AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1172110

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172110 MtrunA17_Chr4g0059241 97.761 134 3 0 4 137 45 178 4.69e-91 261
Msa1172110 MtrunA17_Chr4g0040671 94.545 55 3 0 4 58 45 99 2.38e-30 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1172110 AT1G24450.1 57.353 136 58 0 2 137 55 190 1.14e-50 160

Find 28 sgRNAs with CRISPR-Local

Find 30 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ACTGTTCATGGTCGTGATCT+TGG 0.284490 8_1:-1986640 Msa1172110:CDS
GGTGCTATTTCTCTTGATAC+TGG 0.322054 8_1:-1986694 Msa1172110:CDS
CTGTTCATGGTCGTGATCTT+GGG 0.329301 8_1:-1986639 Msa1172110:CDS
CAAGCGACGGTTCAACTCTT+TGG 0.330495 8_1:+1986852 None:intergenic
TGCCGTTGATGCAATGCGTT+TGG 0.351005 8_1:-1986800 Msa1172110:CDS
ATGAGTCGACATTGGAGATT+AGG 0.358387 8_1:+1986827 None:intergenic
TTCTCTTGATACTGGTAGTT+CGG 0.366585 8_1:-1986686 Msa1172110:CDS
TCTTCCACTGCTGTGGTTTG+TGG 0.372837 8_1:-1986736 Msa1172110:CDS
CACAGCAGTGGAAGAAGAAT+TGG 0.384003 8_1:+1986744 None:intergenic
GAAAGCTTTGTTGTTCTCTT+CGG 0.417815 8_1:+1986948 None:intergenic
TGAGTCGACATTGGAGATTA+GGG 0.444608 8_1:+1986828 None:intergenic
ATGTGTATTACATGATGATC+AGG 0.451757 8_1:-1987026 None:intergenic
CAATTCTTCTTCCACTGCTG+TGG 0.459397 8_1:-1986743 Msa1172110:CDS
GCCGTTGATGCAATGCGTTT+GGG 0.462426 8_1:-1986799 Msa1172110:CDS
ACCCAAACGCATTGCATCAA+CGG 0.482026 8_1:+1986798 None:intergenic
AGTGGAAGAAGAATTGGTCT+TGG 0.487457 8_1:+1986750 None:intergenic
GTGGAAGAAGAATTGGTCTT+GGG 0.501015 8_1:+1986751 None:intergenic
TACTGGTAGTTCGGAGTCTG+CGG 0.528726 8_1:-1986677 Msa1172110:CDS
CTCTTCGGAGAAAGAAGCGT+GGG 0.560654 8_1:+1986963 None:intergenic
GCGACGGTTCAACTCTTTGG+CGG 0.570405 8_1:+1986855 None:intergenic
ACTGGTAGTTCGGAGTCTGC+GGG 0.579104 8_1:-1986676 Msa1172110:CDS
TGTTCATGGTCGTGATCTTG+GGG 0.587592 8_1:-1986638 Msa1172110:CDS
GGCACAAGATGAGTCGACAT+TGG 0.593448 8_1:+1986819 None:intergenic
AGCACCACAAACCACAGCAG+TGG 0.604051 8_1:+1986732 None:intergenic
GCGTTTGGGTTTGCACAAGG+TGG 0.620407 8_1:-1986785 Msa1172110:CDS
AATGCGTTTGGGTTTGCACA+AGG 0.636231 8_1:-1986788 Msa1172110:CDS
TGGAGATTAGGGACAAGCGA+CGG 0.678870 8_1:+1986839 None:intergenic
TCTCTTCGGAGAAAGAAGCG+TGG 0.707050 8_1:+1986962 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AACAAAGCTTTCAGCATTTT+AGG - chr8_1:1986696-1986715 Msa1172110:CDS 30.0%
! AATGTTTTCTTGACTGTTCA+TGG - chr8_1:1986981-1987000 Msa1172110:CDS 30.0%
!! GAAAGCTTTGTTGTTCTCTT+CGG + chr8_1:1986688-1986707 None:intergenic 35.0%
! GGTGCTTTTCGATCAATTTT+TGG - chr8_1:1986918-1986937 Msa1172110:CDS 35.0%
TTCTCTTGATACTGGTAGTT+CGG - chr8_1:1986947-1986966 Msa1172110:CDS 35.0%
TGAGTCGACATTGGAGATTA+GGG + chr8_1:1986808-1986827 None:intergenic 40.0%
ATGAGTCGACATTGGAGATT+AGG + chr8_1:1986809-1986828 None:intergenic 40.0%
!! GTGGAAGAAGAATTGGTCTT+GGG + chr8_1:1986885-1986904 None:intergenic 40.0%
! AGTGGAAGAAGAATTGGTCT+TGG + chr8_1:1986886-1986905 None:intergenic 40.0%
!! GGTGCTATTTCTCTTGATAC+TGG - chr8_1:1986939-1986958 Msa1172110:CDS 40.0%
ACCCAAACGCATTGCATCAA+CGG + chr8_1:1986838-1986857 None:intergenic 45.0%
! AATGCGTTTGGGTTTGCACA+AGG - chr8_1:1986845-1986864 Msa1172110:CDS 45.0%
CACAGCAGTGGAAGAAGAAT+TGG + chr8_1:1986892-1986911 None:intergenic 45.0%
CAATTCTTCTTCCACTGCTG+TGG - chr8_1:1986890-1986909 Msa1172110:CDS 45.0%
ACTGTTCATGGTCGTGATCT+TGG - chr8_1:1986993-1987012 Msa1172110:CDS 45.0%
CTGTTCATGGTCGTGATCTT+GGG - chr8_1:1986994-1987013 Msa1172110:CDS 45.0%
TGTTCATGGTCGTGATCTTG+GGG - chr8_1:1986995-1987014 Msa1172110:CDS 45.0%
! CTCTTCGGAGAAAGAAGCGT+GGG + chr8_1:1986673-1986692 None:intergenic 50.0%
TCTCTTCGGAGAAAGAAGCG+TGG + chr8_1:1986674-1986693 None:intergenic 50.0%
CAAGCGACGGTTCAACTCTT+TGG + chr8_1:1986784-1986803 None:intergenic 50.0%
TGGAGATTAGGGACAAGCGA+CGG + chr8_1:1986797-1986816 None:intergenic 50.0%
GGCACAAGATGAGTCGACAT+TGG + chr8_1:1986817-1986836 None:intergenic 50.0%
TGCCGTTGATGCAATGCGTT+TGG - chr8_1:1986833-1986852 Msa1172110:CDS 50.0%
GCCGTTGATGCAATGCGTTT+GGG - chr8_1:1986834-1986853 Msa1172110:CDS 50.0%
TCTTCCACTGCTGTGGTTTG+TGG - chr8_1:1986897-1986916 Msa1172110:CDS 50.0%
TACTGGTAGTTCGGAGTCTG+CGG - chr8_1:1986956-1986975 Msa1172110:CDS 50.0%
GCGACGGTTCAACTCTTTGG+CGG + chr8_1:1986781-1986800 None:intergenic 55.0%
! GCGTTTGGGTTTGCACAAGG+TGG - chr8_1:1986848-1986867 Msa1172110:CDS 55.0%
AGCACCACAAACCACAGCAG+TGG + chr8_1:1986904-1986923 None:intergenic 55.0%
ACTGGTAGTTCGGAGTCTGC+GGG - chr8_1:1986957-1986976 Msa1172110:CDS 55.0%
Chromosome Type Strat End Strand Name
chr8_1 gene 1986621 1987034 1986621 ID=Msa1172110;Name=Msa1172110
chr8_1 mRNA 1986621 1987034 1986621 ID=Msa1172110-mRNA-1;Parent=Msa1172110;Name=Msa1172110-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|137
chr8_1 exon 1986621 1987034 1986621 ID=Msa1172110-mRNA-1:exon:733;Parent=Msa1172110-mRNA-1
chr8_1 CDS 1986621 1987034 1986621 ID=Msa1172110-mRNA-1:cds;Parent=Msa1172110-mRNA-1
Gene Sequence

>Msa1172110

ATGATCAGGTACACTTTCAAGAGCATAAGTCTTCTTCGTCGTGCAATGACCCACGCTTCTTTCTCCGAAGAGAACAACAAAGCTTTCAGCATTTTAGGCGCTACAATCATTGAAACATCAGTTTCTTTCAATTTGCTTTCGAAAGACGTTGATATTTCCGCCAAAGAGTTGAACCGTCGCTTGTCCCTAATCTCCAATGTCGACTCATCTTGTGCCGTTGATGCAATGCGTTTGGGTTTGCACAAGGTGGTTCGTGTCTCGCCCAAGACCAATTCTTCTTCCACTGCTGTGGTTTGTGGTGCTTTTCGATCAATTTTTGGTGCTATTTCTCTTGATACTGGTAGTTCGGAGTCTGCGGGTAATGTTTTCTTGACTGTTCATGGTCGTGATCTTGGGGTTTACGCTGCTATGTGA
Protein sequence

>Msa1172110

MIRYTFKSISLLRRAMTHASFSEENNKAFSILGATIIETSVSFNLLSKDVDISAKELNRRLSLISNVDSSCAVDAMRLGLHKVVRVSPKTNSSSTAVVCGAFRSIFGAISLDTGSSESAGNVFLTVHGRDLGVYAAM*