AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0604400

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0604400 MtrunA17_Chr8g0375421 81.818 77 10 1 14 90 14 86 2.71e-24 95.1
Msa0604400 MtrunA17_Chr8g0375441 60.811 74 12 2 17 90 1 57 2.49e-19 75.9
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0604400 AT1G14660.2 57.353 68 27 1 30 95 13 80 1.14e-17 76.6
Msa0604400 AT2G01980.1 74.000 50 11 1 48 95 33 82 1.17e-17 76.6
Msa0604400 AT1G14660.1 57.353 68 27 1 30 95 13 80 1.21e-17 76.6

Find 20 sgRNAs with CRISPR-Local

Find 21 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCATCCTTGGCATTGCTCT+TGG 0.232996 4_2:-49952827 Msa0604400:CDS
TCAGATGCAGTTATCTTCTT+TGG 0.260845 4_2:-49952923 Msa0604400:CDS
TTTGGTCTCAGTCTTGCTCT+TGG 0.339821 4_2:-49952905 Msa0604400:CDS
GGCATTGCTCTTGGATCCTT+AGG 0.353533 4_2:-49952818 Msa0604400:CDS
TGATATGTCGTTGTTGTTGA+TGG 0.357807 4_2:-49953071 None:intergenic
ATGAGCAAAGCGACAGTGTA+AGG 0.392815 4_2:+49952845 None:intergenic
CTGAAGCTGAAGCTGAAAGC+AGG 0.455045 4_2:+49952987 None:intergenic
ACTGTCGCTTTGCTCATCCT+TGG 0.476445 4_2:-49952839 Msa0604400:CDS
TGAAGCTGAAAGCAGGGAAA+AGG 0.481172 4_2:+49952994 None:intergenic
GGACTCTAGTCCCACGCAAA+AGG 0.493391 4_2:+49952867 None:intergenic
GATTCATTCTCTGAAGAAGA+AGG 0.493694 4_2:+49952953 None:intergenic
ACCTACTACATACAGAATCA+TGG 0.531172 4_2:-49953035 Msa0604400:CDS
TTAATTAGAAGAAGAACCTA+AGG 0.546743 4_2:+49952802 None:intergenic
AAGAAGATAACTGCATCTGA+TGG 0.552503 4_2:+49952926 None:intergenic
TCCATGATTCTGTATGTAGT+AGG 0.563550 4_2:+49953034 None:intergenic
TGAGCAAAGCGACAGTGTAA+GGG 0.603045 4_2:+49952846 None:intergenic
TGAAGCTGAAGCTGAAAGCA+GGG 0.603810 4_2:+49952988 None:intergenic
TCATTCTCTGAAGAAGAAGG+TGG 0.626461 4_2:+49952956 None:intergenic
AGGATCCAAGAGCAATGCCA+AGG 0.652380 4_2:+49952822 None:intergenic
GAAAGCAGGGAAAAGGAAAG+CGG 0.699197 4_2:+49953001 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TTAATTAGAAGAAGAACCTA+AGG + chr4_2:49953070-49953089 None:intergenic 25.0%
ACCTACTACATACAGAATCA+TGG - chr4_2:49952834-49952853 Msa0604400:CDS 35.0%
TCCATGATTCTGTATGTAGT+AGG + chr4_2:49952838-49952857 None:intergenic 35.0%
! GATTCATTCTCTGAAGAAGA+AGG + chr4_2:49952919-49952938 None:intergenic 35.0%
AAGAAGATAACTGCATCTGA+TGG + chr4_2:49952946-49952965 None:intergenic 35.0%
TCAGATGCAGTTATCTTCTT+TGG - chr4_2:49952946-49952965 Msa0604400:CDS 35.0%
! TCATTCTCTGAAGAAGAAGG+TGG + chr4_2:49952916-49952935 None:intergenic 40.0%
GAAAGCAGGGAAAAGGAAAG+CGG + chr4_2:49952871-49952890 None:intergenic 45.0%
TGAAGCTGAAAGCAGGGAAA+AGG + chr4_2:49952878-49952897 None:intergenic 45.0%
TGAAGCTGAAGCTGAAAGCA+GGG + chr4_2:49952884-49952903 None:intergenic 45.0%
TTTGGTCTCAGTCTTGCTCT+TGG - chr4_2:49952964-49952983 Msa0604400:CDS 45.0%
TGAGCAAAGCGACAGTGTAA+GGG + chr4_2:49953026-49953045 None:intergenic 45.0%
ATGAGCAAAGCGACAGTGTA+AGG + chr4_2:49953027-49953046 None:intergenic 45.0%
CTGAAGCTGAAGCTGAAAGC+AGG + chr4_2:49952885-49952904 None:intergenic 50.0%
! CTTGCAGACACCTTTTGCGT+GGG - chr4_2:49952992-49953011 Msa0604400:CDS 50.0%
!! ACTGTCGCTTTGCTCATCCT+TGG - chr4_2:49953030-49953049 Msa0604400:CDS 50.0%
CTCATCCTTGGCATTGCTCT+TGG - chr4_2:49953042-49953061 Msa0604400:CDS 50.0%
AGGATCCAAGAGCAATGCCA+AGG + chr4_2:49953050-49953069 None:intergenic 50.0%
GGCATTGCTCTTGGATCCTT+AGG - chr4_2:49953051-49953070 Msa0604400:CDS 50.0%
! GCTTGCAGACACCTTTTGCG+TGG - chr4_2:49952991-49953010 Msa0604400:CDS 55.0%
GGACTCTAGTCCCACGCAAA+AGG + chr4_2:49953005-49953024 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 49952802 49953089 49952802 ID=Msa0604400;Name=Msa0604400
chr4_2 mRNA 49952802 49953089 49952802 ID=Msa0604400-mRNA-1;Parent=Msa0604400;Name=Msa0604400-mRNA-1;_AED=0.51;_eAED=1.00;_QI=0|-1|0|1|-1|1|1|0|95
chr4_2 exon 49952802 49953089 49952802 ID=Msa0604400-mRNA-1:exon:11662;Parent=Msa0604400-mRNA-1
chr4_2 CDS 49952802 49953089 49952802 ID=Msa0604400-mRNA-1:cds;Parent=Msa0604400-mRNA-1
Gene Sequence

>Msa0604400

ATGTCGTTGTTGTTGATGGAAGAAGAATCACTACCTACTACATACAGAATCATGGAGCAGCAACAACCGCTTTCCTTTTCCCTGCTTTCAGCTTCAGCTTCAGCTTCTTCTCCACCTTCTTCTTCAGAGAATGAATCAAATCCATCAGATGCAGTTATCTTCTTTGGTCTCAGTCTTGCTCTTGGAATTGCTTGCAGACACCTTTTGCGTGGGACTAGAGTCCCTTACACTGTCGCTTTGCTCATCCTTGGCATTGCTCTTGGATCCTTAGGTTCTTCTTCTAATTAA
Protein sequence

>Msa0604400

MSLLLMEEESLPTTYRIMEQQQPLSFSLLSASASASSPPSSSENESNPSDAVIFFGLSLALGIACRHLLRGTRVPYTVALLILGIALGSLGSSSN*