AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar zhongmu-4 / Msa1380710


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1380710 MtrunA17_Chr7g0229301 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1380710 MtrunA17_Chr6g0454441 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1380710 MtrunA17_Chr4g0016451 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1380710 MtrunA17_Chr6g0466281 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1380710 MtrunA17_CPg0493311 97.512 201 5 0 1 201 1 201 1.37e-143 398
Msa1380710 MtrunA17_Chr7g0229661 84.080 201 13 1 1 201 1 182 1.89e-115 327
Msa1380710 MtrunA17_Chr4g0015291 97.436 156 4 0 1 156 1 156 3.32e-108 307
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
Msa1380710 ATCG00380.1 88.060 201 24 0 1 201 1 201 2.12e-126 355

Find 33 sgRNAs with CRISPR-Local

Find 43 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
ATCAAATAATAGATAGTAAA+TGG 0.189787 tig0020386:-131681 Msa1380710:CDS
GATTGACTAATCCTTTATAT+TGG 0.284280 tig0020386:+131701 None:intergenic
CTTGATCCATTCCAATATAA+AGG 0.291752 tig0020386:-131712 Msa1380710:CDS
CTTAAATACGTTCGTATCGC+TGG 0.342652 tig0020386:-132012 Msa1380710:CDS
ACAATTACTTGAAATGCGTT+TGG 0.359489 tig0020386:-131956 Msa1380710:CDS
TTTGAAAATTAATGAATTGC+TGG 0.365999 tig0020386:-131653 Msa1380710:CDS
ATGGATTGGCAATTCTTCGC+GGG 0.450528 tig0020386:+131741 None:intergenic
TACCAGGACTAACTAGTAAA+CGG 0.463029 tig0020386:-132155 Msa1380710:CDS
TGAGGTTTGCAACGATAACT+TGG 0.468099 tig0020386:+131832 None:intergenic
ACTAATCCTTTATATTGGAA+TGG 0.475526 tig0020386:+131706 None:intergenic
GTCTGTGGTTAACTAATTGA+CGG 0.477609 tig0020386:+131887 None:intergenic
TCAAATAATAGATAGTAAAT+GGG 0.487910 tig0020386:-131680 Msa1380710:CDS
ATAATAGATAGTAAATGGGT+TGG 0.504615 tig0020386:-131676 Msa1380710:CDS
CTAAGTTCGCTTCCAACTGT+AGG 0.508663 tig0020386:+132132 None:intergenic
GGATCAAGAGTCAAATGGAT+TGG 0.511159 tig0020386:+131727 None:intergenic
GGAAAAGCGAAAGGTTCAAC+CGG 0.516182 tig0020386:-131991 Msa1380710:CDS
TCTGTGGTTAACTAATTGAC+GGG 0.521261 tig0020386:+131888 None:intergenic
GGCCGTTTACTAGTTAGTCC+TGG 0.527000 tig0020386:+132153 None:intergenic
AATGGATTGGCAATTCTTCG+CGG 0.545268 tig0020386:+131740 None:intergenic
TCAAGATATTATTACAGCGA+AGG 0.559737 tig0020386:-131812 Msa1380710:CDS
TTCGCTGTAATAATATCTTG+AGG 0.560954 tig0020386:+131814 None:intergenic
TAATTGTAGTAAAACTTGAC+CGG 0.568250 tig0020386:+131972 None:intergenic
ACTAGTAAACGGCCTACAGT+TGG 0.568372 tig0020386:-132144 Msa1380710:CDS
CAAGATATTATTACAGCGAA+GGG 0.569002 tig0020386:-131811 Msa1380710:CDS
TTAACTAATTGACGGGCTTG+AGG 0.581554 tig0020386:+131895 None:intergenic
GGAATGGATCAAGAGTCAAA+TGG 0.582974 tig0020386:+131722 None:intergenic
GATTGGCAATTCTTCGCGGG+GGG 0.584547 tig0020386:+131744 None:intergenic
TGGATTGGCAATTCTTCGCG+GGG 0.610754 tig0020386:+131742 None:intergenic
TGTTTATGTCACGTTACAGA+GGG 0.632465 tig0020386:-132212 None:intergenic
GTGTTTATGTCACGTTACAG+AGG 0.633128 tig0020386:-132213 None:intergenic
CGTATCGCTGGAAAAGCGAA+AGG 0.633501 tig0020386:-132000 Msa1380710:CDS
CATTAACTAAAACATGTCTG+TGG 0.663264 tig0020386:+131872 None:intergenic
GGATTGGCAATTCTTCGCGG+GGG 0.681198 tig0020386:+131743 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! ATCAAATAATAGATAGTAAA+TGG - tig0020386:132150-132169 Msa1380710:CDS 15.0%
!! TCAAATAATAGATAGTAAAT+GGG - tig0020386:132151-132170 Msa1380710:CDS 15.0%
!! TTTGAAAATTAATGAATTGC+TGG - tig0020386:132178-132197 Msa1380710:CDS 20.0%
!! CAAAAATTGCGTTTTCATTA+TGG - tig0020386:131777-131796 Msa1380710:CDS 25.0%
! TAATTGTAGTAAAACTTGAC+CGG + tig0020386:131862-131881 None:intergenic 25.0%
!!! GATAACATACTTTTTCGATT+GGG - tig0020386:131897-131916 Msa1380710:CDS 25.0%
! ACTAATCCTTTATATTGGAA+TGG + tig0020386:132128-132147 None:intergenic 25.0%
! GATTGACTAATCCTTTATAT+TGG + tig0020386:132133-132152 None:intergenic 25.0%
! ATAATAGATAGTAAATGGGT+TGG - tig0020386:132155-132174 Msa1380710:CDS 25.0%
TTTCAAAAAAATACGTCGTC+TGG - tig0020386:131647-131666 Msa1380710:CDS 30.0%
TTCAAAAAAATACGTCGTCT+GGG - tig0020386:131648-131667 Msa1380710:CDS 30.0%
ACAATTACTTGAAATGCGTT+TGG - tig0020386:131875-131894 Msa1380710:CDS 30.0%
!!! GGATAACATACTTTTTCGAT+TGG - tig0020386:131896-131915 Msa1380710:CDS 30.0%
CATTAACTAAAACATGTCTG+TGG + tig0020386:131962-131981 None:intergenic 30.0%
!!! CACAGACATGTTTTAGTTAA+TGG - tig0020386:131960-131979 Msa1380710:CDS 30.0%
TTCGCTGTAATAATATCTTG+AGG + tig0020386:132020-132039 None:intergenic 30.0%
TCAAGATATTATTACAGCGA+AGG - tig0020386:132019-132038 Msa1380710:CDS 30.0%
CAAGATATTATTACAGCGAA+GGG - tig0020386:132020-132039 Msa1380710:CDS 30.0%
CTTGATCCATTCCAATATAA+AGG - tig0020386:132119-132138 Msa1380710:CDS 30.0%
!!! CGACGTATTTTTTTGAAACG+AGG + tig0020386:131645-131664 None:intergenic 35.0%
TCAAAAAAATACGTCGTCTG+GGG - tig0020386:131649-131668 Msa1380710:CDS 35.0%
TACCAGGACTAACTAGTAAA+CGG - tig0020386:131676-131695 Msa1380710:CDS 35.0%
!!! CATACTTTTTCGATTGGGTA+TGG - tig0020386:131902-131921 Msa1380710:CDS 35.0%
TCTGTGGTTAACTAATTGAC+GGG + tig0020386:131946-131965 None:intergenic 35.0%
GTCTGTGGTTAACTAATTGA+CGG + tig0020386:131947-131966 None:intergenic 35.0%
CAAAAAAATACGTCGTCTGG+GGG - tig0020386:131650-131669 Msa1380710:CDS 40.0%
!!! ATTTTTTACTCGAGCGCGAT+TGG + tig0020386:131728-131747 None:intergenic 40.0%
CTTAAATACGTTCGTATCGC+TGG - tig0020386:131819-131838 Msa1380710:CDS 40.0%
!! TTAACTAATTGACGGGCTTG+AGG + tig0020386:131939-131958 None:intergenic 40.0%
TGAGGTTTGCAACGATAACT+TGG + tig0020386:132002-132021 None:intergenic 40.0%
!! AATGGATTGGCAATTCTTCG+CGG + tig0020386:132094-132113 None:intergenic 40.0%
GGATCAAGAGTCAAATGGAT+TGG + tig0020386:132107-132126 None:intergenic 40.0%
GGAATGGATCAAGAGTCAAA+TGG + tig0020386:132112-132131 None:intergenic 40.0%
ACTAGTAAACGGCCTACAGT+TGG - tig0020386:131687-131706 Msa1380710:CDS 45.0%
CTAAGTTCGCTTCCAACTGT+AGG + tig0020386:131702-131721 None:intergenic 45.0%
GGAAAAGCGAAAGGTTCAAC+CGG - tig0020386:131840-131859 Msa1380710:CDS 45.0%
!! ATGGATTGGCAATTCTTCGC+GGG + tig0020386:132093-132112 None:intergenic 45.0%
GGCCGTTTACTAGTTAGTCC+TGG + tig0020386:131681-131700 None:intergenic 50.0%
CGTATCGCTGGAAAAGCGAA+AGG - tig0020386:131831-131850 Msa1380710:CDS 50.0%
!! TGGATTGGCAATTCTTCGCG+GGG + tig0020386:132092-132111 None:intergenic 50.0%
GATTGGCAATTCTTCGCGGG+GGG + tig0020386:132090-132109 None:intergenic 55.0%
! GGATTGGCAATTCTTCGCGG+GGG + tig0020386:132091-132110 None:intergenic 55.0%
CGTCGTCTGGGGGCTTTACC+AGG - tig0020386:131660-131679 Msa1380710:CDS 65.0%
Chromosome Type Strat End Strand Name
tig0020386 gene 131624 132229 131624 ID=Msa1380710;Name=Msa1380710
tig0020386 mRNA 131624 132229 131624 ID=Msa1380710-mRNA-1;Parent=Msa1380710;Name=Msa1380710-mRNA-1;_AED=0.00;_eAED=0.00;_QI=0|-1|0|1|-1|1|1|0|201
tig0020386 exon 131624 132229 131624 ID=Msa1380710-mRNA-1:exon:7181;Parent=Msa1380710-mRNA-1
tig0020386 CDS 131624 132229 131624 ID=Msa1380710-mRNA-1:cds;Parent=Msa1380710-mRNA-1
Gene Sequence

>Msa1380710

ATGTCACGTTACAGAGGGCCTCGTTTCAAAAAAATACGTCGTCTGGGGGCTTTACCAGGACTAACTAGTAAACGGCCTACAGTTGGAAGCGAACTTAGAAACCAATCGCGCTCGAGTAAAAAATCTCAATATCGTATTCGTTTAGAAGAAAAACAAAAATTGCGTTTTCATTATGGTCTTACAGAACGACAATTGCTTAAATACGTTCGTATCGCTGGAAAAGCGAAAGGTTCAACCGGTCAAGTTTTACTACAATTACTTGAAATGCGTTTGGATAACATACTTTTTCGATTGGGTATGGCTTCGACTATTCCTCAAGCCCGTCAATTAGTTAACCACAGACATGTTTTAGTTAATGGTCGTATAGTAGATATACCAAGTTATCGTTGCAAACCTCAAGATATTATTACAGCGAAGGGTGAACAAAAATCTAGAACTCTGATTCAAAATTCTCTTGAATCAGCCCCCCGCGAAGAATTGCCAATCCATTTGACTCTTGATCCATTCCAATATAAAGGATTAGTCAATCAAATAATAGATAGTAAATGGGTTGGTTTGAAAATTAATGAATTGCTGGTTGTAGAATATTATTCTCGTCAGACTTAA

Protein sequence

>Msa1380710

MSRYRGPRFKKIRRLGALPGLTSKRPTVGSELRNQSRSSKKSQYRIRLEEKQKLRFHYGLTERQLLKYVRIAGKAKGSTGQVLLQLLEMRLDNILFRLGMASTIPQARQLVNHRHVLVNGRIVDIPSYRCKPQDIITAKGEQKSRTLIQNSLESAPREELPIHLTLDPFQYKGLVNQIIDSKWVGLKINELLVVEYYSRQT*