AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1335230


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1335230 MtrunA17_Chr8g0341501 96.203 79 3 0 1 79 1 79 1.97e-49 150
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 11 sgRNAs with CRISPR-Local

Find 15 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCAGTTGAGGTGGTGTCTA+TGG 0.235479 tig0000235:-5589 Msa1335230:CDS
CGTCAAGTTAGTGCTCGTTT+TGG 0.356065 tig0000235:-5480 Msa1335230:CDS
AGGAAAGAAGCTGAAAGAAA+TGG 0.356123 tig0000235:-5562 Msa1335230:CDS
CTCCTTCTTTAATTTGTGAA+TGG 0.374793 tig0000235:+5650 None:intergenic
TGAAAGGTGAGATCAAGAAA+TGG 0.464102 tig0000235:-5527 Msa1335230:CDS
GAAAGGTGAGATCAAGAAAT+GGG 0.482363 tig0000235:-5526 Msa1335230:CDS
TACCATTCACAAATTAAAGA+AGG 0.518100 tig0000235:-5652 Msa1335230:CDS
ATGGATTCAAATAAGTTGAA+AGG 0.552282 tig0000235:-5543 Msa1335230:CDS
GAGGTGGTGTCTATGGAGGA+AGG 0.559344 tig0000235:-5582 Msa1335230:CDS
TGAGATCAAGAAATGGGCTA+AGG 0.607413 tig0000235:-5520 Msa1335230:CDS
AGTTGAGGTGGTGTCTATGG+AGG 0.609297 tig0000235:-5586 Msa1335230:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! AAGAAATCTCTATCTTTTAA+TGG - tig0000235:5482-5501 Msa1335230:CDS 20.0%
!! AAATCTCTATCTTTTAATGG+TGG - tig0000235:5485-5504 Msa1335230:CDS 25.0%
! TACCATTCACAAATTAAAGA+AGG - tig0000235:5511-5530 Msa1335230:CDS 25.0%
!! ATGGATTCAAATAAGTTGAA+AGG - tig0000235:5620-5639 Msa1335230:CDS 25.0%
!! CTCCTTCTTTAATTTGTGAA+TGG + tig0000235:5516-5535 None:intergenic 30.0%
!!! TCGTTGTTTTTCTTCAGTTG+AGG - tig0000235:5562-5581 Msa1335230:CDS 35.0%
!! TTGTTTTTCTTCAGTTGAGG+TGG - tig0000235:5565-5584 Msa1335230:CDS 35.0%
AGGAAAGAAGCTGAAAGAAA+TGG - tig0000235:5601-5620 Msa1335230:CDS 35.0%
TGAAAGGTGAGATCAAGAAA+TGG - tig0000235:5636-5655 Msa1335230:CDS 35.0%
GAAAGGTGAGATCAAGAAAT+GGG - tig0000235:5637-5656 Msa1335230:CDS 35.0%
!! TGAGATCAAGAAATGGGCTA+AGG - tig0000235:5643-5662 Msa1335230:CDS 40.0%
TTCAGTTGAGGTGGTGTCTA+TGG - tig0000235:5574-5593 Msa1335230:CDS 45.0%
! CGTCAAGTTAGTGCTCGTTT+TGG - tig0000235:5683-5702 Msa1335230:CDS 45.0%
AGTTGAGGTGGTGTCTATGG+AGG - tig0000235:5577-5596 Msa1335230:CDS 50.0%
GAGGTGGTGTCTATGGAGGA+AGG - tig0000235:5581-5600 Msa1335230:CDS 55.0%
Chromosome Type Strat End Strand Name
tig0000235 gene 5473 5712 5473 ID=Msa1335230;Name=Msa1335230
tig0000235 mRNA 5473 5712 5473 ID=Msa1335230-mRNA-1;Parent=Msa1335230;Name=Msa1335230-mRNA-1;_AED=0.27;_eAED=0.28;_QI=0|-1|0|1|-1|1|1|0|79
tig0000235 exon 5473 5712 5473 ID=Msa1335230-mRNA-1:exon:66;Parent=Msa1335230-mRNA-1
tig0000235 CDS 5473 5712 5473 ID=Msa1335230-mRNA-1:cds;Parent=Msa1335230-mRNA-1
Gene Sequence

>Msa1335230

ATGTCTGTGAAGAAATCTCTATCTTTTAATGGTGGAAGTACCATTCACAAATTAAAGAAGGAGAAATCTACAAAACGAAGACGTTTTGATCGTTGTTTTTCTTCAGTTGAGGTGGTGTCTATGGAGGAAGGAAAGAAGCTGAAAGAAATGGATTCAAATAAGTTGAAAGGTGAGATCAAGAAATGGGCTAAGGCTGTTGTTGCATATGCTCGTCAAGTTAGTGCTCGTTTTGGAAGCTAG

Protein sequence

>Msa1335230

MSVKKSLSFNGGSTIHKLKKEKSTKRRRFDRCFSSVEVVSMEEGKKLKEMDSNKLKGEIKKWAKAVVAYARQVSARFGS*