AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0244270


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 20 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TGATTCCTCTCTACTAAATT+TGG 0.163049 2_2:-22484769 Msa0244270:CDS
AAAAGGAGTTGAAGGAAATT+TGG 0.210940 2_2:-22484851 Msa0244270:CDS
TTTGCAAATGGTTCAGAAAA+AGG 0.225289 2_2:-22484868 Msa0244270:CDS
TGTAGGTTGTTGATCTTTCT+TGG 0.242464 2_2:+22485271 None:intergenic
TGCAAATTCAGCCAGAAAAT+AGG 0.317764 2_2:+22484885 None:intergenic
AGGAAATTTGGAAACTTGTC+TGG 0.342078 2_2:-22484839 Msa0244270:CDS
ATCAAGGATTGCTCCTAGTC+TGG 0.386002 2_2:-22484731 Msa0244270:CDS
TTACCATCACATGGTCAAAA+TGG 0.392220 2_2:-22484815 Msa0244270:CDS
AGAAAATTACTGCATTTGTA+TGG 0.396300 2_2:-22485316 Msa0244270:CDS
TTTCTGGCTGAATTTGCAAA+TGG 0.468682 2_2:-22484880 Msa0244270:CDS
GTTGAAGTGGTAGACGATCA+AGG 0.490025 2_2:-22484747 Msa0244270:CDS
TCTACTAAATTTGGTTGAAG+TGG 0.497703 2_2:-22484760 Msa0244270:CDS
CATCTCATGGGATCCAGACT+AGG 0.520864 2_2:+22484718 None:intergenic
AATTACTGCATTTGTATGGA+AGG 0.523181 2_2:-22485312 Msa0244270:CDS
TTCAACCAAATTTAGTAGAG+AGG 0.552876 2_2:+22484764 None:intergenic
TCTTTCTTGGAACTCTGTCG+AGG 0.571848 2_2:+22485284 None:intergenic
ATTACTGCATTTGTATGGAA+GGG 0.581202 2_2:-22485311 Msa0244270:CDS
CATGGTCAAAATGGATACAA+AGG 0.586800 2_2:-22484806 Msa0244270:CDS
GTTTGCCAAAAGACTAAACA+TGG 0.617800 2_2:+22485420 None:intergenic
TTGTCTGGCTTACCATCACA+TGG 0.649123 2_2:-22484824 Msa0244270:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTAAGATTATATAGTACAAA+TGG + chr2_2:22484747-22484766 None:intergenic 15.0%
!!! TTAAAATACCTTTTTTATGT+AGG + chr2_2:22484889-22484908 None:intergenic 15.0%
!!! TTAATTCAGTTTTGTCAAAA+TGG - chr2_2:22485226-22485245 Msa0244270:intron 20.0%
!!! AATTTTCTGAGGATCAATTT+TGG + chr2_2:22484812-22484831 None:intergenic 25.0%
! AGAAAATTACTGCATTTGTA+TGG - chr2_2:22484824-22484843 Msa0244270:CDS 25.0%
! ATCAACAACCTACATAAAAA+AGG - chr2_2:22484878-22484897 Msa0244270:CDS 25.0%
! TTAGAGTTCCATTTATACTA+TGG - chr2_2:22485112-22485131 Msa0244270:intron 25.0%
! TCACATTACCATAGTATAAA+TGG + chr2_2:22485123-22485142 None:intergenic 25.0%
! ACAAATGCAGTAATTTTCTG+AGG + chr2_2:22484823-22484842 None:intergenic 30.0%
AATTACTGCATTTGTATGGA+AGG - chr2_2:22484828-22484847 Msa0244270:CDS 30.0%
ATTACTGCATTTGTATGGAA+GGG - chr2_2:22484829-22484848 Msa0244270:CDS 30.0%
TAACTACTTAACAGAAAGAC+AGG - chr2_2:22484920-22484939 Msa0244270:intron 30.0%
! AATGGAGTATACCTATTTTC+TGG - chr2_2:22485244-22485263 Msa0244270:intron 30.0%
TTTGCAAATGGTTCAGAAAA+AGG - chr2_2:22485272-22485291 Msa0244270:CDS 30.0%
AAAAGGAGTTGAAGGAAATT+TGG - chr2_2:22485289-22485308 Msa0244270:CDS 30.0%
TGATTCCTCTCTACTAAATT+TGG - chr2_2:22485371-22485390 Msa0244270:intron 30.0%
TTCAACCAAATTTAGTAGAG+AGG + chr2_2:22485379-22485398 None:intergenic 30.0%
TCTACTAAATTTGGTTGAAG+TGG - chr2_2:22485380-22485399 Msa0244270:intron 30.0%
TGTAGGTTGTTGATCTTTCT+TGG + chr2_2:22484872-22484891 None:intergenic 35.0%
! GCAGTTTTTCACATCTCATT+TGG - chr2_2:22485175-22485194 Msa0244270:intron 35.0%
TTTCACATCTCATTTGGCAA+AGG - chr2_2:22485181-22485200 Msa0244270:intron 35.0%
TGCAAATTCAGCCAGAAAAT+AGG + chr2_2:22485258-22485277 None:intergenic 35.0%
!! TTTCTGGCTGAATTTGCAAA+TGG - chr2_2:22485260-22485279 Msa0244270:intron 35.0%
AGGAAATTTGGAAACTTGTC+TGG - chr2_2:22485301-22485320 Msa0244270:CDS 35.0%
TTACCATCACATGGTCAAAA+TGG - chr2_2:22485325-22485344 Msa0244270:CDS 35.0%
!! TATCCATTTTGACCATGTGA+TGG + chr2_2:22485331-22485350 None:intergenic 35.0%
CATGGTCAAAATGGATACAA+AGG - chr2_2:22485334-22485353 Msa0244270:CDS 35.0%
ATGTGAAAAACTGCAGCAGA+AGG + chr2_2:22485169-22485188 None:intergenic 40.0%
GGTTCAGAAAAAGGAGTTGA+AGG - chr2_2:22485281-22485300 Msa0244270:CDS 40.0%
TCTTTCTTGGAACTCTGTCG+AGG + chr2_2:22484859-22484878 None:intergenic 45.0%
CACATCTCATTTGGCAAAGG+TGG - chr2_2:22485184-22485203 Msa0244270:intron 45.0%
!! GCAAAGGTGGTGCTATACTT+GGG - chr2_2:22485197-22485216 Msa0244270:intron 45.0%
! TTGTCTGGCTTACCATCACA+TGG - chr2_2:22485316-22485335 Msa0244270:CDS 45.0%
GTTGAAGTGGTAGACGATCA+AGG - chr2_2:22485393-22485412 Msa0244270:intron 45.0%
ATCAAGGATTGCTCCTAGTC+TGG - chr2_2:22485409-22485428 Msa0244270:intron 45.0%
!! GGCAAAGGTGGTGCTATACT+TGG - chr2_2:22485196-22485215 Msa0244270:intron 50.0%
Chromosome Type Strat End Strand Name
chr2_2 gene 22484722 22485440 22484722 ID=Msa0244270;Name=Msa0244270
chr2_2 mRNA 22484722 22485440 22484722 ID=Msa0244270-mRNA-1;Parent=Msa0244270;Name=Msa0244270-mRNA-1;_AED=0.45;_eAED=0.80;_QI=0|0|0|1|0|0|3|0|108
chr2_2 exon 22485434 22485440 22485434 ID=Msa0244270-mRNA-1:exon:8645;Parent=Msa0244270-mRNA-1
chr2_2 exon 22485263 22485376 22485263 ID=Msa0244270-mRNA-1:exon:8644;Parent=Msa0244270-mRNA-1
chr2_2 exon 22484722 22484927 22484722 ID=Msa0244270-mRNA-1:exon:8643;Parent=Msa0244270-mRNA-1
chr2_2 CDS 22485434 22485440 22485434 ID=Msa0244270-mRNA-1:cds;Parent=Msa0244270-mRNA-1
chr2_2 CDS 22485263 22485376 22485263 ID=Msa0244270-mRNA-1:cds;Parent=Msa0244270-mRNA-1
chr2_2 CDS 22484722 22484927 22484722 ID=Msa0244270-mRNA-1:cds;Parent=Msa0244270-mRNA-1
Gene Sequence

>Msa0244270

ATGTTTAAAAGTTCTTCAGTTGCTTCTTGTCCAAAATTGATCCTCAGAAAATTACTGCATTTGTATGGAAGGGTCATCCTCGACAGAGTTCCAAGAAAGATCAACAACCTACATAAAAAAGTTTTGTCAAAATGGAGTATACCTATTTTCTGGCTGAATTTGCAAATGGTTCAGAAAAAGGAGTTGAAGGAAATTTGGAAACTTGTCTGGCTTACCATCACATGGTCAAAATGGATACAAAGGAGCAAAGTTGCTTTTGATTCCTCTCTACTAAATTTGGTTGAAGTGGTAGACGATCAAGGATTGCTCCTAGTCTGGATCCCATGA

Protein sequence

>Msa0244270

MFKSSSVASCPKLILRKLLHLYGRVILDRVPRKINNLHKKVLSKWSIPIFWLNLQMVQKKELKEIWKLVWLTITWSKWIQRSKVAFDSSLLNLVEVVDDQGLLLVWIP*