AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene003483

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003483.t1 MTR_4g074310 81.507 146 27 0 1 146 1 146 1.52e-85 249
MS.gene003483.t1 MTR_7g057230 69.753 162 28 1 1 141 296 457 1.25e-69 221
MS.gene003483.t1 MTR_4g074320 84.685 111 17 0 1 111 58 168 2.36e-66 200
MS.gene003483.t1 MTR_6g047750 42.767 159 65 3 1 136 297 452 2.66e-30 114
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene003483.t1 AT5G52510 51.613 93 40 2 1 93 270 357 1.80e-18 81.3

Find 24 sgRNAs with CRISPR-Local

Find 37 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GAAGCTGCCACCGCAATTTC+TGG 0.192643 4.2:-34418553 MS.gene003483:CDS
GAAAACCATCGGAGAACTTT+TGG 0.213935 4.2:-34418107 MS.gene003483:CDS
TTGCTTCAAGCTCTCTTTCA+TGG 0.245115 4.2:-34418326 MS.gene003483:CDS
GAAATTTGATCGTTGGTTAT+TGG 0.249208 4.2:-34418467 MS.gene003483:CDS
AGCTTCGAGGATTGCAATAT+TGG 0.276395 4.2:+34418300 None:intergenic
AACGATCAAATTTCAGTCTT+GGG 0.364738 4.2:+34418476 None:intergenic
CAACGATCAAATTTCAGTCT+TGG 0.369194 4.2:+34418475 None:intergenic
GATATGCTAAGTTTAGGAAT+TGG 0.372716 4.2:-34418081 MS.gene003483:CDS
TGAAAATCCACCTGCAATAG+TGG 0.395795 4.2:-34418404 MS.gene003483:CDS
ATATGCTAAGTTTAGGAATT+GGG 0.398441 4.2:-34418080 MS.gene003483:CDS
TGGGTCGATATGCTAAGTTT+AGG 0.418780 4.2:-34418087 MS.gene003483:CDS
TGTGTTGTGGAGTTTGATAA+TGG 0.448667 4.2:-34418241 MS.gene003483:intron
TGAAGCAAATAGAGTGATCA+AGG 0.451795 4.2:+34418341 None:intergenic
TATCTTCAAATGTAGCTTCG+AGG 0.464718 4.2:+34418287 None:intergenic
CAAGACTGAAATTTGATCGT+TGG 0.476052 4.2:-34418474 MS.gene003483:CDS
TCGTTGGTTATTGGATTGCA+TGG 0.560143 4.2:-34418458 MS.gene003483:CDS
CGTGAAGAATCTTTGTGTTG+TGG 0.574036 4.2:-34418254 MS.gene003483:CDS
AAATAGAGTGATCAAGGAGA+AGG 0.585337 4.2:+34418347 None:intergenic
TCGACCCAAAAGTTCTCCGA+TGG 0.589819 4.2:+34418102 None:intergenic
GACGTTCACCGTCACAGTCG+TGG 0.601097 4.2:+34418144 None:intergenic
GACGAGAATCTGAAAACCAT+CGG 0.623313 4.2:-34418118 MS.gene003483:CDS
GTGTTTGAGAGAAACGAGAG+AGG 0.625259 4.2:+34418503 None:intergenic
GCTGCCACCGCAATTTCTGG+AGG 0.664192 4.2:-34418550 MS.gene003483:CDS
GTTGAAGACCACGACTGTGA+CGG 0.707788 4.2:-34418152 MS.gene003483:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! ATATGCTAAGTTTAGGAATT+GGG - chr4.2:34418551-34418570 MS.gene003483:CDS 25.0%
AACGATCAAATTTCAGTCTT+GGG + chr4.2:34418158-34418177 None:intergenic 30.0%
GATATGCTAAGTTTAGGAAT+TGG - chr4.2:34418550-34418569 MS.gene003483:CDS 30.0%
! GAAATTTGATCGTTGGTTAT+TGG - chr4.2:34418164-34418183 MS.gene003483:intron 30.0%
AAAAATTCCACTATTGCAGG+TGG + chr4.2:34418237-34418256 None:intergenic 35.0%
AAATAGAGTGATCAAGGAGA+AGG + chr4.2:34418287-34418306 None:intergenic 35.0%
CAACGATCAAATTTCAGTCT+TGG + chr4.2:34418159-34418178 None:intergenic 35.0%
CAAGACTGAAATTTGATCGT+TGG - chr4.2:34418157-34418176 MS.gene003483:CDS 35.0%
CTGAAAAATTCCACTATTGC+AGG + chr4.2:34418240-34418259 None:intergenic 35.0%
TATCTTCAAATGTAGCTTCG+AGG + chr4.2:34418347-34418366 None:intergenic 35.0%
TGAAGCAAATAGAGTGATCA+AGG + chr4.2:34418293-34418312 None:intergenic 35.0%
TGGAGGAAAAATGGAATATG+CGG - chr4.2:34418098-34418117 MS.gene003483:CDS 35.0%
TGTGTTGTGGAGTTTGATAA+TGG - chr4.2:34418390-34418409 MS.gene003483:CDS 35.0%
! AAAACCATCGGAGAACTTTT+GGG - chr4.2:34418525-34418544 MS.gene003483:CDS 35.0%
! CATTTTTCCTCCAGAAATTG+CGG + chr4.2:34418091-34418110 None:intergenic 35.0%
!! GTGGAGTTTGATAATGGTAA+TGG - chr4.2:34418396-34418415 MS.gene003483:CDS 35.0%
AAACTCCATGCACGTTTCAA+CGG - chr4.2:34418444-34418463 MS.gene003483:CDS 40.0%
AGCTTCGAGGATTGCAATAT+TGG + chr4.2:34418334-34418353 None:intergenic 40.0%
AGGAAAAATGGAATATGCGG+AGG - chr4.2:34418101-34418120 MS.gene003483:CDS 40.0%
CGTGAAGAATCTTTGTGTTG+TGG - chr4.2:34418377-34418396 MS.gene003483:CDS 40.0%
GACGAGAATCTGAAAACCAT+CGG - chr4.2:34418513-34418532 MS.gene003483:CDS 40.0%
TGAAAATCCACCTGCAATAG+TGG - chr4.2:34418227-34418246 MS.gene003483:intron 40.0%
TGGGTCGATATGCTAAGTTT+AGG - chr4.2:34418544-34418563 MS.gene003483:CDS 40.0%
TTGCTTCAAGCTCTCTTTCA+TGG - chr4.2:34418305-34418324 MS.gene003483:CDS 40.0%
! CGCAATTTCTGGAGGAAAAA+TGG - chr4.2:34418089-34418108 MS.gene003483:CDS 40.0%
! GAAAACCATCGGAGAACTTT+TGG - chr4.2:34418524-34418543 MS.gene003483:CDS 40.0%
! TCGTTGGTTATTGGATTGCA+TGG - chr4.2:34418173-34418192 MS.gene003483:intron 40.0%
! TGAAACGTGCATGGAGTTTT+TGG + chr4.2:34418443-34418462 None:intergenic 40.0%
GTGTTTGAGAGAAACGAGAG+AGG + chr4.2:34418131-34418150 None:intergenic 45.0%
GTTAACCGTTGAAACGTGCA+TGG + chr4.2:34418452-34418471 None:intergenic 45.0%
! TTTTCCTCCAGAAATTGCGG+TGG + chr4.2:34418088-34418107 None:intergenic 45.0%
!! GTGCATGGAGTTTTTGGAGA+AGG + chr4.2:34418437-34418456 None:intergenic 45.0%
GTTGAAGACCACGACTGTGA+CGG - chr4.2:34418479-34418498 MS.gene003483:CDS 50.0%
TCGACCCAAAAGTTCTCCGA+TGG + chr4.2:34418532-34418551 None:intergenic 50.0%
GAAGCTGCCACCGCAATTTC+TGG - chr4.2:34418078-34418097 MS.gene003483:CDS 55.0%
GACGTTCACCGTCACAGTCG+TGG + chr4.2:34418490-34418509 None:intergenic 60.0%
! GCTGCCACCGCAATTTCTGG+AGG - chr4.2:34418081-34418100 MS.gene003483:CDS 60.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 34418075 34418578 34418075 ID=MS.gene003483
chr4.2 mRNA 34418075 34418578 34418075 ID=MS.gene003483.t1;Parent=MS.gene003483
chr4.2 exon 34418242 34418578 34418242 ID=MS.gene003483.t1.exon1;Parent=MS.gene003483.t1
chr4.2 CDS 34418242 34418578 34418242 ID=cds.MS.gene003483.t1;Parent=MS.gene003483.t1
chr4.2 exon 34418075 34418178 34418075 ID=MS.gene003483.t1.exon2;Parent=MS.gene003483.t1
chr4.2 CDS 34418075 34418178 34418075 ID=cds.MS.gene003483.t1;Parent=MS.gene003483.t1
Gene Sequence

>MS.gene003483

ATGGAAGCTGCCACCGCAATTTCTGGAGGAAAAATGGAATATGCGGAGGAGATCCTCTCTCGTTTCTCTCAAACACAAAACCCAAGACTGAAATTTGATCGTTGGTTATTGGATTGCATGGCTTTAGCGCTGAAATCGCGTGTGAATAACATTGAAAATCCACCTGCAATAGTGGAATTTTTCAGCAAAGAACATGCTAAGTCGACTCACCTTCTCCTTGATCACTCTATTTGCTTCAAGCTCTCTTTCATGGCTGCCAATATTGCAATCCTCGAAGCTACATTTGAAGATACAACAAAGAGCGTGAAGAATCTTTGTGTTGTGGAGTTTGATAATGGTAATGGAAAACAATACATAAACCTTCTCCAAAAACTCCATGCACGTTTCAACGGTTAACTAGCAATGTTGAAGACCACGACTGTGACGGTGAACGTCGACGACGAGAATCTGAAAACCATCGGAGAACTTTTGGGTCGATATGCTAAGTTTAGGAATTGGGTTTGA
Protein sequence

>MS.gene003483.t1

MEAATAISGGKMEYAEEILSRFSQTQNPRLKFDRWLLDCMALALKSRVNNIENPPAIVEFFSKEHAKSTHLLLDHSICFKLSFMAANIAILEATFEDTTKSVKNLCVVEFDNAMLKTTTVTVNVDDENLKTIGELLGRYAKFRNWV