AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1020720


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1020720 MtrunA17_Chr4g0038821 97.059 68 2 0 1 68 1 68 1.37e-44 137
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1020720 AT3G22210.1 62.500 64 23 1 5 68 6 68 1.55e-20 77.0

Find 23 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGAACATGCAACTATTT+TGG 0.167660 7_1:-44511414 None:intergenic
CAATTCGCTCTTCCAGTATT+GGG 0.341545 7_1:+44510850 Msa1020720:CDS
GTCTTCTAGCTCGCCTCTCT+CGG 0.346161 7_1:-44511083 None:intergenic
GACAGAAATCACTTCAAGAT+TGG 0.349085 7_1:+44511013 Msa1020720:intron
GCCGCAACAATGCCCAATAC+TGG 0.366936 7_1:-44510862 None:intergenic
AGCTCGCCTCTCTCGGGAGC+TGG 0.374844 7_1:-44511076 None:intergenic
GCAATTCGCTCTTCCAGTAT+TGG 0.399436 7_1:+44510849 Msa1020720:CDS
CTCTCTCGGGAGCTGGATGT+TGG 0.452110 7_1:-44511069 None:intergenic
AGTAGCAAATTGTTTGTACT+AGG 0.459932 7_1:+44511218 Msa1020720:three_prime_UTR
TCCAGTATTGGGCATTGTTG+CGG 0.480204 7_1:+44510861 Msa1020720:CDS
ACAGAAATCACTTCAAGATT+GGG 0.482353 7_1:+44511014 Msa1020720:intron
ATTGAAACTCACTGCATAGA+AGG 0.485260 7_1:-44510896 None:intergenic
TCTTCTAGCTCGCCTCTCTC+GGG 0.500761 7_1:-44511082 None:intergenic
CGAGGGAGAAAAGTCATTCA+AGG 0.507786 7_1:-44511448 None:intergenic
ACTAACAAGAACTATTGAAA+AGG 0.512776 7_1:-44511249 None:intergenic
GATGATTCTGAATCAGAGAA+TGG 0.538128 7_1:+44511036 Msa1020720:CDS
TCCAATAGAAAATGGAACAC+GGG 0.570237 7_1:-44511287 None:intergenic
CAACATCCAGCTCCCGAGAG+AGG 0.612999 7_1:+44511070 Msa1020720:CDS
TTCCAATAGAAAATGGAACA+CGG 0.614078 7_1:-44511288 None:intergenic
GAGTTTCAATGAGATTAGAG+AGG 0.641117 7_1:+44510909 Msa1020720:CDS
GATTCTGAATCAGAGAATGG+AGG 0.645594 7_1:+44511039 Msa1020720:CDS
ACAACAAGTTGCACATCCAG+AGG 0.652049 7_1:+44511391 Msa1020720:three_prime_UTR
GTGAGACTAGTCACTGACCC+AGG 0.670217 7_1:-44511370 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! CTGTCATAATTCAATTTTAT+AGG - chr7_1:44510998-44511017 None:intergenic 20.0%
!!! ATTTCTTAATTTTTGATGCT+TGG + chr7_1:44511178-44511197 Msa1020720:three_prime_UTR 20.0%
!!! TACATTTTTCCAATAGAAAA+TGG - chr7_1:44511298-44511317 None:intergenic 20.0%
!!! CATTTGTCGAAGTTATTTTT+TGG - chr7_1:44511124-44511143 None:intergenic 25.0%
! ACTAACAAGAACTATTGAAA+AGG - chr7_1:44511252-44511271 None:intergenic 25.0%
!! AAATGAACATGCAACTATTT+TGG - chr7_1:44511417-44511436 None:intergenic 25.0%
ACAGAAATCACTTCAAGATT+GGG + chr7_1:44511014-44511033 Msa1020720:intron 30.0%
AGTAGCAAATTGTTTGTACT+AGG + chr7_1:44511218-44511237 Msa1020720:three_prime_UTR 30.0%
TTCCAATAGAAAATGGAACA+CGG - chr7_1:44511291-44511310 None:intergenic 30.0%
!!! ACATTTTTTGTGTTTTCTCC+TGG + chr7_1:44511352-44511371 Msa1020720:three_prime_UTR 30.0%
!!! CATTTTTTGTGTTTTCTCCT+GGG + chr7_1:44511353-44511372 Msa1020720:three_prime_UTR 30.0%
ATTGAAACTCACTGCATAGA+AGG - chr7_1:44510899-44510918 None:intergenic 35.0%
GAGTTTCAATGAGATTAGAG+AGG + chr7_1:44510909-44510928 Msa1020720:CDS 35.0%
GACAGAAATCACTTCAAGAT+TGG + chr7_1:44511013-44511032 Msa1020720:intron 35.0%
GATGATTCTGAATCAGAGAA+TGG + chr7_1:44511036-44511055 Msa1020720:CDS 35.0%
TCCAATAGAAAATGGAACAC+GGG - chr7_1:44511290-44511309 None:intergenic 35.0%
CAATTCGCTCTTCCAGTATT+GGG + chr7_1:44510850-44510869 Msa1020720:CDS 40.0%
GATTCTGAATCAGAGAATGG+AGG + chr7_1:44511039-44511058 Msa1020720:CDS 40.0%
GCAATTCGCTCTTCCAGTAT+TGG + chr7_1:44510849-44510868 Msa1020720:CDS 45.0%
! TCCAGTATTGGGCATTGTTG+CGG + chr7_1:44510861-44510880 Msa1020720:CDS 45.0%
! GCCCGTGTTCCATTTTCTAT+TGG + chr7_1:44511286-44511305 Msa1020720:three_prime_UTR 45.0%
ACAACAAGTTGCACATCCAG+AGG + chr7_1:44511391-44511410 Msa1020720:three_prime_UTR 45.0%
!!! CATGCAACTATTTTGGCCTC+TGG - chr7_1:44511410-44511429 None:intergenic 45.0%
GCCGCAACAATGCCCAATAC+TGG - chr7_1:44510865-44510884 None:intergenic 55.0%
!! TCTTCTAGCTCGCCTCTCTC+GGG - chr7_1:44511085-44511104 None:intergenic 55.0%
!! GTCTTCTAGCTCGCCTCTCT+CGG - chr7_1:44511086-44511105 None:intergenic 55.0%
! GTGAGACTAGTCACTGACCC+AGG - chr7_1:44511373-44511392 None:intergenic 55.0%
CTCTCTCGGGAGCTGGATGT+TGG - chr7_1:44511072-44511091 None:intergenic 60.0%
CAACATCCAGCTCCCGAGAG+AGG + chr7_1:44511070-44511089 Msa1020720:CDS 60.0%
AGCTCGCCTCTCTCGGGAGC+TGG - chr7_1:44511079-44511098 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr7_1 gene 44510838 44511464 44510838 ID=Msa1020720;Name=Msa1020720
chr7_1 mRNA 44510838 44511464 44510838 ID=Msa1020720-mRNA-1;Parent=Msa1020720;Name=Msa1020720-mRNA-1;_AED=0.07;_eAED=0.07;_QI=0|1|0.5|1|1|1|2|333|68
chr7_1 exon 44510838 44510930 44510838 ID=Msa1020720-mRNA-1:exon:8653;Parent=Msa1020720-mRNA-1
chr7_1 exon 44511018 44511464 44511018 ID=Msa1020720-mRNA-1:exon:8654;Parent=Msa1020720-mRNA-1
chr7_1 CDS 44510838 44510930 44510838 ID=Msa1020720-mRNA-1:cds;Parent=Msa1020720-mRNA-1
chr7_1 CDS 44511018 44511131 44511018 ID=Msa1020720-mRNA-1:cds;Parent=Msa1020720-mRNA-1
chr7_1 three_prime_UTR 44511132 44511464 44511132 ID=Msa1020720-mRNA-1:three_prime_utr;Parent=Msa1020720-mRNA-1
Gene Sequence

>Msa1020720

ATGGATGCAATGCAATTCGCTCTTCCAGTATTGGGCATTGTTGCGGCTGCAGCAGTGACCTTCTATGCAGTGAGTTTCAATGAGATTAGAGAGAAATCACTTCAAGATTGGGATGATTCTGAATCAGAGAATGGAGGTTTTAGACCAACATCCAGCTCCCGAGAGAGGCGAGCTAGAAGACAAGCTAGTAAAAATACCAAAAAATAA

Protein sequence

>Msa1020720

MDAMQFALPVLGIVAAAAVTFYAVSFNEIREKSLQDWDDSESENGGFRPTSSSRERRARRQASKNTKK*