AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene96662


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene96662.t1 MTR_5g056450 93.038 158 11 0 1 158 1 158 4.78e-98 279
MS.gene96662.t1 MTR_1g041455 58.046 174 50 5 1 158 1 167 1.68e-58 179
MS.gene96662.t1 MTR_1g048880 47.953 171 58 7 1 158 1 153 3.68e-34 117
MS.gene96662.t1 MTR_1g075780 35.032 157 78 6 11 158 4 145 6.06e-14 65.5
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 34 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAAATTGATTTCATTGATT+TGG 0.224195 5.3:+45410380 MS.gene96662:CDS
CATTTGAAGATTCTCCTTCT+AGG 0.234818 5.3:-45410314 None:intergenic
TGAGGAGGAAATTGTCCTTT+AGG 0.244142 5.3:-45410153 None:intergenic
AACCAAAACCAACGGTTATT+CGG 0.300666 5.3:+45410208 MS.gene96662:CDS
GAGGAGGAAATTGTCCTTTA+GGG 0.320849 5.3:-45410152 None:intergenic
AAATCCAATGGATTAACATC+TGG 0.363954 5.3:-45410423 None:intergenic
GGCCGAATAACCGTTGGTTT+TGG 0.365772 5.3:-45410210 None:intergenic
TGCTTCGATTGGTAAGCATT+TGG 0.404776 5.3:-45410291 None:intergenic
CTGGTGAGTTTAGTAATATT+AGG 0.423811 5.3:+45409989 MS.gene96662:CDS
TGAATAAAGCTTTCTGATTG+TGG 0.433760 5.3:-45410115 None:intergenic
TACCAATCGAAGCACCTAGA+AGG 0.448280 5.3:+45410300 MS.gene96662:CDS
CTCCTTCTAGGTGCTTCGAT+TGG 0.488901 5.3:-45410302 None:intergenic
GAAGGAGAATCTTCAAATGA+TGG 0.491518 5.3:+45410318 MS.gene96662:CDS
TAACCCAGATGTTAATCCAT+TGG 0.496678 5.3:+45410419 MS.gene96662:CDS
AATCCAATGGATTAACATCT+GGG 0.500492 5.3:-45410422 None:intergenic
ATCTTCAAATGATGGTACTA+AGG 0.506473 5.3:+45410326 MS.gene96662:CDS
GGCTGAGGCCGAATAACCGT+TGG 0.511549 5.3:-45410216 None:intergenic
AAAGGGTTTCTGCTTGGCTG+AGG 0.532206 5.3:-45410231 None:intergenic
TTCGATTGGTAAGCATTTGG+TGG 0.535435 5.3:-45410288 None:intergenic
CATGATGTGTCAAACTTGGT+AGG 0.541015 5.3:+45410012 MS.gene96662:CDS
TGCAACATCATCACCATGGC+TGG 0.552771 5.3:+45409970 None:intergenic
AATCAGAAAGCTTTATTCAA+CGG 0.559288 5.3:+45410119 MS.gene96662:CDS
TAGGCATGATGTGTCAAACT+TGG 0.564079 5.3:+45410008 MS.gene96662:CDS
AGCTTAAGTGATAAATCCAA+TGG 0.575565 5.3:-45410435 None:intergenic
CAATGTTTGCCACCACATGA+TGG 0.576640 5.3:+45410174 MS.gene96662:CDS
ACGGAGCGTATCAACCCTAA+AGG 0.578711 5.3:+45410138 MS.gene96662:CDS
AACTCACATCGAGTCTCACA+TGG 0.586787 5.3:+45410080 MS.gene96662:CDS
ATTACTAAACTCACCAGCCA+TGG 0.594645 5.3:-45409983 None:intergenic
TCATGTGGTGGCAAACATTG+AGG 0.597472 5.3:-45410171 None:intergenic
GCATTTGCCGATAACCAACA+TGG 0.630189 5.3:-45410260 None:intergenic
ATGATGTGTCAAACTTGGTA+GGG 0.645237 5.3:+45410013 MS.gene96662:CDS
TGTGGTGGCAAACATTGAGG+AGG 0.673338 5.3:-45410168 None:intergenic
GTCTCACATGGAGTACGAAG+AGG 0.675983 5.3:+45410092 MS.gene96662:CDS
AAAATCTTGCCATCATGTGG+TGG 0.685328 5.3:-45410183 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGAAATCAATTTTCTTGAT+AGG - chr5.3:45410375-45410394 None:intergenic 20.0%
!!! GAAAATTGATTTCATTGATT+TGG + chr5.3:45410380-45410399 MS.gene96662:CDS 20.0%
!!! AATCAGAAAGCTTTATTCAA+CGG + chr5.3:45410119-45410138 MS.gene96662:CDS 25.0%
AGCTTAAGTGATAAATCCAA+TGG - chr5.3:45410438-45410457 None:intergenic 30.0%
ATCTTCAAATGATGGTACTA+AGG + chr5.3:45410326-45410345 MS.gene96662:CDS 30.0%
CTGGTGAGTTTAGTAATATT+AGG + chr5.3:45409989-45410008 MS.gene96662:CDS 30.0%
TGAATAAAGCTTTCTGATTG+TGG - chr5.3:45410118-45410137 None:intergenic 30.0%
TTTGAGTGTTTGTGAAAAAG+CGG - chr5.3:45410053-45410072 None:intergenic 30.0%
!! AAATCCAATGGATTAACATC+TGG - chr5.3:45410426-45410445 None:intergenic 30.0%
!! AATCCAATGGATTAACATCT+GGG - chr5.3:45410425-45410444 None:intergenic 30.0%
!! GATTTTTCAACCAAAACCAA+CGG + chr5.3:45410200-45410219 MS.gene96662:CDS 30.0%
AACCAAAACCAACGGTTATT+CGG + chr5.3:45410208-45410227 MS.gene96662:CDS 35.0%
ATGATGTGTCAAACTTGGTA+GGG + chr5.3:45410013-45410032 MS.gene96662:CDS 35.0%
CATTTGAAGATTCTCCTTCT+AGG - chr5.3:45410317-45410336 None:intergenic 35.0%
GAAGGAGAATCTTCAAATGA+TGG + chr5.3:45410318-45410337 MS.gene96662:CDS 35.0%
TAACCCAGATGTTAATCCAT+TGG + chr5.3:45410419-45410438 MS.gene96662:CDS 35.0%
TGAAAAATCTTGCCATCATG+TGG - chr5.3:45410189-45410208 None:intergenic 35.0%
AAAATCTTGCCATCATGTGG+TGG - chr5.3:45410186-45410205 None:intergenic 40.0%
AACCAACATGGCCGAAAAAA+GGG - chr5.3:45410251-45410270 None:intergenic 40.0%
CATGATGTGTCAAACTTGGT+AGG + chr5.3:45410012-45410031 MS.gene96662:CDS 40.0%
GAGGAGGAAATTGTCCTTTA+GGG - chr5.3:45410155-45410174 None:intergenic 40.0%
TAACCAACATGGCCGAAAAA+AGG - chr5.3:45410252-45410271 None:intergenic 40.0%
TAGGCATGATGTGTCAAACT+TGG + chr5.3:45410008-45410027 MS.gene96662:CDS 40.0%
TGAGGAGGAAATTGTCCTTT+AGG - chr5.3:45410156-45410175 None:intergenic 40.0%
TGCTTCGATTGGTAAGCATT+TGG - chr5.3:45410294-45410313 None:intergenic 40.0%
TTCGATTGGTAAGCATTTGG+TGG - chr5.3:45410291-45410310 None:intergenic 40.0%
!! TTTTCGGCCATGTTGGTTAT+CGG + chr5.3:45410253-45410272 MS.gene96662:CDS 40.0%
!!! CCAAGCAGAAACCCTTTTTT+CGG + chr5.3:45410237-45410256 MS.gene96662:CDS 40.0%
AACTCACATCGAGTCTCACA+TGG + chr5.3:45410080-45410099 MS.gene96662:CDS 45.0%
CAATGTTTGCCACCACATGA+TGG + chr5.3:45410174-45410193 MS.gene96662:CDS 45.0%
CCGAAAAAAGGGTTTCTGCT+TGG - chr5.3:45410240-45410259 None:intergenic 45.0%
GCATTTGCCGATAACCAACA+TGG - chr5.3:45410263-45410282 None:intergenic 45.0%
TCATGTGGTGGCAAACATTG+AGG - chr5.3:45410174-45410193 None:intergenic 45.0%
! TACCAATCGAAGCACCTAGA+AGG + chr5.3:45410300-45410319 MS.gene96662:CDS 45.0%
!!! AACCCTTTTTTCGGCCATGT+TGG + chr5.3:45410246-45410265 MS.gene96662:CDS 45.0%
AAAGGGTTTCTGCTTGGCTG+AGG - chr5.3:45410234-45410253 None:intergenic 50.0%
ACGGAGCGTATCAACCCTAA+AGG + chr5.3:45410138-45410157 MS.gene96662:CDS 50.0%
CTCCTTCTAGGTGCTTCGAT+TGG - chr5.3:45410305-45410324 None:intergenic 50.0%
GTCTCACATGGAGTACGAAG+AGG + chr5.3:45410092-45410111 MS.gene96662:CDS 50.0%
TGTGGTGGCAAACATTGAGG+AGG - chr5.3:45410171-45410190 None:intergenic 50.0%
!!! GGCCGAATAACCGTTGGTTT+TGG - chr5.3:45410213-45410232 None:intergenic 50.0%
GGCTGAGGCCGAATAACCGT+TGG - chr5.3:45410219-45410238 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr5.3 gene 45409985 45410461 45409985 ID=MS.gene96662
chr5.3 mRNA 45409985 45410461 45409985 ID=MS.gene96662.t1;Parent=MS.gene96662
chr5.3 exon 45409985 45410461 45409985 ID=MS.gene96662.t1.exon1;Parent=MS.gene96662.t1
chr5.3 CDS 45409985 45410461 45409985 ID=cds.MS.gene96662.t1;Parent=MS.gene96662.t1
Gene Sequence

>MS.gene96662

ATGGCTGGTGAGTTTAGTAATATTAGGCATGATGTGTCAAACTTGGTAGGGTGTAAATATTGCAACCGCTTTTTCACAAACACTCAAACACTCGTAACTCACATCGAGTCTCACATGGAGTACGAAGAGGCCACAATCAGAAAGCTTTATTCAACGGAGCGTATCAACCCTAAAGGACAATTTCCTCCTCAATGTTTGCCACCACATGATGGCAAGATTTTTCAACCAAAACCAACGGTTATTCGGCCTCAGCCAAGCAGAAACCCTTTTTTCGGCCATGTTGGTTATCGGCAAATGCAACTTCCACCAAATGCTTACCAATCGAAGCACCTAGAAGGAGAATCTTCAAATGATGGTACTAAGGCATATATCAAGCAACTTGAGAAACCTATCAAGAAAATTGATTTCATTGATTTGGTTAATAATGATGATGATAACCCAGATGTTAATCCATTGGATTTATCACTTAAGCTCTAG

Protein sequence

>MS.gene96662.t1

MAGEFSNIRHDVSNLVGCKYCNRFFTNTQTLVTHIESHMEYEEATIRKLYSTERINPKGQFPPQCLPPHDGKIFQPKPTVIRPQPSRNPFFGHVGYRQMQLPPNAYQSKHLEGESSNDGTKAYIKQLEKPIKKIDFIDLVNNDDDNPDVNPLDLSLKL