AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0662810

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0662810 MtrunA17_Chr8g0346001 94.737 133 7 0 1 133 302 434 8.92e-64 200
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 30 sgRNAs with CRISPR-Local

Find 29 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AAGTTGATGATGATGATTTA+AGG 0.268850 4_4:-611954 None:intergenic
ATGGACAAACTGAGGCTTCT+AGG 0.319602 4_4:+611863 Msa0662810:CDS
GTGATGGTGGTCTTACTAAT+TGG 0.352073 4_4:+611806 Msa0662810:CDS
TCTTACTAATTGGGTAGCTT+TGG 0.361121 4_4:+611816 Msa0662810:CDS
CTTGTTGCTTCTCAATTGAA+TGG 0.385288 4_4:+611844 Msa0662810:CDS
AACTGAGGCTTCTAGGCAAT+TGG 0.397982 4_4:+611870 Msa0662810:CDS
GATGATGATGATGCCTCTAA+TGG 0.411646 4_4:-611766 None:intergenic
TGCTTTAATGACCCCACAAT+GGG 0.424079 4_4:+611895 Msa0662810:CDS
CATGGTTAATAATCCATTAG+AGG 0.428212 4_4:+611753 None:intergenic
TGATGGTGGTCTTACTAATT+GGG 0.469019 4_4:+611807 Msa0662810:CDS
AGTTGATGATGATGATTTAA+GGG 0.477571 4_4:-611953 None:intergenic
CTAATTGGGTAGCTTTGGAT+AGG 0.478615 4_4:+611821 Msa0662810:CDS
TTAGTGCAATATCCCATTGT+GGG 0.521916 4_4:-611907 None:intergenic
GTTCCAGAGGTCAATCTCAC+TGG 0.538763 4_4:-612061 None:intergenic
AGAGGCATCATCATCATCAA+TGG 0.541656 4_4:+611771 Msa0662810:CDS
GATGATGATGATTTAAGGGT+GGG 0.578828 4_4:-611949 None:intergenic
TCAATTGAATGGACAAACTG+AGG 0.592361 4_4:+611855 Msa0662810:CDS
ATGCCAGTGAGATTGACCTC+TGG 0.596304 4_4:+612058 Msa0662810:CDS
ATTAGTGCAATATCCCATTG+TGG 0.600538 4_4:-611908 None:intergenic
TTGCTTTAATGACCCCACAA+TGG 0.606154 4_4:+611894 Msa0662810:CDS
TGATGATGATGATTTAAGGG+TGG 0.618237 4_4:-611950 None:intergenic
CTCACTGGCATAGTCATGTG+AGG 0.627225 4_4:-612046 None:intergenic
ATGGTGATAGCATGTGGTGA+TGG 0.628336 4_4:+611790 Msa0662810:CDS
GTGATAGCATGTGGTGATGG+TGG 0.637758 4_4:+611793 Msa0662810:CDS
TCACTGGCATAGTCATGTGA+GGG 0.651790 4_4:-612045 None:intergenic
TCGATCGAGCAAAGTTCCAG+AGG 0.677993 4_4:-612074 None:intergenic
TAGTGCAATATCCCATTGTG+GGG 0.681689 4_4:-611906 None:intergenic
TCATCAATGGTGATAGCATG+TGG 0.720641 4_4:+611784 Msa0662810:CDS
GTATTCGACACGTGACACAG+TGG 0.748440 4_4:-612123 None:intergenic
TTCAGAAGATGACAACAACG+AGG 0.812789 4_4:-612100 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AGTTGATGATGATGATTTAA+GGG - chr4_4:611956-611975 None:intergenic 25.0%
!!! AAGTTGATGATGATGATTTA+AGG - chr4_4:611957-611976 None:intergenic 25.0%
!! TGATGGTGGTCTTACTAATT+GGG + chr4_4:611807-611826 Msa0662810:CDS 35.0%
TCTTACTAATTGGGTAGCTT+TGG + chr4_4:611816-611835 Msa0662810:CDS 35.0%
! CTTGTTGCTTCTCAATTGAA+TGG + chr4_4:611844-611863 Msa0662810:CDS 35.0%
TCAATTGAATGGACAAACTG+AGG + chr4_4:611855-611874 Msa0662810:CDS 35.0%
TTAGTGCAATATCCCATTGT+GGG - chr4_4:611910-611929 None:intergenic 35.0%
ATTAGTGCAATATCCCATTG+TGG - chr4_4:611911-611930 None:intergenic 35.0%
! GATGATGATGATTTAAGGGT+GGG - chr4_4:611952-611971 None:intergenic 35.0%
! TGATGATGATGATTTAAGGG+TGG - chr4_4:611953-611972 None:intergenic 35.0%
! GATGATGATGATGCCTCTAA+TGG - chr4_4:611769-611788 None:intergenic 40.0%
!! AGAGGCATCATCATCATCAA+TGG + chr4_4:611771-611790 Msa0662810:CDS 40.0%
TCATCAATGGTGATAGCATG+TGG + chr4_4:611784-611803 Msa0662810:CDS 40.0%
!! GTGATGGTGGTCTTACTAAT+TGG + chr4_4:611806-611825 Msa0662810:CDS 40.0%
!! CTAATTGGGTAGCTTTGGAT+AGG + chr4_4:611821-611840 Msa0662810:CDS 40.0%
TTGCTTTAATGACCCCACAA+TGG + chr4_4:611894-611913 Msa0662810:CDS 40.0%
TGCTTTAATGACCCCACAAT+GGG + chr4_4:611895-611914 Msa0662810:CDS 40.0%
TAGTGCAATATCCCATTGTG+GGG - chr4_4:611909-611928 None:intergenic 40.0%
TTCAGAAGATGACAACAACG+AGG - chr4_4:612103-612122 None:intergenic 40.0%
ATGGTGATAGCATGTGGTGA+TGG + chr4_4:611790-611809 Msa0662810:CDS 45.0%
ATGGACAAACTGAGGCTTCT+AGG + chr4_4:611863-611882 Msa0662810:CDS 45.0%
AACTGAGGCTTCTAGGCAAT+TGG + chr4_4:611870-611889 Msa0662810:CDS 45.0%
TCACTGGCATAGTCATGTGA+GGG - chr4_4:612048-612067 None:intergenic 45.0%
!! GTGATAGCATGTGGTGATGG+TGG + chr4_4:611793-611812 Msa0662810:CDS 50.0%
CTCACTGGCATAGTCATGTG+AGG - chr4_4:612049-612068 None:intergenic 50.0%
ATGCCAGTGAGATTGACCTC+TGG + chr4_4:612058-612077 Msa0662810:CDS 50.0%
GTTCCAGAGGTCAATCTCAC+TGG - chr4_4:612064-612083 None:intergenic 50.0%
TCGATCGAGCAAAGTTCCAG+AGG - chr4_4:612077-612096 None:intergenic 50.0%
GTATTCGACACGTGACACAG+TGG - chr4_4:612126-612145 None:intergenic 50.0%
Chromosome Type Strat End Strand Name
chr4_4 gene 611754 612155 611754 ID=Msa0662810;Name=Msa0662810
chr4_4 mRNA 611754 612155 611754 ID=Msa0662810-mRNA-1;Parent=Msa0662810;Name=Msa0662810-mRNA-1;_AED=0.47;_eAED=0.47;_QI=0|-1|0|1|-1|1|1|0|133
chr4_4 exon 611754 612155 611754 ID=Msa0662810-mRNA-1:exon:308;Parent=Msa0662810-mRNA-1
chr4_4 CDS 611754 612155 611754 ID=Msa0662810-mRNA-1:cds;Parent=Msa0662810-mRNA-1
Gene Sequence

>Msa0662810

ATGGTTAATAATCCATTAGAGGCATCATCATCATCAATGGTGATAGCATGTGGTGATGGTGGTCTTACTAATTGGGTAGCTTTGGATAGGCTTGTTGCTTCTCAATTGAATGGACAAACTGAGGCTTCTAGGCAATTGGCTTGCTTTAATGACCCCACAATGGGATATTGCACTAATGATCAAGATCTTCAACTTCCCACCCTTAAATCATCATCATCAACTTCATCACTATCAACACAAGTCAGAGCTACTACTACTTCTACTACTACTACAGCTACTACTTACATTAGTCCCTCACATGACTATGCCAGTGAGATTGACCTCTGGAACTTTGCTCGATCGACTTCCTCGTTGTTGTCATCTTCTGAACCACTGTGTCACGTGTCGAATACGTCAGTGTGA
Protein sequence

>Msa0662810

MVNNPLEASSSSMVIACGDGGLTNWVALDRLVASQLNGQTEASRQLACFNDPTMGYCTNDQDLQLPTLKSSSSTSSLSTQVRATTTSTTTTATTYISPSHDYASEIDLWNFARSTSSLLSSSEPLCHVSNTSV*