AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa ssp. caerulea / MsaG013108

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG013108 MtrunA17_Chr3g0092141 89.286 196 17 2 34 229 1 192 5.36e-126 354
MsaG013108 MtrunA17_Chr4g0060761 51.562 192 82 6 27 208 82 272 3.74e-54 175
MsaG013108 MtrunA17_Chr3g0127001 49.107 112 51 1 94 205 154 259 1.56e-30 113
MsaG013108 MtrunA17_Chr1g0182631 47.321 112 53 1 94 205 127 232 1.70e-28 107
MsaG013108 MtrunA17_Chr5g0406901 36.719 128 73 2 80 200 188 314 3.33e-22 92.8
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MsaG013108 AT1G18790.1 62.500 128 41 2 81 201 112 239 3.34e-50 165
MsaG013108 AT1G74480.1 61.207 116 40 2 87 197 127 242 2.29e-42 145
MsaG013108 AT5G66990.1 50.746 134 59 2 75 203 142 273 4.61e-41 142
MsaG013108 AT5G53040.1 55.340 103 40 2 99 201 153 249 5.28e-31 115
MsaG013108 AT4G35590.2 37.313 134 72 2 94 220 192 320 2.40e-19 85.5
MsaG013108 AT4G35590.1 37.313 134 72 2 94 220 242 370 4.40e-19 85.1

Find 41 sgRNAs with CRISPR-Local

Find sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTACTTGTACATTCTTTATA+AGG 0.172964 3:+40995142 None:intergenic
TGATAACCTTCTATGCTTAA+TGG 0.225802 3:+40995563 None:intergenic
AGAGTTTCATTTCGAAATTC+AGG 0.227635 3:+40995611 None:intergenic
TTCCATGAAAGGATCAAAAT+TGG 0.229603 3:+40995643 None:intergenic
AACTTGATGAAAACACAAAA+AGG 0.320323 3:-40994246 MsaT013108.1:CDS
TCTCTAGCAGCTTGAGATAT+TGG 0.323623 3:+40995255 None:intergenic
AAGAAAAGGTGTAGGGATCT+TGG 0.330015 3:-40995207 MsaT013108.1:CDS
GCTCATGGTTATGAGGTTAA+TGG 0.347444 3:-40994182 MsaT013108.1:CDS
TACTTGTACATTCTTTATAA+GGG 0.359802 3:+40995143 None:intergenic
ACTTGATGCTGGAAATTATT+CGG 0.365304 3:-40995418 MsaT013108.1:CDS
GGTGCAGGTACAAGTAATTC+AGG 0.392094 3:+40995584 None:intergenic
CCTGCACCATTAAGCATAGA+AGG 0.395032 3:-40995569 MsaT013108.1:intron
TCAATGACAGACTATGGTTA+TGG 0.408759 3:-40995474 MsaT013108.1:intron
GGCTTACACATTTGAAGAAA+AGG 0.415724 3:-40995221 MsaT013108.1:CDS
CATTCTTTATAAGGGTTTGA+AGG 0.417292 3:+40995151 None:intergenic
TATGAGGTTAATGGAACAAC+AGG 0.443913 3:-40994173 MsaT013108.1:CDS
ATCAAAATTGGTATCTTGCA+TGG 0.445144 3:+40995655 None:intergenic
CTGCTAGAGACCTTAATGTT+GGG 0.489436 3:-40995242 MsaT013108.1:CDS
GAAAGAAATGAAGAAGGTAG+AGG 0.489935 3:-40994284 MsaT013108.1:CDS
GCTTAGACAAGCATGTTTCA+AGG 0.494981 3:-40994224 MsaT013108.1:CDS
CCTTCTATGCTTAATGGTGC+AGG 0.511925 3:+40995569 None:intergenic
ATTGCAGAAAGAAATGAAGA+AGG 0.517898 3:-40994290 MsaT013108.1:CDS
AGAGAAGGCTCATGGTTATG+AGG 0.522137 3:-40994189 MsaT013108.1:CDS
GCTGCTAGAGACCTTAATGT+TGG 0.523622 3:-40995243 MsaT013108.1:CDS
AATGTGTAAGCCCAACATTA+AGG 0.530566 3:+40995232 None:intergenic
ATGTGGAATGAACTTGATGC+TGG 0.531093 3:-40995429 MsaT013108.1:CDS
CACATTTGAAGAAAAGGTGT+AGG 0.540159 3:-40995215 MsaT013108.1:CDS
AGGCTCATTAATTTCCTATG+TGG 0.543250 3:+40995171 None:intergenic
GAATTCAAAGGTGGCCACAT+AGG 0.544869 3:-40995185 MsaT013108.1:CDS
TCAAAATTGGTATCTTGCAT+GGG 0.545683 3:+40995656 None:intergenic
TACTGGAGAAAATGTTGCAA+AGG 0.556786 3:-40995367 MsaT013108.1:CDS
AGGCTAATTACAAGAAGAGA+AGG 0.568624 3:-40994204 MsaT013108.1:CDS
TGTTGCAAAGGAAATTGTGA+AGG 0.572064 3:-40995355 MsaT013108.1:CDS
ACATTTGAAGAAAAGGTGTA+GGG 0.575896 3:-40995214 MsaT013108.1:CDS
TTATTGGTGGTGCAGGAGCA+GGG 0.581874 3:-40994352 MsaT013108.1:intron
TTACAAGAAGAGAAGGCTCA+TGG 0.590126 3:-40994197 MsaT013108.1:CDS
GTAGGGATCTTGGAATTCAA+AGG 0.603743 3:-40995197 MsaT013108.1:CDS
GTTGCAAAGGAAATTGTGAA+GGG 0.628143 3:-40995354 MsaT013108.1:CDS
GCATCAAGTTCATTCCACAT+TGG 0.632758 3:+40995432 None:intergenic
GCAGGTACAAGTAATTCAGG+TGG 0.663503 3:+40995587 None:intergenic
GGGATCTTGGAATTCAAAGG+TGG 0.676630 3:-40995194 MsaT013108.1:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
Chromosome Type Strat End Strand Name
Chr3 gene 40994102 40995675 40994102 ID=MsaG013108
Chr3 mRNA 40994102 40995675 40994102 ID=MsaT013108.1;Parent=MsaG013108
Chr3 exon 40994102 40994359 40994102 ID=MsaT013108.1.exon3;Parent=MsaT013108.1
Chr3 CDS 40994102 40994359 40994102 ID=cds.MsaT013108.1;Parent=MsaT013108.1
Chr3 exon 40995146 40995486 40995146 ID=MsaT013108.1.exon2;Parent=MsaT013108.1
Chr3 CDS 40995146 40995486 40995146 ID=cds.MsaT013108.1;Parent=MsaT013108.1
Chr3 exon 40995570 40995675 40995570 ID=MsaT013108.1.exon1;Parent=MsaT013108.1
Chr3 CDS 40995570 40995675 40995570 ID=cds.MsaT013108.1;Parent=MsaT013108.1
Gene Sequence

>MsaT013108.1

ATGCAAGATACCAATTTTGATCCTTTCATGGAAAATTATTATCCTGAATTTCGAAATGAAACTCTTCCACCTGAATTACTTGTACCTGCACCATTAAGCATAGAAGACTATGGTTATGGTGATGCTAAAAATGTGGTTCCAATGTGGAATGAACTTGATGCTGGAAATTATTCGGATAAACATATCTTTTCTATTAGCAACATTACTGGAGAAAATGTTGCAAAGGAAATTGTGAAGGGTAAGAGATGTAGAGAAGAGAATACTAATAGTGCAAGAATGCTAACAAAAGAAACAATTTCTGAGTACTTCTATGTGCCAATATCTCAAGCTGCTAGAGACCTTAATGTTGGGCTTACACATTTGAAGAAAAGGTGTAGGGATCTTGGAATTCAAAGGTGGCCACATAGGAAATTAATGAGCCTTCAAACCCTTATAAAGAATGTACAAGAGCAGGGTAATGAATGTGATGAAAAAATAAGAAATGCTGTGGAAGTATTGCAGAAAGAAATGAAGAAGGTAGAGGAAAAGCCAGATTTGCAACTTGATGAAAACACAAAAAGGCTTAGACAAGCATGTTTCAAGGCTAATTACAAGAAGAGAAGGCTCATGGTTATGAGGTTAATGGAACAACAGGAGTCTTCTCTCAGTGAAAGTGCAAGTGTTGATGATCACAAAAAGTCAAATTTCTTCTTAACATCATGTTAA
Protein sequence

>MsaT013108.1

MQDTNFDPFMENYYPEFRNETLPPELLVPAPLSIEDYGYGDAKNVVPMWNELDAGNYSDKHIFSISNITGENVAKEIVKGKRCREENTNSARMLTKETISEYFYVPISQAARDLNVGLTHLKKRCRDLGIQRWPHRKLMSLQTLIKNVQEQGNECDEKIRNAVEVLQKEMKKVEEKPDLQLDENTKRLRQACFKANYKKRRLMVMRLMEQQESSLSESASVDDHKKSNFFLTSC*