AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0607200


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0607200 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
Msa0607200 AT3G22210.1 62.500 64 23 1 5 68 6 68 1.55e-20 77.0

Find 19 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAATGAACATGCAACTATTT+TGG 0.213384 4_2:-53975200 None:intergenic
GCAATTCGCTCTTCCAGTTT+TGG 0.231911 4_2:+53974632 Msa0607200:CDS
CGAGGGAGAAAAGTCATTTA+AGG 0.295877 4_2:-53975234 None:intergenic
GTCTTCTAGCTCGCCTCTCT+CGG 0.346161 4_2:-53974862 None:intergenic
GACAGAAATCACTTCAAGAT+TGG 0.349085 4_2:+53974792 Msa0607200:intron
GCTGCAACAATGCCCAAAAC+TGG 0.365881 4_2:-53974645 None:intergenic
AGCTCGCCTCTCTCGGGAGC+TGG 0.374844 4_2:-53974855 None:intergenic
GAGAGATATATCATCAGAAA+TGG 0.429163 4_2:+53974602 Msa0607200:exon
CTCTCTCGGGAGCTGGATGT+TGG 0.452110 4_2:-53974848 None:intergenic
AGTAGCAAATTGTTTGTACT+AGG 0.459932 4_2:+53974999 Msa0607200:three_prime_UTR
ACAGAAATCACTTCAAGATT+GGG 0.482353 4_2:+53974793 Msa0607200:intron
ATTGAAACTCACTGCATAGA+AGG 0.485260 4_2:-53974679 None:intergenic
TCTTCTAGCTCGCCTCTCTC+GGG 0.500761 4_2:-53974861 None:intergenic
ACCAACAAGAACTATTGAAA+AGG 0.500770 4_2:-53975030 None:intergenic
GATGATTCTGAATCAGAGAA+TGG 0.538128 4_2:+53974815 Msa0607200:CDS
CAACATCCAGCTCCCGAGAG+AGG 0.612999 4_2:+53974849 Msa0607200:CDS
GAGTTTCAATGAGATTAGAG+AGG 0.641117 4_2:+53974692 Msa0607200:CDS
GATTCTGAATCAGAGAATGG+AGG 0.645594 4_2:+53974818 Msa0607200:CDS
ACTAGTCACTGACCCAACCC+AGG 0.668265 4_2:-53975151 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! TACATTTTTCTAATAGAAAA+TGG - chr4_2:53975079-53975098 None:intergenic 15.0%
!!! TTCTTGTTGAAGTTATTTTT+TGG - chr4_2:53974903-53974922 None:intergenic 20.0%
!!! ATTTCTTAATTTTTGATGCT+TGG + chr4_2:53974959-53974978 Msa0607200:three_prime_UTR 20.0%
!! AAATGAACATGCAACTATTT+TGG - chr4_2:53975203-53975222 None:intergenic 25.0%
GAGAGATATATCATCAGAAA+TGG + chr4_2:53974602-53974621 Msa0607200:exon 30.0%
ACAGAAATCACTTCAAGATT+GGG + chr4_2:53974793-53974812 Msa0607200:intron 30.0%
AGTAGCAAATTGTTTGTACT+AGG + chr4_2:53974999-53975018 Msa0607200:three_prime_UTR 30.0%
! ACCTTTTCAATAGTTCTTGT+TGG + chr4_2:53975029-53975048 Msa0607200:three_prime_UTR 30.0%
ACCAACAAGAACTATTGAAA+AGG - chr4_2:53975033-53975052 None:intergenic 30.0%
!!! ACATTTTTTGTGTTTTCTCC+TGG + chr4_2:53975133-53975152 Msa0607200:three_prime_UTR 30.0%
!!! CATTTTTTGTGTTTTCTCCT+GGG + chr4_2:53975134-53975153 Msa0607200:three_prime_UTR 30.0%
ATTGAAACTCACTGCATAGA+AGG - chr4_2:53974682-53974701 None:intergenic 35.0%
GAGTTTCAATGAGATTAGAG+AGG + chr4_2:53974692-53974711 Msa0607200:CDS 35.0%
GACAGAAATCACTTCAAGAT+TGG + chr4_2:53974792-53974811 Msa0607200:intron 35.0%
GATGATTCTGAATCAGAGAA+TGG + chr4_2:53974815-53974834 Msa0607200:CDS 35.0%
! CAATTCGCTCTTCCAGTTTT+GGG + chr4_2:53974633-53974652 Msa0607200:CDS 40.0%
GATTCTGAATCAGAGAATGG+AGG + chr4_2:53974818-53974837 Msa0607200:CDS 40.0%
! TTTTGTGTTTTCTCCTGGGT+TGG + chr4_2:53975138-53975157 Msa0607200:three_prime_UTR 40.0%
! TTTGTGTTTTCTCCTGGGTT+GGG + chr4_2:53975139-53975158 Msa0607200:three_prime_UTR 40.0%
!!! CATGCAACTATTTTGGTCTC+TGG - chr4_2:53975196-53975215 None:intergenic 40.0%
! GCAATTCGCTCTTCCAGTTT+TGG + chr4_2:53974632-53974651 Msa0607200:CDS 45.0%
GCTGCAACAATGCCCAAAAC+TGG - chr4_2:53974648-53974667 None:intergenic 50.0%
!! TCTTCTAGCTCGCCTCTCTC+GGG - chr4_2:53974864-53974883 None:intergenic 55.0%
!! GTCTTCTAGCTCGCCTCTCT+CGG - chr4_2:53974865-53974884 None:intergenic 55.0%
ACTAGTCACTGACCCAACCC+AGG - chr4_2:53975154-53975173 None:intergenic 55.0%
CTCTCTCGGGAGCTGGATGT+TGG - chr4_2:53974851-53974870 None:intergenic 60.0%
CAACATCCAGCTCCCGAGAG+AGG + chr4_2:53974849-53974868 Msa0607200:CDS 60.0%
AGCTCGCCTCTCTCGGGAGC+TGG - chr4_2:53974858-53974877 None:intergenic 70.0%
Chromosome Type Strat End Strand Name
chr4_2 gene 53974571 53975250 53974571 ID=Msa0607200;Name=Msa0607200
chr4_2 mRNA 53974571 53975250 53974571 ID=Msa0607200-mRNA-1;Parent=Msa0607200;Name=Msa0607200-mRNA-1;_AED=0.01;_eAED=0.01;_QI=50|1|1|1|1|1|2|340|68
chr4_2 exon 53974571 53974713 53974571 ID=Msa0607200-mRNA-1:exon:13400;Parent=Msa0607200-mRNA-1
chr4_2 exon 53974797 53975250 53974797 ID=Msa0607200-mRNA-1:exon:13401;Parent=Msa0607200-mRNA-1
chr4_2 five_prime_UTR 53974571 53974620 53974571 ID=Msa0607200-mRNA-1:five_prime_utr;Parent=Msa0607200-mRNA-1
chr4_2 CDS 53974621 53974713 53974621 ID=Msa0607200-mRNA-1:cds;Parent=Msa0607200-mRNA-1
chr4_2 CDS 53974797 53974910 53974797 ID=Msa0607200-mRNA-1:cds;Parent=Msa0607200-mRNA-1
chr4_2 three_prime_UTR 53974911 53975250 53974911 ID=Msa0607200-mRNA-1:three_prime_utr;Parent=Msa0607200-mRNA-1
Gene Sequence

>Msa0607200

ATGGATGCAATGCAATTCGCTCTTCCAGTTTTGGGCATTGTTGCAGCTGCTGCTGTGACCTTCTATGCAGTGAGTTTCAATGAGATTAGAGAGAAATCACTTCAAGATTGGGATGATTCTGAATCAGAGAATGGAGGTTTTAGACCAACATCCAGCTCCCGAGAGAGGCGAGCTAGAAGACAAGCTAGTAAAAATACCAAAAAATAA

Protein sequence

>Msa0607200

MDAMQFALPVLGIVAAAAVTFYAVSFNEIREKSLQDWDDSESENGGFRPTSSSRERRARRQASKNTKK*