AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0744040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0744040 MtrunA17_Chr5g0446481 57.143 105 24 3 6 94 8 107 1.51e-21 87.4
Msa0744040 MtrunA17_Chr5g0447051 79.592 49 10 0 1 49 24 72 5.71e-20 76.6
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTTCCCAACCACCAATTT+TGG 0.163736 5_1:+64693924 None:intergenic
ACAGATAACGATACCAAAAT+TGG 0.306382 5_1:-64693937 Msa0744040:CDS
GGATAACGAAGTCAAAGATT+TGG 0.387444 5_1:-64694060 Msa0744040:CDS
CGATACCAAAATTGGTGGTT+GGG 0.404154 5_1:-64693929 Msa0744040:CDS
GAGGATAAGAAAGTTGATGA+AGG 0.462866 5_1:-64693895 Msa0744040:CDS
ATTGCCATTTGAGTCAGTCT+TGG 0.463769 5_1:+64694157 None:intergenic
AGACTGACTCAAATGGCAAT+AGG 0.467994 5_1:-64694154 Msa0744040:CDS
ACCAAAATTGGTGGTTGGGA+AGG 0.477978 5_1:-64693925 Msa0744040:CDS
ACGATACCAAAATTGGTGGT+TGG 0.479374 5_1:-64693930 Msa0744040:CDS
TGGGGTGGAAGAACTAGAAA+TGG 0.500417 5_1:-64693995 Msa0744040:intron
AAAGAGGATGAGAAAGATGT+TGG 0.522340 5_1:-64693862 Msa0744040:CDS
GTTTCCAAGACTGACTCAAA+TGG 0.535048 5_1:-64694161 Msa0744040:CDS
AGATGACATGGGTGAAAAGA+AGG 0.535573 5_1:-64694114 Msa0744040:CDS
AGGATAAGAAAGTTGATGAA+GGG 0.547120 5_1:-64693894 Msa0744040:CDS
TGAAGGGAAAGAAACAAAAG+AGG 0.565665 5_1:-64693878 Msa0744040:CDS
TAACGAAGTCAAAGATTTGG+AGG 0.567042 5_1:-64694057 Msa0744040:CDS
GAAGTCAAAGATTTGGAGGA+TGG 0.574033 5_1:-64694053 Msa0744040:intron
AAGGACCTGGAACCTAAAGT+AGG 0.578565 5_1:-64694095 Msa0744040:CDS
GATAACGATACCAAAATTGG+TGG 0.582971 5_1:-64693934 Msa0744040:CDS
AGAAAACCACCTAGATGACA+TGG 0.586850 5_1:-64694126 Msa0744040:CDS
CATGGGTGAAAAGAAGGACC+TGG 0.596256 5_1:-64694108 Msa0744040:CDS
TTTCACCCATGTCATCTAGG+TGG 0.597167 5_1:+64694120 None:intergenic
TGGTTGGGAAGGAATAAAAG+AGG 0.648604 5_1:-64693914 Msa0744040:CDS
GAAAACCACCTAGATGACAT+GGG 0.708635 5_1:-64694125 Msa0744040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTGATAAAAAAAAACTGA+TGG - chr5_1:64694050-64694069 Msa0744040:intron 20.0%
!!! GTTGATAAAAAAAAACTGAT+GGG - chr5_1:64694051-64694070 Msa0744040:intron 20.0%
!! TTGATAAAAAAAAACTGATG+GGG - chr5_1:64694052-64694071 Msa0744040:intron 20.0%
!!! CTACATTGGTTTCATTAAAT+TGG + chr5_1:64693869-64693888 None:intergenic 25.0%
ATATTATCTGAGCACTACAT+TGG + chr5_1:64693883-64693902 None:intergenic 30.0%
ATAAAAAAAAACTGATGGGG+TGG - chr5_1:64694055-64694074 Msa0744040:CDS 30.0%
GATGATAAAAAAGCTGATGA+TGG - chr5_1:64694095-64694114 Msa0744040:CDS 30.0%
ACAGATAACGATACCAAAAT+TGG - chr5_1:64694128-64694147 Msa0744040:CDS 30.0%
!! AGGATAAGAAAGTTGATGAA+GGG - chr5_1:64694171-64694190 Msa0744040:CDS 30.0%
!! TTTTTCCTACTTTAGGTTCC+AGG + chr5_1:64693978-64693997 None:intergenic 35.0%
ACCTAAAGTAGGAAAAATCG+TGG - chr5_1:64693981-64694000 Msa0744040:CDS 35.0%
! TCCACGATTTTTCCTACTTT+AGG + chr5_1:64693985-64694004 None:intergenic 35.0%
TAAAGTAGGAAAAATCGTGG+AGG - chr5_1:64693984-64694003 Msa0744040:CDS 35.0%
GGATAACGAAGTCAAAGATT+TGG - chr5_1:64694005-64694024 Msa0744040:intron 35.0%
TAACGAAGTCAAAGATTTGG+AGG - chr5_1:64694008-64694027 Msa0744040:intron 35.0%
GATAACGATACCAAAATTGG+TGG - chr5_1:64694131-64694150 Msa0744040:CDS 35.0%
!! GAGGATAAGAAAGTTGATGA+AGG - chr5_1:64694170-64694189 Msa0744040:CDS 35.0%
TGAAGGGAAAGAAACAAAAG+AGG - chr5_1:64694187-64694206 Msa0744040:intron 35.0%
AAAGAGGATGAGAAAGATGT+TGG - chr5_1:64694203-64694222 Msa0744040:intron 35.0%
! GTTTCCAAGACTGACTCAAA+TGG - chr5_1:64693904-64693923 Msa0744040:CDS 40.0%
! ATTGCCATTTGAGTCAGTCT+TGG + chr5_1:64693911-64693930 None:intergenic 40.0%
! AGACTGACTCAAATGGCAAT+AGG - chr5_1:64693911-64693930 Msa0744040:CDS 40.0%
AGAAAACCACCTAGATGACA+TGG - chr5_1:64693939-64693958 Msa0744040:CDS 40.0%
GAAAACCACCTAGATGACAT+GGG - chr5_1:64693940-64693959 Msa0744040:CDS 40.0%
! TCTTTTCACCCATGTCATCT+AGG + chr5_1:64693951-64693970 None:intergenic 40.0%
AGATGACATGGGTGAAAAGA+AGG - chr5_1:64693951-64693970 Msa0744040:CDS 40.0%
GAAGTCAAAGATTTGGAGGA+TGG - chr5_1:64694012-64694031 Msa0744040:intron 40.0%
! ACGATACCAAAATTGGTGGT+TGG - chr5_1:64694135-64694154 Msa0744040:CDS 40.0%
! CGATACCAAAATTGGTGGTT+GGG - chr5_1:64694136-64694155 Msa0744040:CDS 40.0%
TGGTTGGGAAGGAATAAAAG+AGG - chr5_1:64694151-64694170 Msa0744040:CDS 40.0%
TTTCACCCATGTCATCTAGG+TGG + chr5_1:64693948-64693967 None:intergenic 45.0%
AAGGACCTGGAACCTAAAGT+AGG - chr5_1:64693970-64693989 Msa0744040:CDS 45.0%
GGAGGATGGTATGAAAGCAA+TGG - chr5_1:64694026-64694045 Msa0744040:intron 45.0%
TGGGGTGGAAGAACTAGAAA+TGG - chr5_1:64694070-64694089 Msa0744040:CDS 45.0%
! ACCAAAATTGGTGGTTGGGA+AGG - chr5_1:64694140-64694159 Msa0744040:CDS 45.0%
! TCCTTCCCAACCACCAATTT+TGG + chr5_1:64694144-64694163 None:intergenic 45.0%
CATGGGTGAAAAGAAGGACC+TGG - chr5_1:64693957-64693976 Msa0744040:CDS 50.0%
Chromosome Type Strat End Strand Name
chr5_1 gene 64693855 64694232 64693855 ID=Msa0744040;Name=Msa0744040
chr5_1 mRNA 64693855 64694232 64693855 ID=Msa0744040-mRNA-1;Parent=Msa0744040;Name=Msa0744040-mRNA-1;_AED=0.42;_eAED=0.45;_QI=0|0|0|1|0|0|3|0|100
chr5_1 exon 64694227 64694232 64694227 ID=Msa0744040-mRNA-1:exon:19185;Parent=Msa0744040-mRNA-1
chr5_1 exon 64694054 64694198 64694054 ID=Msa0744040-mRNA-1:exon:19184;Parent=Msa0744040-mRNA-1
chr5_1 exon 64693855 64694006 64693855 ID=Msa0744040-mRNA-1:exon:19183;Parent=Msa0744040-mRNA-1
chr5_1 CDS 64694227 64694232 64694227 ID=Msa0744040-mRNA-1:cds;Parent=Msa0744040-mRNA-1
chr5_1 CDS 64694054 64694198 64694054 ID=Msa0744040-mRNA-1:cds;Parent=Msa0744040-mRNA-1
chr5_1 CDS 64693855 64694006 64693855 ID=Msa0744040-mRNA-1:cds;Parent=Msa0744040-mRNA-1
Gene Sequence

>Msa0744040

GCACAATGCTCAGATAATATAGTTTCCAAGACTGACTCAAATGGCAATAGGATGCTAGAAAACCACCTAGATGACATGGGTGAAAAGAAGGACCTGGAACCTAAAGTAGGAAAAATCGTGGAGGATAACGAAGTCAAAGATTTGGAGGATGAACTAGAAATGGAAGATGATAAAAAAGCTGATGATGGTGATGTCATAACAGATAACGATACCAAAATTGGTGGTTGGGAAGGAATAAAAGAGGATAAGAAAGTTGATGAAGGGAAAGAAACAAAAGAGGATGAGAAAGATGTTGGCATATGA

Protein sequence

>Msa0744040

AQCSDNIVSKTDSNGNRMLENHLDDMGEKKDLEPKVGKIVEDNEVKDLEDELEMEDDKKADDGDVITDNDTKIGGWEGIKEDKKVDEGKETKEDEKDVGI*