AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1342040


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342040 MtrunA17_Chr4g0015761 100.000 71 0 0 7 77 1 71 4.03e-47 144
Msa1342040 MtrunA17_CPg0492811 100.000 71 0 0 7 77 1 71 4.03e-47 144
Msa1342040 MtrunA17_Chr8g0355631 98.592 71 1 0 7 77 1 71 1.74e-46 142
Msa1342040 MtrunA17_Chr4g0016861 100.000 35 0 0 41 75 1 35 1.92e-18 71.2
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1342040 ATCG00600.1 97.222 36 1 0 41 76 1 36 5.01e-18 70.1

Find 18 sgRNAs with CRISPR-Local

Find 26 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGATTGAAGTTTCTCTATT+TGG 0.115333 tig0005022:+12142 Msa1342040:CDS
TCAATACAGATTCCTATTTA+AGG 0.207264 tig0005022:+12077 Msa1342040:CDS
TCATGTCAATTGCCAATTCT+TGG 0.245809 tig0005022:+12038 Msa1342040:CDS
GGTAATATCTATCCTTAAAT+AGG 0.247970 tig0005022:-12089 None:intergenic
AATAATCCAGCCAAAGTAAT+AGG 0.315680 tig0005022:-12184 None:intergenic
AAACTTCAATCATTTGAGTT+TGG 0.328054 tig0005022:-12132 None:intergenic
AAAGGCTGACATAGATGTTA+TGG 0.351732 tig0005022:+11839 None:intergenic
CTAATTCCTATTACTTTGGC+TGG 0.352028 tig0005022:+12178 Msa1342040:CDS
TCTCTATTTGGAATCGTGTT+AGG 0.358426 tig0005022:+12154 Msa1342040:CDS
AGGTCTAATTCCTATTACTT+TGG 0.388074 tig0005022:+12174 Msa1342040:CDS
ATCATTTGAGTTTGGTTGAA+AGG 0.406278 tig0005022:-12124 None:intergenic
GAATCTCAATGACCAAGAAT+TGG 0.414372 tig0005022:-12050 None:intergenic
AATTGGCAATTGACATGATA+AGG 0.448909 tig0005022:-12033 None:intergenic
TTCTTGGTCATTGAGATTCA+CGG 0.471290 tig0005022:+12054 Msa1342040:CDS
AAGGCTGACATAGATGTTAT+GGG 0.482368 tig0005022:+11840 None:intergenic
ATATCGACGTGGTGATCAGT+TGG 0.572503 tig0005022:+12225 Msa1342040:CDS
TTTGGCTGGATTATTTGTAA+CGG 0.592623 tig0005022:+12192 Msa1342040:CDS
GCATATTTACAATATCGACG+TGG 0.789819 tig0005022:+12214 Msa1342040:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AGAAAAATTTAAGAGATAGA+TGG - tig0005022:11889-11908 None:intergenic 20.0%
!!! TCTCTTAAATTTTTCTGTAA+AGG + tig0005022:11893-11912 Msa1342040:intron 20.0%
!!! TTGAGATGAATTGTAAATTT+TGG + tig0005022:11987-12006 Msa1342040:intron 20.0%
! TCAATACAGATTCCTATTTA+AGG + tig0005022:12077-12096 Msa1342040:CDS 25.0%
! GGTAATATCTATCCTTAAAT+AGG - tig0005022:12092-12111 None:intergenic 25.0%
!! AAACTTCAATCATTTGAGTT+TGG - tig0005022:12135-12154 None:intergenic 25.0%
! ATGATTGAAGTTTCTCTATT+TGG + tig0005022:12142-12161 Msa1342040:CDS 25.0%
AATTGGCAATTGACATGATA+AGG - tig0005022:12036-12055 None:intergenic 30.0%
TGGTTGAAAGGAAAAAAAGT+GGG - tig0005022:12115-12134 None:intergenic 30.0%
TTGGTTGAAAGGAAAAAAAG+TGG - tig0005022:12116-12135 None:intergenic 30.0%
! ATCATTTGAGTTTGGTTGAA+AGG - tig0005022:12127-12146 None:intergenic 30.0%
AGGTCTAATTCCTATTACTT+TGG + tig0005022:12174-12193 Msa1342040:CDS 30.0%
AATAATCCAGCCAAAGTAAT+AGG - tig0005022:12187-12206 None:intergenic 30.0%
TTTGGCTGGATTATTTGTAA+CGG + tig0005022:12192-12211 Msa1342040:CDS 30.0%
TCATGTCAATTGCCAATTCT+TGG + tig0005022:12038-12057 Msa1342040:CDS 35.0%
GAATCTCAATGACCAAGAAT+TGG - tig0005022:12053-12072 None:intergenic 35.0%
TTCTTGGTCATTGAGATTCA+CGG + tig0005022:12054-12073 Msa1342040:CDS 35.0%
GTTGAAAGGAAAAAAAGTGG+GGG - tig0005022:12113-12132 None:intergenic 35.0%
GGTTGAAAGGAAAAAAAGTG+GGG - tig0005022:12114-12133 None:intergenic 35.0%
! TCTCTATTTGGAATCGTGTT+AGG + tig0005022:12154-12173 Msa1342040:CDS 35.0%
CTAATTCCTATTACTTTGGC+TGG + tig0005022:12178-12197 Msa1342040:CDS 35.0%
GCATATTTACAATATCGACG+TGG + tig0005022:12214-12233 Msa1342040:CDS 35.0%
GCTGAATGAAACAATAACCG+CGG + tig0005022:11917-11936 Msa1342040:intron 40.0%
CTGAATGAAACAATAACCGC+GGG + tig0005022:11918-11937 Msa1342040:intron 40.0%
CAGACTAATAAAAAGACCCG+CGG - tig0005022:11937-11956 None:intergenic 40.0%
ATATCGACGTGGTGATCAGT+TGG + tig0005022:12225-12244 Msa1342040:CDS 45.0%
Chromosome Type Strat End Strand Name
tig0005022 gene 11853 12255 11853 ID=Msa1342040;Name=Msa1342040
tig0005022 mRNA 11853 12255 11853 ID=Msa1342040-mRNA-1;Parent=Msa1342040;Name=Msa1342040-mRNA-1;_AED=0.35;_eAED=0.35;_QI=0|0|0|0.5|0|0|2|0|77
tig0005022 exon 11853 11861 11853 ID=Msa1342040-mRNA-1:exon:3441;Parent=Msa1342040-mRNA-1
tig0005022 exon 12031 12255 12031 ID=Msa1342040-mRNA-1:exon:3442;Parent=Msa1342040-mRNA-1
tig0005022 CDS 11853 11861 11853 ID=Msa1342040-mRNA-1:cds;Parent=Msa1342040-mRNA-1
tig0005022 CDS 12031 12255 12031 ID=Msa1342040-mRNA-1:cds;Parent=Msa1342040-mRNA-1
Gene Sequence

>Msa1342040

ATGTTATGGTTCCTTATCATGTCAATTGCCAATTCTTGGTCATTGAGATTCACGGTCAATACAGATTCCTATTTAAGGATAGATATTACCCCCACTTTTTTTCCTTTCAACCAAACTCAAATGATTGAAGTTTCTCTATTTGGAATCGTGTTAGGTCTAATTCCTATTACTTTGGCTGGATTATTTGTAACGGCATATTTACAATATCGACGTGGTGATCAGTTGGATATTTGA

Protein sequence

>Msa1342040

MLWFLIMSIANSWSLRFTVNTDSYLRIDITPTFFPFNQTQMIEVSLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDI*