AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0347600


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0347600 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
Msa0347600 AT1G55670.1 70.303 165 41 3 1 162 1 160 1.44e-77 228

Find 23 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GGTTATGATCCAAGTTTCTT+TGG 0.278269 3_1:-8760523 Msa0347600:CDS
TTGCTCAGGTAAGCCTTGTT+TGG 0.325198 3_1:+8760705 None:intergenic
TATTGTTGCTTACTATATCT+TGG 0.334380 3_1:-8760560 Msa0347600:CDS
GTTAAAACCAACAGGATCAT+TGG 0.338510 3_1:+8760618 None:intergenic
CCTTGGAAGGACAAGCTTGA+TGG 0.371656 3_1:+8760904 None:intergenic
CAAGGCTTACCTGAGCAAAA+TGG 0.416510 3_1:-8760700 Msa0347600:CDS
TCAACAAGGTTAAAACCAAC+AGG 0.475786 3_1:+8760610 None:intergenic
CCATCAAGCTTGTCCTTCCA+AGG 0.477711 3_1:-8760904 Msa0347600:CDS
TTGTGAGAGGGTTGAAACCT+TGG 0.480579 3_1:+8760887 None:intergenic
CTTAAATCCAATGATCCTGT+TGG 0.489692 3_1:-8760625 Msa0347600:CDS
CTTAAGCTTATCACAAGTGA+AGG 0.506695 3_1:+8760790 None:intergenic
AAATATTAACCAAAGAAACT+TGG 0.511509 3_1:+8760514 None:intergenic
AGCTGGTGACAAACGTGCTA+AGG 0.525842 3_1:-8760662 Msa0347600:CDS
TAATGCATGAGTTGATATCA+TGG 0.550417 3_1:+8760966 None:intergenic
ATCTTGGCTACTTCTAGCAA+TGG 0.561786 3_1:-8760544 Msa0347600:CDS
AGAGAAAATGTAGCCAAACA+AGG 0.605177 3_1:-8760718 Msa0347600:CDS
CTTGTGATAAGCTTAAGCAC+TGG 0.608219 3_1:-8760784 Msa0347600:CDS
AAGGTTTCAACCCTCTCACA+AGG 0.615424 3_1:-8760885 Msa0347600:CDS
GAGAGGGTTGAAACCTTGGA+AGG 0.623355 3_1:+8760891 None:intergenic
TTAAGCTTATCACAAGTGAA+GGG 0.638403 3_1:+8760791 None:intergenic
ATGAGTTGATATCATGGATG+AGG 0.640889 3_1:+8760972 None:intergenic
GGTGTGACACACTTTGAAGC+TGG 0.654419 3_1:-8760679 Msa0347600:CDS
CCCAAGCCAAAACATCAACA+AGG 0.663918 3_1:+8760596 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTTTAACCTTGTTGATGTTT+TGG - chr3_1:8760902-8760921 Msa0347600:CDS 25.0%
!! TATTGTTGCTTACTATATCT+TGG - chr3_1:8760944-8760963 Msa0347600:CDS 25.0%
!! TAATGCATGAGTTGATATCA+TGG + chr3_1:8760541-8760560 None:intergenic 30.0%
!! AGTTTTGTGTTTTTGAATGG+TGG + chr3_1:8760568-8760587 None:intergenic 30.0%
!! GTGAGTTTTGTGTTTTTGAA+TGG + chr3_1:8760571-8760590 None:intergenic 30.0%
!!! CTTGAAAACCTTTTTTTGCT+TGG + chr3_1:8760669-8760688 None:intergenic 30.0%
TTAAGCTTATCACAAGTGAA+GGG + chr3_1:8760716-8760735 None:intergenic 30.0%
!!! ACTGGTCTTTCATTGTTTTT+AGG - chr3_1:8760738-8760757 Msa0347600:CDS 30.0%
!!! GTCTTTCATTGTTTTTAGGA+AGG - chr3_1:8760742-8760761 Msa0347600:CDS 30.0%
!! ATGAGTTGATATCATGGATG+AGG + chr3_1:8760535-8760554 None:intergenic 35.0%
CATTCACACCAAGCAAAAAA+AGG - chr3_1:8760658-8760677 Msa0347600:CDS 35.0%
CTTAAGCTTATCACAAGTGA+AGG + chr3_1:8760717-8760736 None:intergenic 35.0%
! GTTTGGCTACATTTTCTCTT+TGG + chr3_1:8760785-8760804 None:intergenic 35.0%
AGAGAAAATGTAGCCAAACA+AGG - chr3_1:8760786-8760805 Msa0347600:CDS 35.0%
CTTAAATCCAATGATCCTGT+TGG - chr3_1:8760879-8760898 Msa0347600:CDS 35.0%
GTTAAAACCAACAGGATCAT+TGG + chr3_1:8760889-8760908 None:intergenic 35.0%
TCAACAAGGTTAAAACCAAC+AGG + chr3_1:8760897-8760916 None:intergenic 35.0%
GGTTATGATCCAAGTTTCTT+TGG - chr3_1:8760981-8761000 Msa0347600:CDS 35.0%
! CTTTTGTTGACCTTGTGAGA+GGG + chr3_1:8760632-8760651 None:intergenic 40.0%
! ACTTTTGTTGACCTTGTGAG+AGG + chr3_1:8760633-8760652 None:intergenic 40.0%
CTTGTGATAAGCTTAAGCAC+TGG - chr3_1:8760720-8760739 Msa0347600:CDS 40.0%
!!! ACCTTGTTGATGTTTTGGCT+TGG - chr3_1:8760907-8760926 Msa0347600:CDS 40.0%
!!! CCTTGTTGATGTTTTGGCTT+GGG - chr3_1:8760908-8760927 Msa0347600:CDS 40.0%
!!! CTTGTTGATGTTTTGGCTTG+GGG - chr3_1:8760909-8760928 Msa0347600:CDS 40.0%
ATCTTGGCTACTTCTAGCAA+TGG - chr3_1:8760960-8760979 Msa0347600:CDS 40.0%
TTGTGAGAGGGTTGAAACCT+TGG + chr3_1:8760620-8760639 None:intergenic 45.0%
AAGGTTTCAACCCTCTCACA+AGG - chr3_1:8760619-8760638 Msa0347600:CDS 45.0%
!! TTGCTCAGGTAAGCCTTGTT+TGG + chr3_1:8760802-8760821 None:intergenic 45.0%
CAAGGCTTACCTGAGCAAAA+TGG - chr3_1:8760804-8760823 Msa0347600:CDS 45.0%
! TGTGTCACACCATTTTGCTC+AGG + chr3_1:8760816-8760835 None:intergenic 45.0%
CCCAAGCCAAAACATCAACA+AGG + chr3_1:8760911-8760930 None:intergenic 45.0%
!!! GTTTTGGCTTGGGGTTCTTT+AGG - chr3_1:8760918-8760937 Msa0347600:CDS 45.0%
CCTTGGAAGGACAAGCTTGA+TGG + chr3_1:8760603-8760622 None:intergenic 50.0%
CCATCAAGCTTGTCCTTCCA+AGG - chr3_1:8760600-8760619 Msa0347600:CDS 50.0%
GAGAGGGTTGAAACCTTGGA+AGG + chr3_1:8760616-8760635 None:intergenic 50.0%
!! GGTGTGACACACTTTGAAGC+TGG - chr3_1:8760825-8760844 Msa0347600:CDS 50.0%
AGCTGGTGACAAACGTGCTA+AGG - chr3_1:8760842-8760861 Msa0347600:CDS 50.0%
Chromosome Type Strat End Strand Name
chr3_1 gene 8760519 8761007 8760519 ID=Msa0347600;Name=Msa0347600
chr3_1 mRNA 8760519 8761007 8760519 ID=Msa0347600-mRNA-1;Parent=Msa0347600;Name=Msa0347600-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|162
chr3_1 exon 8760519 8761007 8760519 ID=Msa0347600-mRNA-1:exon:2523;Parent=Msa0347600-mRNA-1
chr3_1 CDS 8760519 8761007 8760519 ID=Msa0347600-mRNA-1:cds;Parent=Msa0347600-mRNA-1
Gene Sequence

>Msa0347600

ATGGCAGCTTCAGCCTCATCCATGATATCAACTCATGCATTAACAACCACCATTCAAAAACACAAAACTCACAATCTCAAGCCATCAAGCTTGTCCTTCCAAGGTTTCAACCCTCTCACAAGGTCAACAAAAGTCAACACATTCACACCAAGCAAAAAAAGGTTTTCAAGTGTTGTTGTCAAAGCTGAACTCAACCCTTCACTTGTGATAAGCTTAAGCACTGGTCTTTCATTGTTTTTAGGAAGGTTTGTGTTTTTCAACTTCCAAAGAGAAAATGTAGCCAAACAAGGCTTACCTGAGCAAAATGGTGTGACACACTTTGAAGCTGGTGACAAACGTGCTAAGGAATATGTTAGCTTGCTTAAATCCAATGATCCTGTTGGTTTTAACCTTGTTGATGTTTTGGCTTGGGGTTCTTTAGGTCATATTGTTGCTTACTATATCTTGGCTACTTCTAGCAATGGTTATGATCCAAGTTTCTTTGGTTAA

Protein sequence

>Msa0347600

MAASASSMISTHALTTTIQKHKTHNLKPSSLSFQGFNPLTRSTKVNTFTPSKKRFSSVVVKAELNPSLVISLSTGLSLFLGRFVFFNFQRENVAKQGLPEQNGVTHFEAGDKRAKEYVSLLKSNDPVGFNLVDVLAWGSLGHIVAYYILATSSNGYDPSFFG*