AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0489620


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0489620 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
Msa0489620 AT1G55670.1 70.303 165 41 3 1 162 1 160 1.44e-77 228

Find 27 sgRNAs with CRISPR-Local

Find 38 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGGCCTTTCATTGTTTCT+AGG 0.274659 3_4:+10200076 Msa0489620:CDS
GGTTATGATCCAAGTTTCTT+TGG 0.281064 3_4:+10200319 Msa0489620:CDS
TTGCTCAGGTAAGCCTTGTT+TGG 0.325198 3_4:-10200137 None:intergenic
TATTGTTGCTTACTATATCT+TGG 0.334380 3_4:+10200282 Msa0489620:CDS
GTTAAAACCAACAGGATCAT+TGG 0.338510 3_4:-10200224 None:intergenic
CCTTGGAAGGACAAGCTTGA+TGG 0.371656 3_4:-10199938 None:intergenic
CAAGGCTTACCTGAGCAAAA+TGG 0.416510 3_4:+10200142 Msa0489620:CDS
GCCTTTCATTGTTTCTAGGA+AGG 0.456316 3_4:+10200080 Msa0489620:CDS
TCAACAAGGTTAAAACCAAC+AGG 0.475786 3_4:-10200232 None:intergenic
CCATCAAGCTTGTCCTTCCA+AGG 0.477711 3_4:+10199938 Msa0489620:CDS
TTGTGAGAGGGTTGAAACCT+TGG 0.480579 3_4:-10199955 None:intergenic
CTTAAATCCAATGATCCTGT+TGG 0.489692 3_4:+10200217 Msa0489620:CDS
AAATATCAACCAAAGAAACT+TGG 0.505006 3_4:-10200328 None:intergenic
CTTAAGCTTATCACAAGTGA+AGG 0.506695 3_4:-10200052 None:intergenic
AGCTGGTGACAAACGTGCTA+AGG 0.525842 3_4:+10200180 Msa0489620:CDS
TAATGCATGAGTTGATATCA+TGG 0.550417 3_4:-10199876 None:intergenic
AGAGAAAATGTAGCCAAACA+AGG 0.605177 3_4:+10200124 Msa0489620:CDS
TTAAGCTTATCACAAGTGAA+GGG 0.611825 3_4:-10200051 None:intergenic
AAGGTTTCAACCCTCTCACA+AGG 0.615424 3_4:+10199957 Msa0489620:CDS
CTTGTGATAAGCTTAAGCAC+TGG 0.620138 3_4:+10200058 Msa0489620:CDS
GAGAGGGTTGAAACCTTGGA+AGG 0.623355 3_4:-10199951 None:intergenic
ATCTTGGCTACCTCTAGCAA+TGG 0.629294 3_4:+10200298 Msa0489620:CDS
ATGAGTTGATATCATGGATG+AGG 0.640889 3_4:-10199870 None:intergenic
GGTGTGACACACTTTGAAGC+TGG 0.654419 3_4:+10200163 Msa0489620:CDS
ACCTTCCTAGAAACAATGAA+AGG 0.658705 3_4:-10200081 None:intergenic
TGGATCATAACCATTGCTAG+AGG 0.663829 3_4:-10200308 None:intergenic
CCCAAGCCAAAACATCAACA+AGG 0.663918 3_4:-10200246 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTAACCTTGTTGATGTTT+TGG + chr3_4:10200240-10200259 Msa0489620:CDS 25.0%
!! TATTGTTGCTTACTATATCT+TGG + chr3_4:10200282-10200301 Msa0489620:CDS 25.0%
!! TAATGCATGAGTTGATATCA+TGG - chr3_4:10199879-10199898 None:intergenic 30.0%
!! AGTTTTGTGTTTTTGAATGG+TGG - chr3_4:10199906-10199925 None:intergenic 30.0%
!! GTGAGTTTTGTGTTTTTGAA+TGG - chr3_4:10199909-10199928 None:intergenic 30.0%
! CTTGAAAATCTCTTTTTGCT+TGG - chr3_4:10200007-10200026 None:intergenic 30.0%
TTAAGCTTATCACAAGTGAA+GGG - chr3_4:10200054-10200073 None:intergenic 30.0%
!! ATGAGTTGATATCATGGATG+AGG - chr3_4:10199873-10199892 None:intergenic 35.0%
CTTAAGCTTATCACAAGTGA+AGG - chr3_4:10200055-10200074 None:intergenic 35.0%
ACCTTCCTAGAAACAATGAA+AGG - chr3_4:10200084-10200103 None:intergenic 35.0%
! GTTTGGCTACATTTTCTCTT+TGG - chr3_4:10200123-10200142 None:intergenic 35.0%
AGAGAAAATGTAGCCAAACA+AGG + chr3_4:10200124-10200143 Msa0489620:CDS 35.0%
CTTAAATCCAATGATCCTGT+TGG + chr3_4:10200217-10200236 Msa0489620:CDS 35.0%
GTTAAAACCAACAGGATCAT+TGG - chr3_4:10200227-10200246 None:intergenic 35.0%
TCAACAAGGTTAAAACCAAC+AGG - chr3_4:10200235-10200254 None:intergenic 35.0%
GGTTATGATCCAAGTTTCTT+TGG + chr3_4:10200319-10200338 Msa0489620:CDS 35.0%
! CTTTTGTTGACCTTGTGAGA+GGG - chr3_4:10199970-10199989 None:intergenic 40.0%
! ACTTTTGTTGACCTTGTGAG+AGG - chr3_4:10199971-10199990 None:intergenic 40.0%
CTTGTGATAAGCTTAAGCAC+TGG + chr3_4:10200058-10200077 Msa0489620:CDS 40.0%
!! ACTGGCCTTTCATTGTTTCT+AGG + chr3_4:10200076-10200095 Msa0489620:CDS 40.0%
!! GCCTTTCATTGTTTCTAGGA+AGG + chr3_4:10200080-10200099 Msa0489620:CDS 40.0%
!!! ACCTTGTTGATGTTTTGGCT+TGG + chr3_4:10200245-10200264 Msa0489620:CDS 40.0%
!!! CCTTGTTGATGTTTTGGCTT+GGG + chr3_4:10200246-10200265 Msa0489620:CDS 40.0%
!!! CTTGTTGATGTTTTGGCTTG+GGG + chr3_4:10200247-10200266 Msa0489620:CDS 40.0%
TGGATCATAACCATTGCTAG+AGG - chr3_4:10200311-10200330 None:intergenic 40.0%
TTGTGAGAGGGTTGAAACCT+TGG - chr3_4:10199958-10199977 None:intergenic 45.0%
AAGGTTTCAACCCTCTCACA+AGG + chr3_4:10199957-10199976 Msa0489620:CDS 45.0%
!! TTGCTCAGGTAAGCCTTGTT+TGG - chr3_4:10200140-10200159 None:intergenic 45.0%
CAAGGCTTACCTGAGCAAAA+TGG + chr3_4:10200142-10200161 Msa0489620:CDS 45.0%
! TGTGTCACACCATTTTGCTC+AGG - chr3_4:10200154-10200173 None:intergenic 45.0%
CCCAAGCCAAAACATCAACA+AGG - chr3_4:10200249-10200268 None:intergenic 45.0%
!!! GTTTTGGCTTGGGGTTCTTT+AGG + chr3_4:10200256-10200275 Msa0489620:CDS 45.0%
ATCTTGGCTACCTCTAGCAA+TGG + chr3_4:10200298-10200317 Msa0489620:CDS 45.0%
CCTTGGAAGGACAAGCTTGA+TGG - chr3_4:10199941-10199960 None:intergenic 50.0%
CCATCAAGCTTGTCCTTCCA+AGG + chr3_4:10199938-10199957 Msa0489620:CDS 50.0%
GAGAGGGTTGAAACCTTGGA+AGG - chr3_4:10199954-10199973 None:intergenic 50.0%
!! GGTGTGACACACTTTGAAGC+TGG + chr3_4:10200163-10200182 Msa0489620:CDS 50.0%
AGCTGGTGACAAACGTGCTA+AGG + chr3_4:10200180-10200199 Msa0489620:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_4 gene 10199857 10200345 10199857 ID=Msa0489620;Name=Msa0489620
chr3_4 mRNA 10199857 10200345 10199857 ID=Msa0489620-mRNA-1;Parent=Msa0489620;Name=Msa0489620-mRNA-1;_AED=0.00;_eAED=0.08;_QI=0|-1|0|1|-1|1|1|0|162
chr3_4 exon 10199857 10200345 10199857 ID=Msa0489620-mRNA-1:exon:3312;Parent=Msa0489620-mRNA-1
chr3_4 CDS 10199857 10200345 10199857 ID=Msa0489620-mRNA-1:cds;Parent=Msa0489620-mRNA-1
Gene Sequence

>Msa0489620

ATGGCAGCTTCAGCCTCATCCATGATATCAACTCATGCATTAACAACCACCATTCAAAAACACAAAACTCACAATCTCAAGCCATCAAGCTTGTCCTTCCAAGGTTTCAACCCTCTCACAAGGTCAACAAAAGTCAACACATTCACACCAAGCAAAAAGAGATTTTCAAGTGTTGTTGTCAAAGCTGAACTAAACCCTTCACTTGTGATAAGCTTAAGCACTGGCCTTTCATTGTTTCTAGGAAGGTTTGTGTTTTTCAACTTCCAAAGAGAAAATGTAGCCAAACAAGGCTTACCTGAGCAAAATGGTGTGACACACTTTGAAGCTGGTGACAAACGTGCTAAGGAATATGTTAGCTTGCTTAAATCCAATGATCCTGTTGGTTTTAACCTTGTTGATGTTTTGGCTTGGGGTTCTTTAGGTCATATTGTTGCTTACTATATCTTGGCTACCTCTAGCAATGGTTATGATCCAAGTTTCTTTGGTTGA

Protein sequence

>Msa0489620

MAASASSMISTHALTTTIQKHKTHNLKPSSLSFQGFNPLTRSTKVNTFTPSKKRFSSVVVKAELNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDKRAKEYVSLLKSNDPVGFNLVDVLAWGSLGHIVAYYILATSSNGYDPSFFG*