AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0381970

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0381970 MtrunA17_Chr3g0136171 97.500 120 3 0 1 120 24 143 1.15e-79 230
Msa0381970 MtrunA17_Chr1g0150841 66.129 124 37 2 1 119 1 124 5.72e-48 149
Msa0381970 MtrunA17_Chr4g0070691 57.851 121 44 5 1 119 1 116 3.70e-35 117
Msa0381970 MtrunA17_Chr2g0300351 55.738 122 48 3 1 119 1 119 1.72e-24 90.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0381970 AT2G06520.1 52.427 103 46 1 20 119 13 115 2.24e-24 90.1

Find 22 sgRNAs with CRISPR-Local

Find 32 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCTATACTTGGAGCTGTTAT+TGG 0.192002 3_1:+84397173 Msa0381970:CDS
TTTGACTGTGTGATCCTCTT+TGG 0.259959 3_1:-84396975 None:intergenic
CTATACTTGGAGCTGTTATT+GGG 0.283981 3_1:+84397174 Msa0381970:CDS
TTTGGTTGTGTGATGGGTAA+TGG 0.333839 3_1:-84396957 None:intergenic
CTTAATTAAGCTCTCTTAAC+CGG 0.367220 3_1:-84397212 None:intergenic
AGATGCATTAATTTCAACCT+TGG 0.419109 3_1:-84397000 None:intergenic
TAATGCATCTTTGAAAGAAA+AGG 0.433518 3_1:+84397013 Msa0381970:CDS
CCTGATGTGGCTCATGCAGC+TGG 0.437171 3_1:+84397083 Msa0381970:CDS
ATCCTCTTTGGTTGTGTGAT+GGG 0.438365 3_1:-84396963 None:intergenic
GATCCTCTTTGGTTGTGTGA+TGG 0.472817 3_1:-84396964 None:intergenic
TGGGGTTTCCAACTTTGATC+CGG 0.483190 3_1:+84397193 Msa0381970:CDS
CCAGCTGCATGAGCCACATC+AGG 0.505992 3_1:-84397083 None:intergenic
CTCCATGGTTATACCTGATG+TGG 0.524546 3_1:+84397070 Msa0381970:CDS
TCTCTTAACCGGATCAAAGT+TGG 0.532912 3_1:-84397201 None:intergenic
TGCATCCTTGACAGCCTCCA+TGG 0.539158 3_1:+84397055 Msa0381970:CDS
GCTGTGCTAACAGCTATACT+TGG 0.540967 3_1:+84397161 Msa0381970:CDS
TATACTTGGAGCTGTTATTG+GGG 0.562747 3_1:+84397175 Msa0381970:CDS
TATAACCATGGAGGCTGTCA+AGG 0.564152 3_1:-84397060 None:intergenic
TACCCATCACACAACCAAAG+AGG 0.615865 3_1:+84396961 Msa0381970:CDS
GATCACACAGTCAAAATCCA+AGG 0.634917 3_1:+84396983 Msa0381970:CDS
AGCCACATCAGGTATAACCA+TGG 0.670542 3_1:-84397072 None:intergenic
CACATCAGGTATAACCATGG+AGG 0.712255 3_1:-84397069 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TAATGCATCTTTGAAAGAAA+AGG + chr3_1:84397013-84397032 Msa0381970:CDS 25.0%
!! TGGATTTTTCAGCTTGTTTT+GGG - chr3_1:84396916-84396935 None:intergenic 30.0%
!! ATGGATTTTTCAGCTTGTTT+TGG - chr3_1:84396917-84396936 None:intergenic 30.0%
TAATGGCCTGAAAAATGATT+CGG - chr3_1:84396943-84396962 None:intergenic 30.0%
AGATGCATTAATTTCAACCT+TGG - chr3_1:84397003-84397022 None:intergenic 30.0%
AAATGCTTAGCAAAAAGTTC+TGG - chr3_1:84397130-84397149 None:intergenic 30.0%
! TTTTTGCTAAGCATTTTTGC+TGG + chr3_1:84397134-84397153 Msa0381970:CDS 30.0%
CTATACTTGGAGCTGTTATT+GGG + chr3_1:84397174-84397193 Msa0381970:CDS 35.0%
TATACTTGGAGCTGTTATTG+GGG + chr3_1:84397175-84397194 Msa0381970:CDS 35.0%
! CTGAAAAATGATTCGGAGGA+TGG - chr3_1:84396936-84396955 None:intergenic 40.0%
!! CATCCTCCGAATCATTTTTC+AGG + chr3_1:84396934-84396953 Msa0381970:CDS 40.0%
!! TTTGGTTGTGTGATGGGTAA+TGG - chr3_1:84396960-84396979 None:intergenic 40.0%
ATCCTCTTTGGTTGTGTGAT+GGG - chr3_1:84396966-84396985 None:intergenic 40.0%
TTTGACTGTGTGATCCTCTT+TGG - chr3_1:84396978-84396997 None:intergenic 40.0%
GATCACACAGTCAAAATCCA+AGG + chr3_1:84396983-84397002 Msa0381970:CDS 40.0%
!! AGCAAAAAGTTCTGGAGAGA+TGG - chr3_1:84397122-84397141 None:intergenic 40.0%
! TTGCTAAGCATTTTTGCTGG+TGG + chr3_1:84397137-84397156 Msa0381970:CDS 40.0%
GCTATACTTGGAGCTGTTAT+TGG + chr3_1:84397173-84397192 Msa0381970:CDS 40.0%
TCTCTTAACCGGATCAAAGT+TGG - chr3_1:84397204-84397223 None:intergenic 40.0%
!! TTTTGGGTAGCAGAACTCAG+TGG - chr3_1:84396900-84396919 None:intergenic 45.0%
! TGGCCTGAAAAATGATTCGG+AGG - chr3_1:84396940-84396959 None:intergenic 45.0%
TACCCATCACACAACCAAAG+AGG + chr3_1:84396961-84396980 Msa0381970:CDS 45.0%
GATCCTCTTTGGTTGTGTGA+TGG - chr3_1:84396967-84396986 None:intergenic 45.0%
TATAACCATGGAGGCTGTCA+AGG - chr3_1:84397063-84397082 None:intergenic 45.0%
CACATCAGGTATAACCATGG+AGG - chr3_1:84397072-84397091 None:intergenic 45.0%
CTCCATGGTTATACCTGATG+TGG + chr3_1:84397070-84397089 Msa0381970:CDS 45.0%
AGCCACATCAGGTATAACCA+TGG - chr3_1:84397075-84397094 None:intergenic 45.0%
GCTGTGCTAACAGCTATACT+TGG + chr3_1:84397161-84397180 Msa0381970:CDS 45.0%
TGGGGTTTCCAACTTTGATC+CGG + chr3_1:84397193-84397212 Msa0381970:CDS 45.0%
TGCATCCTTGACAGCCTCCA+TGG + chr3_1:84397055-84397074 Msa0381970:CDS 55.0%
CCAGCTGCATGAGCCACATC+AGG - chr3_1:84397086-84397105 None:intergenic 60.0%
CCTGATGTGGCTCATGCAGC+TGG + chr3_1:84397083-84397102 Msa0381970:CDS 60.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 84396867 84397229 84396867 ID=Msa0381970;Name=Msa0381970
chr3_1 mRNA 84396867 84397229 84396867 ID=Msa0381970-mRNA-1;Parent=Msa0381970;Name=Msa0381970-mRNA-1;_AED=0.46;_eAED=0.46;_QI=0|-1|0|1|-1|1|1|0|120
chr3_1 exon 84396867 84397229 84396867 ID=Msa0381970-mRNA-1:exon:21925;Parent=Msa0381970-mRNA-1
chr3_1 CDS 84396867 84397229 84396867 ID=Msa0381970-mRNA-1:cds;Parent=Msa0381970-mRNA-1
Gene Sequence

>Msa0381970

ATGGCTTCTGCTTCTGTTGCAACAGCTTTGCCACTGAGTTCTGCTACCCAAAACAAGCTGAAAAATCCATCCTCCGAATCATTTTTCAGGCCATTACCCATCACACAACCAAAGAGGATCACACAGTCAAAATCCAAGGTTGAAATTAATGCATCTTTGAAAGAAAAGGCAGTGACAGCACTTACAGCTGCATCCTTGACAGCCTCCATGGTTATACCTGATGTGGCTCATGCAGCTGGATCTGATCTCTCACCATCTCTCCAGAACTTTTTGCTAAGCATTTTTGCTGGTGGAGCTGTGCTAACAGCTATACTTGGAGCTGTTATTGGGGTTTCCAACTTTGATCCGGTTAAGAGAGCTTAA
Protein sequence

>Msa0381970

MASASVATALPLSSATQNKLKNPSSESFFRPLPITQPKRITQSKSKVEINASLKEKAVTALTAASLTASMVIPDVAHAAGSDLSPSLQNFLLSIFAGGAVLTAILGAVIGVSNFDPVKRA*