AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0584920

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0584920 MtrunA17_Chr4g0019481 82.051 117 20 1 1 116 1 117 2.62e-59 178
Msa0584920 MtrunA17_Chr4g0019471 73.282 131 20 2 1 116 1 131 8.12e-55 167
Msa0584920 MtrunA17_Chr4g0019551 77.778 117 25 1 1 116 1 117 3.16e-47 147
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 16 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCTGGTTCAGGCTGGTTATT+TGG 0.185355 4_2:-5162011 None:intergenic
TCTCATTCATCTGGTGTATA+AGG 0.203991 4_2:-5162212 None:intergenic
ACTCGATTCTAATATAAAAT+CGG 0.323743 4_2:-5161973 None:intergenic
CTCATTCATCTGGTGTATAA+GGG 0.375685 4_2:-5162211 None:intergenic
CTCGATTCTAATATAAAATC+GGG 0.421980 4_2:-5161972 None:intergenic
GGAGGTTGGTTCAAGTCAAA+TGG 0.461699 4_2:-5162164 None:intergenic
TCAGGCTGGTTATTTGGTGA+TGG 0.492034 4_2:-5162005 None:intergenic
TTGAGGTCGAAAGCTCGAAC+AGG 0.496472 4_2:-5162185 None:intergenic
AAGTCAAATGGTTGCACATG+TGG 0.522527 4_2:-5162152 None:intergenic
AATGGTTGCACATGTGGAGG+TGG 0.555990 4_2:-5162146 None:intergenic
CGAAAGCTCGAACAGGAGGT+TGG 0.564077 4_2:-5162178 None:intergenic
ACTGCTAAAGCTTCTCGAGA+TGG 0.596385 4_2:-5161927 None:intergenic
CTGGTGTATAAGGGAGATTG+AGG 0.611261 4_2:-5162202 None:intergenic
ATATTAGAATCGAGTAAACA+AGG 0.624706 4_2:+5161981 Msa0584920:CDS
AGGTCGAAAGCTCGAACAGG+AGG 0.636300 4_2:-5162182 None:intergenic
TCAAATGGTTGCACATGTGG+AGG 0.671560 4_2:-5162149 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ACTCGATTCTAATATAAAAT+CGG - chr4_2:5161976-5161995 None:intergenic 20.0%
! CTCGATTCTAATATAAAATC+GGG - chr4_2:5161975-5161994 None:intergenic 25.0%
! ATATTAGAATCGAGTAAACA+AGG + chr4_2:5161981-5162000 Msa0584920:CDS 25.0%
! TGTTCAACATTTTGTGGTTG+AGG - chr4_2:5162047-5162066 None:intergenic 35.0%
!! GGTTGATGTTCAACATTTTG+TGG - chr4_2:5162053-5162072 None:intergenic 35.0%
! TGTTGTTCAACATTTTGTGG+TGG - chr4_2:5162092-5162111 None:intergenic 35.0%
!! GGTTGTTGTTCAACATTTTG+TGG - chr4_2:5162095-5162114 None:intergenic 35.0%
AAGTCAAATGGTTGCACATG+TGG - chr4_2:5162155-5162174 None:intergenic 40.0%
ACTGCTAAAGCTTCTCGAGA+TGG - chr4_2:5161930-5161949 None:intergenic 45.0%
! TCAGGCTGGTTATTTGGTGA+TGG - chr4_2:5162008-5162027 None:intergenic 45.0%
! TCTGGTTCAGGCTGGTTATT+TGG - chr4_2:5162014-5162033 None:intergenic 45.0%
!! TCAACATTTTGTGGTGGAGC+TGG - chr4_2:5162086-5162105 None:intergenic 45.0%
TCAAATGGTTGCACATGTGG+AGG - chr4_2:5162152-5162171 None:intergenic 45.0%
! GGAGGTTGGTTCAAGTCAAA+TGG - chr4_2:5162167-5162186 None:intergenic 45.0%
CTGGTGTATAAGGGAGATTG+AGG - chr4_2:5162205-5162224 None:intergenic 45.0%
!!! GAGCATTTTCTGGTTCAGGC+TGG - chr4_2:5162022-5162041 None:intergenic 50.0%
!!! GGCTGAGCATTTTCTGGTTC+AGG - chr4_2:5162026-5162045 None:intergenic 50.0%
! GGTTGAGGCTGAGCATTTTC+TGG - chr4_2:5162032-5162051 None:intergenic 50.0%
! TGTGGAGGTGGTGCATTTTG+TGG - chr4_2:5162137-5162156 None:intergenic 50.0%
AATGGTTGCACATGTGGAGG+TGG - chr4_2:5162149-5162168 None:intergenic 50.0%
TTGAGGTCGAAAGCTCGAAC+AGG - chr4_2:5162188-5162207 None:intergenic 50.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:5162074-5162093 None:intergenic 55.0%
! GGTGGAGCTGGTGCATTTTG+TGG - chr4_2:5162074-5162093 None:intergenic 55.0%
!! GGTGCATTTTGTGGTGGAGC+TGG - chr4_2:5162128-5162147 None:intergenic 55.0%
! GGAGGTGGTGCATTTTGTGG+TGG - chr4_2:5162134-5162153 None:intergenic 55.0%
CGAAAGCTCGAACAGGAGGT+TGG - chr4_2:5162181-5162200 None:intergenic 55.0%
AGGTCGAAAGCTCGAACAGG+AGG - chr4_2:5162185-5162204 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 5161882 5162232 5161882 ID=Msa0584920;Name=Msa0584920
chr4_2 mRNA 5161882 5162232 5161882 ID=Msa0584920-mRNA-1;Parent=Msa0584920;Name=Msa0584920-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|116
chr4_2 exon 5161882 5162232 5161882 ID=Msa0584920-mRNA-1:exon:1248;Parent=Msa0584920-mRNA-1
chr4_2 CDS 5161882 5162232 5161882 ID=Msa0584920-mRNA-1:cds;Parent=Msa0584920-mRNA-1
Gene Sequence

>Msa0584920

ATGTCAAAGCTAGAATTCTTATGCAGTGAATGTGACACAATGTTTCCATCTCGAGAAGCTTTAGCAGTGCATGTTATCGAAGAACATCATCCCGATTTTATATTAGAATCGAGTAAACAAGGTCCATCACCAAATAACCAGCCTGAACCAGAAAATGCTCAGCCTCAACCACAAAATGTTGAACATCAACCACAAAATGCACCAGCTCCACCACAAAATGTTGAACAACAACCACAAAATGCACCAGCTCCACCACAAAATGCACCACCTCCACATGTGCAACCATTTGACTTGAACCAACCTCCTGTTCGAGCTTTCGACCTCAATCTCCCTTATACACCAGATGAATGA
Protein sequence

>Msa0584920

MSKLEFLCSECDTMFPSREALAVHVIEEHHPDFILESSKQGPSPNNQPEPENAQPQPQNVEHQPQNAPAPPQNVEQQPQNAPAPPQNAPPPHVQPFDLNQPPVRAFDLNLPYTPDE*