AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0394330


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394330 MtrunA17_Chr3g0079941 99.383 162 1 0 1 162 51 212 5.81e-116 327
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0394330 AT1G55670.1 70.303 165 41 3 1 162 1 160 1.44e-77 228

Find 23 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTATGATCCAAGTTTCTT+TGG 0.281064 3_2:-8902909 Msa0394330:CDS
TTGCTCAGGTAAGCCTTGTT+TGG 0.325198 3_2:+8903091 None:intergenic
TATTGTTGCTTACTATATCT+TGG 0.334380 3_2:-8902946 Msa0394330:CDS
GTTAAAACCAACAGGATCAT+TGG 0.338510 3_2:+8903004 None:intergenic
CCTTGGAAGGACAAGCTTGA+TGG 0.371656 3_2:+8903290 None:intergenic
CAAGGCTTACCTGAGCAAAA+TGG 0.416510 3_2:-8903086 Msa0394330:CDS
TCAACAAGGTTAAAACCAAC+AGG 0.475786 3_2:+8902996 None:intergenic
CCATCAAGCTTGTCCTTCCA+AGG 0.477711 3_2:-8903290 Msa0394330:CDS
TTGTGAGAGGGTTGAAACCT+TGG 0.480579 3_2:+8903273 None:intergenic
CTTAAATCCAATGATCCTGT+TGG 0.489692 3_2:-8903011 Msa0394330:CDS
AAATATCAACCAAAGAAACT+TGG 0.505006 3_2:+8902900 None:intergenic
CTTAAGCTTATCACAAGTGA+AGG 0.506695 3_2:+8903176 None:intergenic
AGCTGGTGACAAACGTGCTA+AGG 0.525842 3_2:-8903048 Msa0394330:CDS
TAATGCATGAGTTGATATCA+TGG 0.550417 3_2:+8903352 None:intergenic
ATCTTGGCTACTTCTAGCAA+TGG 0.561786 3_2:-8902930 Msa0394330:CDS
AGAGAAAATGTAGCCAAACA+AGG 0.605177 3_2:-8903104 Msa0394330:CDS
CTTGTGATAAGCTTAAGCAC+TGG 0.608219 3_2:-8903170 Msa0394330:CDS
GGTGTTACACACTTTGAAGC+TGG 0.611835 3_2:-8903065 Msa0394330:CDS
AAGGTTTCAACCCTCTCACA+AGG 0.615424 3_2:-8903271 Msa0394330:CDS
GAGAGGGTTGAAACCTTGGA+AGG 0.623355 3_2:+8903277 None:intergenic
TTAAGCTTATCACAAGTGAA+GGG 0.638403 3_2:+8903177 None:intergenic
ATGAGTTGATATCATGGATG+AGG 0.640889 3_2:+8903358 None:intergenic
CCCAAGCCAAAACATCAACA+AGG 0.663918 3_2:+8902982 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTAACCTTGTTGATGTTT+TGG - chr3_2:8903288-8903307 Msa0394330:CDS 25.0%
!! TATTGTTGCTTACTATATCT+TGG - chr3_2:8903330-8903349 Msa0394330:CDS 25.0%
!! TAATGCATGAGTTGATATCA+TGG + chr3_2:8902927-8902946 None:intergenic 30.0%
!! AGTTTTGTGTTTTTGAATGG+TGG + chr3_2:8902954-8902973 None:intergenic 30.0%
!! GTGAGTTTTGTGTTTTTGAA+TGG + chr3_2:8902957-8902976 None:intergenic 30.0%
! CTTGAAAATCTCTTTTTGCT+TGG + chr3_2:8903055-8903074 None:intergenic 30.0%
TTAAGCTTATCACAAGTGAA+GGG + chr3_2:8903102-8903121 None:intergenic 30.0%
!!! ACTGGTCTTTCATTGTTTTT+AGG - chr3_2:8903124-8903143 Msa0394330:CDS 30.0%
!!! GTCTTTCATTGTTTTTAGGA+AGG - chr3_2:8903128-8903147 Msa0394330:CDS 30.0%
!! ATGAGTTGATATCATGGATG+AGG + chr3_2:8902921-8902940 None:intergenic 35.0%
CTTAAGCTTATCACAAGTGA+AGG + chr3_2:8903103-8903122 None:intergenic 35.0%
! GTTTGGCTACATTTTCTCTT+TGG + chr3_2:8903171-8903190 None:intergenic 35.0%
AGAGAAAATGTAGCCAAACA+AGG - chr3_2:8903172-8903191 Msa0394330:CDS 35.0%
CTTAAATCCAATGATCCTGT+TGG - chr3_2:8903265-8903284 Msa0394330:CDS 35.0%
GTTAAAACCAACAGGATCAT+TGG + chr3_2:8903275-8903294 None:intergenic 35.0%
TCAACAAGGTTAAAACCAAC+AGG + chr3_2:8903283-8903302 None:intergenic 35.0%
GGTTATGATCCAAGTTTCTT+TGG - chr3_2:8903367-8903386 Msa0394330:CDS 35.0%
! CTTTTGTTGACCTTGTGAGA+GGG + chr3_2:8903018-8903037 None:intergenic 40.0%
! ACTTTTGTTGACCTTGTGAG+AGG + chr3_2:8903019-8903038 None:intergenic 40.0%
CTTGTGATAAGCTTAAGCAC+TGG - chr3_2:8903106-8903125 Msa0394330:CDS 40.0%
! TGTGTAACACCATTTTGCTC+AGG + chr3_2:8903202-8903221 None:intergenic 40.0%
!!! ACCTTGTTGATGTTTTGGCT+TGG - chr3_2:8903293-8903312 Msa0394330:CDS 40.0%
!!! CCTTGTTGATGTTTTGGCTT+GGG - chr3_2:8903294-8903313 Msa0394330:CDS 40.0%
!!! CTTGTTGATGTTTTGGCTTG+GGG - chr3_2:8903295-8903314 Msa0394330:CDS 40.0%
ATCTTGGCTACTTCTAGCAA+TGG - chr3_2:8903346-8903365 Msa0394330:CDS 40.0%
TTGTGAGAGGGTTGAAACCT+TGG + chr3_2:8903006-8903025 None:intergenic 45.0%
AAGGTTTCAACCCTCTCACA+AGG - chr3_2:8903005-8903024 Msa0394330:CDS 45.0%
!! TTGCTCAGGTAAGCCTTGTT+TGG + chr3_2:8903188-8903207 None:intergenic 45.0%
CAAGGCTTACCTGAGCAAAA+TGG - chr3_2:8903190-8903209 Msa0394330:CDS 45.0%
!! GGTGTTACACACTTTGAAGC+TGG - chr3_2:8903211-8903230 Msa0394330:CDS 45.0%
CCCAAGCCAAAACATCAACA+AGG + chr3_2:8903297-8903316 None:intergenic 45.0%
!!! GTTTTGGCTTGGGGTTCTTT+AGG - chr3_2:8903304-8903323 Msa0394330:CDS 45.0%
CCTTGGAAGGACAAGCTTGA+TGG + chr3_2:8902989-8903008 None:intergenic 50.0%
CCATCAAGCTTGTCCTTCCA+AGG - chr3_2:8902986-8903005 Msa0394330:CDS 50.0%
GAGAGGGTTGAAACCTTGGA+AGG + chr3_2:8903002-8903021 None:intergenic 50.0%
AGCTGGTGACAAACGTGCTA+AGG - chr3_2:8903228-8903247 Msa0394330:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_2 gene 8902905 8903393 8902905 ID=Msa0394330;Name=Msa0394330
chr3_2 mRNA 8902905 8903393 8902905 ID=Msa0394330-mRNA-1;Parent=Msa0394330;Name=Msa0394330-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|162
chr3_2 exon 8902905 8903393 8902905 ID=Msa0394330-mRNA-1:exon:2340;Parent=Msa0394330-mRNA-1
chr3_2 CDS 8902905 8903393 8902905 ID=Msa0394330-mRNA-1:cds;Parent=Msa0394330-mRNA-1
Gene Sequence

>Msa0394330

ATGGCAGCTTCAGCCTCATCCATGATATCAACTCATGCATTAACAACCACCATTCAAAAACACAAAACTCACAATCTCAAGCCATCAAGCTTGTCCTTCCAAGGTTTCAACCCTCTCACAAGGTCAACAAAAGTCAACACATTCACACCAAGCAAAAAGAGATTTTCAAGTGTTGTTGTCAAAGCTGAACTCAACCCTTCACTTGTGATAAGCTTAAGCACTGGTCTTTCATTGTTTTTAGGAAGGTTTGTGTTTTTCAACTTCCAAAGAGAAAATGTAGCCAAACAAGGCTTACCTGAGCAAAATGGTGTTACACACTTTGAAGCTGGTGACAAACGTGCTAAGGAATATGTTAGCTTGCTTAAATCCAATGATCCTGTTGGTTTTAACCTTGTTGATGTTTTGGCTTGGGGTTCTTTAGGTCATATTGTTGCTTACTATATCTTGGCTACTTCTAGCAATGGTTATGATCCAAGTTTCTTTGGTTGA

Protein sequence

>Msa0394330

MAASASSMISTHALTTTIQKHKTHNLKPSSLSFQGFNPLTRSTKVNTFTPSKKRFSSVVVKAELNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDKRAKEYVSLLKSNDPVGFNLVDVLAWGSLGHIVAYYILATSSNGYDPSFFG*