AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1169000


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 29 sgRNAs with CRISPR-Local

Find 45 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTGCAGGTCAAGGCTGATTT+TGG 0.138857 7_4:+61915010 Msa1169000:intron
AACCCGCATTTCTAACTTAA+TGG 0.155002 7_4:-61915084 None:intergenic
TACTGGTGATGTTTCTAAAA+AGG 0.173626 7_4:+61914785 Msa1169000:five_prime_UTR
TCGGATTAACCAACACAATT+AGG 0.275265 7_4:+61914719 Msa1169000:five_prime_UTR
TGAGTTGAGAAGGTTGAATA+AGG 0.323601 7_4:+61914518 Msa1169000:five_prime_UTR
CACTTGTAGGCTCTCTTCTA+TGG 0.338739 7_4:+61914566 Msa1169000:five_prime_UTR
ATTTCTAACTTAATGGTACT+TGG 0.426986 7_4:-61915077 None:intergenic
TTAACTTAAATCATACTGAT+AGG 0.430639 7_4:+61914894 Msa1169000:CDS
AACCAACACAATTAGGCTCT+TGG 0.438251 7_4:+61914726 Msa1169000:five_prime_UTR
GATAAGAGGAAGCGGTGAAG+GGG 0.453973 7_4:+61914451 None:intergenic
TACCATTAAGTTAGAAATGC+GGG 0.455867 7_4:+61915082 Msa1169000:exon
TTGTAATAGAAGATATGAAT+AGG 0.461497 7_4:+61914690 Msa1169000:five_prime_UTR
AGCCTTGCTCTGCAAATACT+TGG 0.488191 7_4:-61915053 None:intergenic
AGATAAGAGGAAGCGGTGAA+GGG 0.491215 7_4:+61914450 None:intergenic
AGATATGAATAGGCTCTCTT+CGG 0.510356 7_4:+61914700 Msa1169000:five_prime_UTR
AGAAGAGGAACCTCACTTGT+AGG 0.517175 7_4:+61914553 Msa1169000:five_prime_UTR
GTCCAAGTATTTGCAGAGCA+AGG 0.527011 7_4:+61915051 Msa1169000:CDS
AGCCAAGAGCCTAATTGTGT+TGG 0.531992 7_4:-61914728 None:intergenic
TTACTGAGTTGGACTTAAAG+TGG 0.536061 7_4:+61914838 Msa1169000:five_prime_UTR
ATAAGAGGAAGCGGTGAAGG+GGG 0.538898 7_4:+61914452 None:intergenic
TTGAAGTTGTTGAGTTGAGA+AGG 0.559117 7_4:+61914508 Msa1169000:five_prime_UTR
TGTATGCTATCTTACTGAGT+TGG 0.580470 7_4:+61914827 Msa1169000:five_prime_UTR
AGGAGCTGCATATGTAGAAG+AGG 0.591272 7_4:+61914538 Msa1169000:five_prime_UTR
ATGATTTAAGTTAATAACCA+TGG 0.599391 7_4:-61914885 None:intergenic
GTACCATTAAGTTAGAAATG+CGG 0.611734 7_4:+61915081 Msa1169000:exon
TCATACTGATAGGACAGTGA+TGG 0.631868 7_4:+61914904 Msa1169000:CDS
TAGAAGAGAGCCTACAAGTG+AGG 0.633933 7_4:-61914563 None:intergenic
TAGTTGTGCCTGCCAAAACA+CGG 0.641537 7_4:-61914764 None:intergenic
TAACTTGCTGAGAAATACCA+TGG 0.684621 7_4:+61914868 Msa1169000:exon

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! TTGTAATAGAAGATATGAAT+AGG + chr7_4:61914690-61914709 Msa1169000:five_prime_UTR 20.0%
!!! ATGATTTAAGTTAATAACCA+TGG - chr7_4:61914888-61914907 None:intergenic 20.0%
!! TTAACTTAAATCATACTGAT+AGG + chr7_4:61914894-61914913 Msa1169000:CDS 20.0%
!! TGACATAATTTCTTTTCTCA+TGG + chr7_4:61914658-61914677 Msa1169000:five_prime_UTR 25.0%
!! GACATAATTTCTTTTCTCAT+GGG + chr7_4:61914659-61914678 Msa1169000:five_prime_UTR 25.0%
! ATTTCTAACTTAATGGTACT+TGG - chr7_4:61915080-61915099 None:intergenic 25.0%
! TACTGGTGATGTTTCTAAAA+AGG + chr7_4:61914785-61914804 Msa1169000:five_prime_UTR 30.0%
! ACTGGTGATGTTTCTAAAAA+GGG + chr7_4:61914786-61914805 Msa1169000:five_prime_UTR 30.0%
!! AGTACTTGATAACCTCATTT+TGG - chr7_4:61914963-61914982 None:intergenic 30.0%
GTACCATTAAGTTAGAAATG+CGG + chr7_4:61915081-61915100 Msa1169000:exon 30.0%
TACCATTAAGTTAGAAATGC+GGG + chr7_4:61915082-61915101 Msa1169000:exon 30.0%
TAAAAAGTAAACAAGCAGCA+AGG - chr7_4:61915122-61915141 None:intergenic 30.0%
!!! TTGCTGCTTGTTTACTTTTT+AGG + chr7_4:61915121-61915140 Msa1169000:three_prime_UTR 30.0%
!! TTGAAGTTGTTGAGTTGAGA+AGG + chr7_4:61914508-61914527 Msa1169000:five_prime_UTR 35.0%
! TGAGTTGAGAAGGTTGAATA+AGG + chr7_4:61914518-61914537 Msa1169000:five_prime_UTR 35.0%
AGATATGAATAGGCTCTCTT+CGG + chr7_4:61914700-61914719 Msa1169000:five_prime_UTR 35.0%
TCGGATTAACCAACACAATT+AGG + chr7_4:61914719-61914738 Msa1169000:five_prime_UTR 35.0%
!! TTTTGATTGATGCCGTGTTT+TGG + chr7_4:61914752-61914771 Msa1169000:five_prime_UTR 35.0%
! ATGTTTCTAAAAAGGGTCGA+TGG + chr7_4:61914793-61914812 Msa1169000:five_prime_UTR 35.0%
TGTATGCTATCTTACTGAGT+TGG + chr7_4:61914827-61914846 Msa1169000:five_prime_UTR 35.0%
! TTACTGAGTTGGACTTAAAG+TGG + chr7_4:61914838-61914857 Msa1169000:five_prime_UTR 35.0%
!! TAACTTGCTGAGAAATACCA+TGG + chr7_4:61914868-61914887 Msa1169000:exon 35.0%
TTTGGACAGAGTAAACTTCA+AGG - chr7_4:61914945-61914964 None:intergenic 35.0%
AGTTTACTCTGTCCAAAATG+AGG + chr7_4:61914948-61914967 Msa1169000:intron 35.0%
AACCCGCATTTCTAACTTAA+TGG - chr7_4:61915087-61915106 None:intergenic 35.0%
AACCAACACAATTAGGCTCT+TGG + chr7_4:61914726-61914745 Msa1169000:five_prime_UTR 40.0%
TCATACTGATAGGACAGTGA+TGG + chr7_4:61914904-61914923 Msa1169000:CDS 40.0%
CAGTAGAGGATAGGCAAATT+GGG - chr7_4:61914993-61915012 None:intergenic 40.0%
AGGAGCTGCATATGTAGAAG+AGG + chr7_4:61914538-61914557 Msa1169000:five_prime_UTR 45.0%
AGAAGAGGAACCTCACTTGT+AGG + chr7_4:61914553-61914572 Msa1169000:five_prime_UTR 45.0%
TAGAAGAGAGCCTACAAGTG+AGG - chr7_4:61914566-61914585 None:intergenic 45.0%
CACTTGTAGGCTCTCTTCTA+TGG + chr7_4:61914566-61914585 Msa1169000:five_prime_UTR 45.0%
AGCCAAGAGCCTAATTGTGT+TGG - chr7_4:61914731-61914750 None:intergenic 45.0%
TAGTTGTGCCTGCCAAAACA+CGG - chr7_4:61914767-61914786 None:intergenic 45.0%
GCAGTAGAGGATAGGCAAAT+TGG - chr7_4:61914994-61915013 None:intergenic 45.0%
ATTTGCCTATCCTCTACTGC+AGG + chr7_4:61914994-61915013 Msa1169000:intron 45.0%
!! TGCAGGTCAAGGCTGATTTT+GGG + chr7_4:61915011-61915030 Msa1169000:intron 45.0%
GTCCAAGTATTTGCAGAGCA+AGG + chr7_4:61915051-61915070 Msa1169000:CDS 45.0%
AGCCTTGCTCTGCAAATACT+TGG - chr7_4:61915056-61915075 None:intergenic 45.0%
!!! GATTGATGCCGTGTTTTGGC+AGG + chr7_4:61914756-61914775 Msa1169000:five_prime_UTR 50.0%
!! GTTTTGGCAGGCACAACTAC+TGG + chr7_4:61914768-61914787 Msa1169000:five_prime_UTR 50.0%
CTTGACCTGCAGTAGAGGAT+AGG - chr7_4:61915002-61915021 None:intergenic 50.0%
CTATCCTCTACTGCAGGTCA+AGG + chr7_4:61915000-61915019 Msa1169000:intron 50.0%
!! CTGCAGGTCAAGGCTGATTT+TGG + chr7_4:61915010-61915029 Msa1169000:intron 50.0%
TCAGCCTTGACCTGCAGTAG+AGG - chr7_4:61915007-61915026 None:intergenic 55.0%
Chromosome Type Strat End Strand Name
chr7_4 gene 61914465 61915164 61914465 ID=Msa1169000;Name=Msa1169000
chr7_4 mRNA 61914465 61915164 61914465 ID=Msa1169000-mRNA-1;Parent=Msa1169000;Name=Msa1169000-mRNA-1;_AED=0.28;_eAED=0.28;_QI=422|1|1|1|1|1|2|74|37
chr7_4 exon 61914465 61914925 61914465 ID=Msa1169000-mRNA-1:exon:19540;Parent=Msa1169000-mRNA-1
chr7_4 exon 61915016 61915164 61915016 ID=Msa1169000-mRNA-1:exon:19541;Parent=Msa1169000-mRNA-1
chr7_4 five_prime_UTR 61914465 61914886 61914465 ID=Msa1169000-mRNA-1:five_prime_utr;Parent=Msa1169000-mRNA-1
chr7_4 CDS 61914887 61914925 61914887 ID=Msa1169000-mRNA-1:cds;Parent=Msa1169000-mRNA-1
chr7_4 CDS 61915016 61915090 61915016 ID=Msa1169000-mRNA-1:cds;Parent=Msa1169000-mRNA-1
chr7_4 three_prime_UTR 61915091 61915164 61915091 ID=Msa1169000-mRNA-1:three_prime_utr;Parent=Msa1169000-mRNA-1
Gene Sequence

>Msa1169000

ATGGTTATTAACTTAAATCATACTGATAGGACAGTGATGGTCAAGGCTGATTTTGGGTCTGTTATTGATGCTTTGTCCAAGTATTTGCAGAGCAAGGCTGCCAAGTACCATTAA

Protein sequence

>Msa1169000

MVINLNHTDRTVMVKADFGSVIDALSKYLQSKAAKYH*