITELEMEVSEHSLVLNAIQPLDQSRRCYRMIGGVLVERTIKEVLPAVQRNKEGLEEVVARLNETLEKKKREIAEFETKYKIRMRKADAEVNDESGKKEGSAQGVLVGSAGGSE*