AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0624070

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0624070 MtrunA17_Chr4g0019481 73.504 117 17 2 1 103 1 117 7.03e-49 151
Msa0624070 MtrunA17_Chr4g0019551 76.923 117 13 2 1 103 1 117 8.20e-49 150
Msa0624070 MtrunA17_Chr4g0019471 65.649 131 17 2 1 103 1 131 3.98e-46 144
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 18 sgRNAs with CRISPR-Local

Find 22 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTCATTCATCTGGTGTATA+AGG 0.184471 4_3:+1896990 None:intergenic
TGTGGTTGAGGCTGATTATT+TGG 0.247122 4_3:+1897152 None:intergenic
CTCGATTCTAATATTAAATC+TGG 0.264896 4_3:+1897191 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.356164 4_3:+1896991 None:intergenic
AGGTCGAAAGCGCGAACATT+AGG 0.356569 4_3:+1897020 None:intergenic
GGAGGTTGGTTCAAATCAAA+TGG 0.432622 4_3:+1897041 None:intergenic
CTGGTGTATAAGGGATATTA+AGG 0.496508 4_3:+1897000 None:intergenic
TGAGGCTGATTATTTGGTGG+TGG 0.505165 4_3:+1897158 None:intergenic
AAATCAAATGGTTGCACGCG+TGG 0.532950 4_3:+1897053 None:intergenic
AAGCGCGAACATTAGGAGGT+TGG 0.540533 4_3:+1897027 None:intergenic
TCGAAAGCGCGAACATTAGG+AGG 0.542553 4_3:+1897023 None:intergenic
ACTGCTAAAGCTTGTGGAGA+TGG 0.545041 4_3:+1897236 None:intergenic
AATGGTTGCACGCGTGGAGG+TGG 0.556418 4_3:+1897059 None:intergenic
ACATGCACTGCTAAAGCTTG+TGG 0.565788 4_3:+1897230 None:intergenic
GGTTGAGGCTGATTATTTGG+TGG 0.570406 4_3:+1897155 None:intergenic
TCAAATGGTTGCACGCGTGG+AGG 0.626989 4_3:+1897056 None:intergenic
GCATCAACCACAAAATGCAC+CGG 0.637007 4_3:-1897120 Msa0624070:CDS
ATATTAGAATCGAGTAAACA+AGG 0.646902 4_3:-1897182 Msa0624070:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! CTCGATTCTAATATTAAATC+TGG + chr4_3:1897085-1897104 None:intergenic 25.0%
! ATATTAGAATCGAGTAAACA+AGG - chr4_3:1897091-1897110 Msa0624070:CDS 25.0%
CTGGTGTATAAGGGATATTA+AGG + chr4_3:1897276-1897295 None:intergenic 35.0%
TGTGGTTGAGGCTGATTATT+TGG + chr4_3:1897124-1897143 None:intergenic 40.0%
! TGCTCATCATTTTGTGGTTG+AGG + chr4_3:1897136-1897155 None:intergenic 40.0%
!! GGTTGATGCTCATCATTTTG+TGG + chr4_3:1897142-1897161 None:intergenic 40.0%
!! GGTTGATGTTCAGCATTTTG+TGG + chr4_3:1897184-1897203 None:intergenic 40.0%
! GGAGGTTGGTTCAAATCAAA+TGG + chr4_3:1897235-1897254 None:intergenic 40.0%
ACTGCTAAAGCTTGTGGAGA+TGG + chr4_3:1897040-1897059 None:intergenic 45.0%
ACATGCACTGCTAAAGCTTG+TGG + chr4_3:1897046-1897065 None:intergenic 45.0%
! TGAGGCTGATTATTTGGTGG+TGG + chr4_3:1897118-1897137 None:intergenic 45.0%
GGTTGAGGCTGATTATTTGG+TGG + chr4_3:1897121-1897140 None:intergenic 45.0%
GCATCAACCACAAAATGCAC+CGG - chr4_3:1897153-1897172 Msa0624070:CDS 45.0%
! TCAGCATTTTGTGGTAGAGC+CGG + chr4_3:1897175-1897194 None:intergenic 45.0%
AAATCAAATGGTTGCACGCG+TGG + chr4_3:1897223-1897242 None:intergenic 45.0%
AAGCGCGAACATTAGGAGGT+TGG + chr4_3:1897249-1897268 None:intergenic 50.0%
! TCGAAAGCGCGAACATTAGG+AGG + chr4_3:1897253-1897272 None:intergenic 50.0%
! AGGTCGAAAGCGCGAACATT+AGG + chr4_3:1897256-1897275 None:intergenic 50.0%
! GGTAGAGCCGGTGCATTTTG+TGG + chr4_3:1897163-1897182 None:intergenic 55.0%
! CGTGGAGGTGGTGCATTTTG+TGG + chr4_3:1897205-1897224 None:intergenic 55.0%
TCAAATGGTTGCACGCGTGG+AGG + chr4_3:1897220-1897239 None:intergenic 55.0%
AATGGTTGCACGCGTGGAGG+TGG + chr4_3:1897217-1897236 None:intergenic 60.0%
Chromosome Type Strat End Strand Name
chr4_3 gene 1896992 1897303 1896992 ID=Msa0624070;Name=Msa0624070
chr4_3 mRNA 1896992 1897303 1896992 ID=Msa0624070-mRNA-1;Parent=Msa0624070;Name=Msa0624070-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|103
chr4_3 exon 1896992 1897303 1896992 ID=Msa0624070-mRNA-1:exon:518;Parent=Msa0624070-mRNA-1
chr4_3 CDS 1896992 1897303 1896992 ID=Msa0624070-mRNA-1:cds;Parent=Msa0624070-mRNA-1
Gene Sequence

>Msa0624070

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCCACAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCAGATTTAATATTAGAATCGAGTAAACAAGGTCCACCACCAAATAATCAGCCTCAACCACAAAATGATGAGCATCAACCACAAAATGCACCGGCTCTACCACAAAATGCTGAACATCAACCACAAAATGCACCACCTCCACGCGTGCAACCATTTGATTTGAACCAACCTCCTAATGTTCGCGCTTTCGACCTTAATATCCCTTATACACCAGATGAATGA
Protein sequence

>Msa0624070

MSKLEFLCSECDTMFPSPQALAVHVIEEHHPDLILESSKQGPPPNNQPQPQNDEHQPQNAPALPQNAEHQPQNAPPPRVQPFDLNQPPNVRAFDLNIPYTPDE*