AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1377940

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377940 MtrunA17_Chr8g0339041 77.419 124 28 0 1 124 139 262 8.43e-65 201
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1377940 AT1G79220.1 46.400 125 66 1 1 124 165 289 5.44e-31 114

Find 24 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CCTTCGTTGCTATGTGAAAA+TGG 0.268635 tig0020032:-150039 Msa1377940:CDS
TCTTACAAAGTTTGGTTTAT+CGG 0.270206 tig0020032:-149785 Msa1377940:CDS
AAATATGTGGTGACGTTAAT+AGG 0.278279 tig0020032:-149847 Msa1377940:CDS
GTTGACAATGTCATAATATT+AGG 0.285517 tig0020032:+149730 None:intergenic
GAAAATGGCTATGACATTAA+AGG 0.301086 tig0020032:-150024 Msa1377940:CDS
TATGACATTGTCAACTGATA+TGG 0.327135 tig0020032:-149722 Msa1377940:CDS
GTGTTAAATCTTACAAAGTT+TGG 0.362500 tig0020032:-149793 Msa1377940:CDS
GTTGCACAATATGAAGAGTT+AGG 0.395236 tig0020032:-149997 Msa1377940:CDS
AAGAGTTAGGCGTATTGAAA+AGG 0.444866 tig0020032:-149984 Msa1377940:CDS
TTCCTTTGATGATGAGAAGA+TGG 0.470731 tig0020032:-149914 Msa1377940:CDS
ATGGTATATATAAGCAGGAC+TGG 0.475180 tig0020032:-149895 Msa1377940:CDS
AGGCGTATTGAAAAGGGACT+TGG 0.493691 tig0020032:-149977 Msa1377940:CDS
TTATCGGATGATGAGATAGT+TGG 0.498981 tig0020032:-149769 Msa1377940:CDS
TGCAGCCGGCGATTATTACA+AGG 0.503215 tig0020032:-149939 Msa1377940:CDS
AGAAGATGGTATATATAAGC+AGG 0.519672 tig0020032:-149900 Msa1377940:CDS
CAACGAAGGGTTTCTTGCAA+TGG 0.530280 tig0020032:+150053 None:intergenic
AGAGTTAGGCGTATTGAAAA+GGG 0.532449 tig0020032:-149983 Msa1377940:CDS
TGGTATATATAAGCAGGACT+GGG 0.532776 tig0020032:-149894 Msa1377940:CDS
TGCAAAATTGTACAAATATG+TGG 0.567808 tig0020032:-149860 Msa1377940:CDS
GAAGTCCTTGTAATAATCGC+CGG 0.570186 tig0020032:+149934 None:intergenic
TACCATCTTCTCATCATCAA+AGG 0.572098 tig0020032:+149912 None:intergenic
CGTGGAAATGATTCACGCAA+AGG 0.597282 tig0020032:-149815 Msa1377940:CDS
GTTAATAGGAATCTCTCGCG+TGG 0.661196 tig0020032:-149833 Msa1377940:CDS
GGTATATATAAGCAGGACTG+GGG 0.703023 tig0020032:-149893 Msa1377940:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TGCAAAATTGTACAAATATG+TGG - tig0020032:149920-149939 Msa1377940:CDS 25.0%
! GTGTTAAATCTTACAAAGTT+TGG - tig0020032:149987-150006 Msa1377940:CDS 25.0%
!! TCTTACAAAGTTTGGTTTAT+CGG - tig0020032:149995-150014 Msa1377940:CDS 25.0%
! GTTGACAATGTCATAATATT+AGG + tig0020032:150053-150072 None:intergenic 25.0%
GAAAATGGCTATGACATTAA+AGG - tig0020032:149756-149775 Msa1377940:CDS 30.0%
AGAAGATGGTATATATAAGC+AGG - tig0020032:149880-149899 Msa1377940:CDS 30.0%
! AAATATGTGGTGACGTTAAT+AGG - tig0020032:149933-149952 Msa1377940:CDS 30.0%
TATGACATTGTCAACTGATA+TGG - tig0020032:150058-150077 Msa1377940:CDS 30.0%
! CATTTTCACATAGCAACGAA+GGG + tig0020032:149743-149762 None:intergenic 35.0%
GTTGCACAATATGAAGAGTT+AGG - tig0020032:149783-149802 Msa1377940:CDS 35.0%
AAGAGTTAGGCGTATTGAAA+AGG - tig0020032:149796-149815 Msa1377940:CDS 35.0%
AGAGTTAGGCGTATTGAAAA+GGG - tig0020032:149797-149816 Msa1377940:CDS 35.0%
!! TTCCTTTGATGATGAGAAGA+TGG - tig0020032:149866-149885 Msa1377940:CDS 35.0%
TACCATCTTCTCATCATCAA+AGG + tig0020032:149871-149890 None:intergenic 35.0%
ATGGTATATATAAGCAGGAC+TGG - tig0020032:149885-149904 Msa1377940:CDS 35.0%
TGGTATATATAAGCAGGACT+GGG - tig0020032:149886-149905 Msa1377940:CDS 35.0%
TTATCGGATGATGAGATAGT+TGG - tig0020032:150011-150030 Msa1377940:CDS 35.0%
!!! GATGAGATAGTTGGTCTTTT+TGG - tig0020032:150020-150039 Msa1377940:CDS 35.0%
! CCATTTTCACATAGCAACGA+AGG + tig0020032:149744-149763 None:intergenic 40.0%
CCTTCGTTGCTATGTGAAAA+TGG - tig0020032:149741-149760 Msa1377940:CDS 40.0%
!!! TCAAATGCTGATTTTGCAGC+CGG - tig0020032:149827-149846 Msa1377940:CDS 40.0%
GAAGTCCTTGTAATAATCGC+CGG + tig0020032:149849-149868 None:intergenic 40.0%
GGTATATATAAGCAGGACTG+GGG - tig0020032:149887-149906 Msa1377940:CDS 40.0%
CAACGAAGGGTTTCTTGCAA+TGG + tig0020032:149730-149749 None:intergenic 45.0%
AGGCGTATTGAAAAGGGACT+TGG - tig0020032:149803-149822 Msa1377940:CDS 45.0%
GTTAATAGGAATCTCTCGCG+TGG - tig0020032:149947-149966 Msa1377940:CDS 45.0%
CGTGGAAATGATTCACGCAA+AGG - tig0020032:149965-149984 Msa1377940:CDS 45.0%
TGCAGCCGGCGATTATTACA+AGG - tig0020032:149841-149860 Msa1377940:CDS 50.0%
!! AAGCAGGACTGGGGTTTTGA+AGG - tig0020032:149896-149915 Msa1377940:CDS 50.0%
Chromosome Type Strat End Strand Name
tig0020032 gene 149714 150088 149714 ID=Msa1377940;Name=Msa1377940
tig0020032 mRNA 149714 150088 149714 ID=Msa1377940-mRNA-1;Parent=Msa1377940;Name=Msa1377940-mRNA-1;_AED=0.28;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|124
tig0020032 exon 149714 150088 149714 ID=Msa1377940-mRNA-1:exon:5835;Parent=Msa1377940-mRNA-1
tig0020032 CDS 149714 150088 149714 ID=Msa1377940-mRNA-1:cds;Parent=Msa1377940-mRNA-1
Gene Sequence

>Msa1377940

ATGCTTCATAAGACCATTGCAAGAAACCCTTCGTTGCTATGTGAAAATGGCTATGACATTAAAGGTATTGTTGCACAATATGAAGAGTTAGGCGTATTGAAAAGGGACTTGGTTCAAATGCTGATTTTGCAGCCGGCGATTATTACAAGGACTTCCTTTGATGATGAGAAGATGGTATATATAAGCAGGACTGGGGTTTTGAAGGATGCAAAATTGTACAAATATGTGGTGACGTTAATAGGAATCTCTCGCGTGGAAATGATTCACGCAAAGGTGTTAAATCTTACAAAGTTTGGTTTATCGGATGATGAGATAGTTGGTCTTTTTGGTAAGTCTCCTAATATTATGACATTGTCAACTGATATGGCACAATGA
Protein sequence

>Msa1377940

MLHKTIARNPSLLCENGYDIKGIVAQYEELGVLKRDLVQMLILQPAIITRTSFDDEKMVYISRTGVLKDAKLYKYVVTLIGISRVEMIHAKVLNLTKFGLSDDEIVGLFGKSPNIMTLSTDMAQ*