AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1420270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1420270 MtrunA17_Chr5g0404011 91.919 99 5 1 1 99 1 96 7.44e-61 180
Msa1420270 MtrunA17_Chr5g0403991 71.569 102 26 1 1 99 1 102 3.41e-49 151
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 22 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGAACACAAGAAGAATAAA+AGG 0.259149 tig0024770:+60932 Msa1420270:CDS
ATATTCTTCATTTGTCTCCA+TGG 0.393537 tig0024770:-60911 None:intergenic
CTCCTCCGCCTCGTTGGGAC+TGG 0.394195 tig0024770:-60998 None:intergenic
AAGAAGAATAAAAGGGGTAT+TGG 0.401583 tig0024770:+60940 Msa1420270:CDS
CGTCACCTCCTCCGCCTCGT+TGG 0.403234 tig0024770:-61004 None:intergenic
GTCACCTCCTCCGCCTCGTT+GGG 0.405210 tig0024770:-61003 None:intergenic
ATCAGTCACCACCCTTGAAC+TGG 0.436123 tig0024770:-61081 None:intergenic
TCGGAATGTGTTAAAGTTGG+TGG 0.447025 tig0024770:+60868 Msa1420270:CDS
CAGTCCCAACGAGGCGGAGG+AGG 0.463123 tig0024770:+60999 Msa1420270:CDS
GGAGGAGGTGACGGTGAAGA+AGG 0.476982 tig0024770:+61014 Msa1420270:CDS
TGAACACAAGAAGAATAAAA+GGG 0.482825 tig0024770:+60933 Msa1420270:CDS
ATCATCAGAATCTGTAACTT+CGG 0.488685 tig0024770:+60849 Msa1420270:CDS
TTCCAGTCCCAACGAGGCGG+AGG 0.517997 tig0024770:+60996 Msa1420270:CDS
AGGAGAAGAAACGTTCGTCT+TGG 0.533201 tig0024770:+61034 Msa1420270:CDS
CAACGAGGCGGAGGAGGTGA+CGG 0.560055 tig0024770:+61005 Msa1420270:CDS
ACTTCGGAATGTGTTAAAGT+TGG 0.563777 tig0024770:+60865 Msa1420270:CDS
GTTAGGTTGTCAAGATCAGA+AGG 0.595454 tig0024770:+60817 Msa1420270:CDS
TGAAAGACTCTCACAAACCA+TGG 0.604467 tig0024770:+60894 Msa1420270:CDS
AACGTTGGCCAGTTCAAGGG+TGG 0.624083 tig0024770:+61073 Msa1420270:CDS
GAACACAAGAAGAATAAAAG+GGG 0.652443 tig0024770:+60934 Msa1420270:CDS
GAGAATTTCCAGTCCCAACG+AGG 0.655349 tig0024770:+60990 Msa1420270:CDS
AATTTCCAGTCCCAACGAGG+CGG 0.689181 tig0024770:+60993 Msa1420270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TGGAATTTAGAAAAAGTGTT+AGG + tig0024770:60800-60819 Msa1420270:CDS 25.0%
! ATGAACACAAGAAGAATAAA+AGG + tig0024770:60932-60951 Msa1420270:CDS 25.0%
! TGAACACAAGAAGAATAAAA+GGG + tig0024770:60933-60952 Msa1420270:CDS 25.0%
ATCATCAGAATCTGTAACTT+CGG + tig0024770:60849-60868 Msa1420270:CDS 30.0%
ATATTCTTCATTTGTCTCCA+TGG - tig0024770:60914-60933 None:intergenic 30.0%
GAACACAAGAAGAATAAAAG+GGG + tig0024770:60934-60953 Msa1420270:CDS 30.0%
! AAGAAGAATAAAAGGGGTAT+TGG + tig0024770:60940-60959 Msa1420270:CDS 30.0%
ACTTCGGAATGTGTTAAAGT+TGG + tig0024770:60865-60884 Msa1420270:CDS 35.0%
! GTTAGGTTGTCAAGATCAGA+AGG + tig0024770:60817-60836 Msa1420270:CDS 40.0%
TCGGAATGTGTTAAAGTTGG+TGG + tig0024770:60868-60887 Msa1420270:CDS 40.0%
TGAAAGACTCTCACAAACCA+TGG + tig0024770:60894-60913 Msa1420270:CDS 40.0%
TTCCAGATCCACAAAAACGT+TGG + tig0024770:61058-61077 Msa1420270:CDS 40.0%
AAAAACGTTGGCCAGTTCAA+GGG + tig0024770:61070-61089 Msa1420270:CDS 40.0%
AGGAGAAGAAACGTTCGTCT+TGG + tig0024770:61034-61053 Msa1420270:CDS 45.0%
! TGAACTGGCCAACGTTTTTG+TGG - tig0024770:61069-61088 None:intergenic 45.0%
CAAAAACGTTGGCCAGTTCA+AGG + tig0024770:61069-61088 Msa1420270:CDS 45.0%
GAGAATTTCCAGTCCCAACG+AGG + tig0024770:60990-61009 Msa1420270:CDS 50.0%
AATTTCCAGTCCCAACGAGG+CGG + tig0024770:60993-61012 Msa1420270:CDS 50.0%
! GGCCAACGTTTTTGTGGATC+TGG - tig0024770:61063-61082 None:intergenic 50.0%
AACGTTGGCCAGTTCAAGGG+TGG + tig0024770:61073-61092 Msa1420270:CDS 55.0%
! GGAGGAGGTGACGGTGAAGA+AGG + tig0024770:61014-61033 Msa1420270:CDS 60.0%
TTCCAGTCCCAACGAGGCGG+AGG + tig0024770:60996-61015 Msa1420270:CDS 65.0%
GTCACCTCCTCCGCCTCGTT+GGG - tig0024770:61006-61025 None:intergenic 65.0%
CAACGAGGCGGAGGAGGTGA+CGG + tig0024770:61005-61024 Msa1420270:CDS 65.0%
CTCCTCCGCCTCGTTGGGAC+TGG - tig0024770:61001-61020 None:intergenic 70.0%
CAGTCCCAACGAGGCGGAGG+AGG + tig0024770:60999-61018 Msa1420270:CDS 70.0%
CGTCACCTCCTCCGCCTCGT+TGG - tig0024770:61007-61026 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
tig0024770 gene 60799 61098 60799 ID=Msa1420270;Name=Msa1420270
tig0024770 mRNA 60799 61098 60799 ID=Msa1420270-mRNA-1;Parent=Msa1420270;Name=Msa1420270-mRNA-1;_AED=0.26;_eAED=0.26;_QI=0|-1|0|1|-1|1|1|0|99
tig0024770 exon 60799 61098 60799 ID=Msa1420270-mRNA-1:exon:1387;Parent=Msa1420270-mRNA-1
tig0024770 CDS 60799 61098 60799 ID=Msa1420270-mRNA-1:cds;Parent=Msa1420270-mRNA-1
Gene Sequence

>Msa1420270

ATGGAATTTAGAAAAAGTGTTAGGTTGTCAAGATCAGAAGGTATATTACTATCATCAGAATCTGTAACTTCGGAATGTGTTAAAGTTGGTGGTTATGAAAGACTCTCACAAACCATGGAGACAAATGAAGAATATGAACACAAGAAGAATAAAAGGGGTATTGGATTTCTAAGTAAAGTATTAAATTTAACGAGAATTTCCAGTCCCAACGAGGCGGAGGAGGTGACGGTGAAGAAGGAGAAGAAACGTTCGTCTTGGCTTCCAGATCCACAAAAACGTTGGCCAGTTCAAGGGTGGTGA

Protein sequence

>Msa1420270

MEFRKSVRLSRSEGILLSSESVTSECVKVGGYERLSQTMETNEEYEHKKNKRGIGFLSKVLNLTRISSPNEAEEVTVKKEKKRSSWLPDPQKRWPVQGW*