AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa0095150


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095150 MtrunA17_Chr8g0355631 97.872 47 1 0 29 75 25 71 7.25e-28 95.5
Msa0095150 MtrunA17_Chr4g0015761 97.872 47 1 0 29 75 25 71 8.54e-28 95.1
Msa0095150 MtrunA17_CPg0492811 97.872 47 1 0 29 75 25 71 8.54e-28 95.1
Msa0095150 MtrunA17_Chr4g0016861 100.000 35 0 0 39 73 1 35 3.92e-18 70.1
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa0095150 ATCG00600.1 97.222 36 1 0 39 74 1 36 1.27e-17 68.9

Find 16 sgRNAs with CRISPR-Local

Find 36 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATGATTGAAGTTTCTCTATT+TGG 0.115333 1_2:-79013252 Msa0095150:CDS
TCATGTCAATTGCCAATTCT+TGG 0.245809 1_2:-79013355 Msa0095150:CDS
AATAATCCAGCCAAAGTAAT+AGG 0.315680 1_2:+79013210 None:intergenic
AAACTTCAATCATTTGAGTT+TGG 0.328054 1_2:+79013262 None:intergenic
CTAATTCCTATTACTTTGGC+TGG 0.352028 1_2:-79013216 Msa0095150:CDS
TCTCTATTTGGAATCGTGTT+AGG 0.358426 1_2:-79013240 Msa0095150:CDS
GGTAATATCTATCCTTCAAT+AGG 0.374355 1_2:+79013304 None:intergenic
AGGTCTAATTCCTATTACTT+TGG 0.388074 1_2:-79013220 Msa0095150:CDS
ATCATTTGAGTTTGGTTGAA+AGG 0.406278 1_2:+79013270 None:intergenic
GAATCTCAATGACCAAGAAT+TGG 0.414372 1_2:+79013343 None:intergenic
AATTGGCAATTGACATGATA+AGG 0.448909 1_2:+79013360 None:intergenic
TTCTTGGTCATTGAGATTCA+CGG 0.471290 1_2:-79013339 Msa0095150:CDS
TCAATACAGATTCCTATTGA+AGG 0.532626 1_2:-79013316 Msa0095150:CDS
ATATCGACGTGGTGATCAGT+TGG 0.572503 1_2:-79013169 Msa0095150:CDS
TTTGGCTGGATTATTTGTAA+CGG 0.592623 1_2:-79013202 Msa0095150:CDS
GCATATTTACAATATCGACG+TGG 0.789819 1_2:-79013180 Msa0095150:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAATAAAAATATAGTTACAT+AGG + chr1_2:79013200-79013219 None:intergenic 10.0%
!!! TTTATTTTTGAGATAAAAAT+AGG + chr1_2:79013299-79013318 None:intergenic 10.0%
!!! ATTTTTATCTCAAAAATAAA+TGG - chr1_2:79013299-79013318 Msa0095150:CDS 10.0%
!! GATTCATGAATCAATTATTA+CGG + chr1_2:79013230-79013249 None:intergenic 20.0%
!! TCAAAAATAAATGGAAACTT+AGG - chr1_2:79013308-79013327 Msa0095150:CDS 20.0%
!!! TTGAGATGAATTGTAAATTT+TGG - chr1_2:79013489-79013508 Msa0095150:intron 20.0%
! TTTCAATTGTATCTTTCAAG+TGG - chr1_2:79013256-79013275 Msa0095150:CDS 25.0%
!!! ATCTTTCAAGTGGTATTTTT+TGG - chr1_2:79013266-79013285 Msa0095150:CDS 25.0%
!! AAACTTCAATCATTTGAGTT+TGG + chr1_2:79013636-79013655 None:intergenic 25.0%
! ATGATTGAAGTTTCTCTATT+TGG - chr1_2:79013643-79013662 Msa0095150:intron 25.0%
TAGTAGAAAACCGAAATAAC+TGG + chr1_2:79013400-79013419 None:intergenic 30.0%
AATTGGCAATTGACATGATA+AGG + chr1_2:79013538-79013557 None:intergenic 30.0%
TCAATACAGATTCCTATTGA+AGG - chr1_2:79013579-79013598 Msa0095150:intron 30.0%
GGTAATATCTATCCTTCAAT+AGG + chr1_2:79013594-79013613 None:intergenic 30.0%
TTGGTTGAAAGGAAAAAAGT+GGG + chr1_2:79013617-79013636 None:intergenic 30.0%
TTTGGTTGAAAGGAAAAAAG+TGG + chr1_2:79013618-79013637 None:intergenic 30.0%
! ATCATTTGAGTTTGGTTGAA+AGG + chr1_2:79013628-79013647 None:intergenic 30.0%
AGGTCTAATTCCTATTACTT+TGG - chr1_2:79013675-79013694 Msa0095150:intron 30.0%
AATAATCCAGCCAAAGTAAT+AGG + chr1_2:79013688-79013707 None:intergenic 30.0%
TTTGGCTGGATTATTTGTAA+CGG - chr1_2:79013693-79013712 Msa0095150:intron 30.0%
CCGAAATAACTGGTTATAGT+GGG + chr1_2:79013390-79013409 None:intergenic 35.0%
CCCACTATAACCAGTTATTT+CGG - chr1_2:79013387-79013406 Msa0095150:intron 35.0%
ACCGAAATAACTGGTTATAG+TGG + chr1_2:79013391-79013410 None:intergenic 35.0%
!! AGCAGTTTTAACAATAACCG+CGG - chr1_2:79013419-79013438 Msa0095150:intron 35.0%
TCATGTCAATTGCCAATTCT+TGG - chr1_2:79013540-79013559 Msa0095150:intron 35.0%
GAATCTCAATGACCAAGAAT+TGG + chr1_2:79013555-79013574 None:intergenic 35.0%
TTCTTGGTCATTGAGATTCA+CGG - chr1_2:79013556-79013575 Msa0095150:intron 35.0%
TGGTTGAAAGGAAAAAAGTG+GGG + chr1_2:79013616-79013635 None:intergenic 35.0%
! TCTCTATTTGGAATCGTGTT+AGG - chr1_2:79013655-79013674 Msa0095150:intron 35.0%
CTAATTCCTATTACTTTGGC+TGG - chr1_2:79013679-79013698 Msa0095150:intron 35.0%
GCATATTTACAATATCGACG+TGG - chr1_2:79013715-79013734 Msa0095150:intron 35.0%
!! AACTGGTTATAGTGGGCATA+AGG + chr1_2:79013383-79013402 None:intergenic 40.0%
!! GCAGTTTTAACAATAACCGC+GGG - chr1_2:79013420-79013439 Msa0095150:intron 40.0%
CAGACTAATAAAAAGACCCG+CGG + chr1_2:79013439-79013458 None:intergenic 40.0%
GGTTGAAAGGAAAAAAGTGG+GGG + chr1_2:79013615-79013634 None:intergenic 40.0%
ATATCGACGTGGTGATCAGT+TGG - chr1_2:79013726-79013745 Msa0095150:intron 45.0%
Chromosome Type Strat End Strand Name
chr1_2 gene 79013161 79013756 79013161 ID=Msa0095150;Name=Msa0095150
chr1_2 mRNA 79013161 79013756 79013161 ID=Msa0095150-mRNA-1;Parent=Msa0095150;Name=Msa0095150-mRNA-1;_AED=0.42;_eAED=0.42;_QI=0|0|0|0.5|1|1|2|0|75
chr1_2 exon 79013753 79013756 79013753 ID=Msa0095150-mRNA-1:exon:28066;Parent=Msa0095150-mRNA-1
chr1_2 exon 79013161 79013384 79013161 ID=Msa0095150-mRNA-1:exon:28065;Parent=Msa0095150-mRNA-1
chr1_2 CDS 79013753 79013756 79013753 ID=Msa0095150-mRNA-1:cds;Parent=Msa0095150-mRNA-1
chr1_2 CDS 79013161 79013384 79013161 ID=Msa0095150-mRNA-1:cds;Parent=Msa0095150-mRNA-1
Gene Sequence

>Msa0095150

ATGGTTCCTTATCATGTCAATTGCCAATTCTTGGTCATTGAGATTCACGGTCAATACAGATTCCTATTGAAGGATAGATATTACCCCCACTTTTTTCCTTTCAACCAAACTCAAATGATTGAAGTTTCTCTATTTGGAATCGTGTTAGGTCTAATTCCTATTACTTTGGCTGGATTATTTGTAACGGCATATTTACAATATCGACGTGGTGATCAGTTGGATATTTGA

Protein sequence

>Msa0095150

MVPYHVNCQFLVIEIHGQYRFLLKDRYYPHFFPFNQTQMIEVSLFGIVLGLIPITLAGLFVTAYLQYRRGDQLDI*