AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene44273

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44273.t1 MTR_5g032580 94.915 177 3 1 1 171 1 177 6.91e-120 336
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene44273.t1 AT1G26290 42.017 119 60 3 1 115 1 114 1.86e-16 72.4

Find 30 sgRNAs with CRISPR-Local

Find 42 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
AGAATTAGAAGAGGAGATTA+AGG 0.231798 5.4:+22812251 MS.gene44273:CDS
TAACAAAGAAGCAAATAAAA+AGG 0.238986 5.4:+22812425 MS.gene44273:CDS
TCAAGCCCTATTCCTGTAAA+AGG 0.284131 5.4:+22812534 MS.gene44273:CDS
CACTTTCTGAGGTGATTATA+AGG 0.320343 5.4:+22812361 MS.gene44273:CDS
AAGAAGTGAAGAAGATTGAT+TGG 0.347744 5.4:+22812490 MS.gene44273:CDS
TTCAACTCCTCTGCTGAAAC+AGG 0.402447 5.4:-22812195 None:intergenic
ATCTTGCTCGTCGATTGCTT+CGG 0.414612 5.4:+22812286 MS.gene44273:CDS
GGATAAGAAGCTACTTCAAT+TGG 0.436350 5.4:+22812617 MS.gene44273:CDS
TTGATTGGGAGAAGAGTTTG+AGG 0.445900 5.4:+22812505 MS.gene44273:CDS
AGGAACTAAAATTGAAATCA+AGG 0.471855 5.4:+22812398 MS.gene44273:CDS
TTAGAAGAGGAGATTAAGGA+AGG 0.474485 5.4:+22812255 MS.gene44273:CDS
GGTGATTATAAGGATGAGAA+TGG 0.489148 5.4:+22812371 MS.gene44273:CDS
TGATTGGGAGAAGAGTTTGA+GGG 0.505362 5.4:+22812506 MS.gene44273:CDS
AAAGGATAAGATAATGATGA+GGG 0.511757 5.4:+22812578 MS.gene44273:CDS
GCTACTTCAATTGGTGTGGA+AGG 0.513216 5.4:+22812626 MS.gene44273:CDS
TGAGGTTCCTGTTTCAGCAG+AGG 0.528276 5.4:+22812188 MS.gene44273:CDS
ATTATAAGGATGAGAATGGA+AGG 0.528677 5.4:+22812375 MS.gene44273:CDS
AGAAGTGAAGAAGATTGATT+GGG 0.529976 5.4:+22812491 MS.gene44273:CDS
AATAATAACATGGATCATCA+TGG 0.531079 5.4:+22812025 None:intergenic
ATATGTTAGATCAAAGCAAA+AGG 0.536682 5.4:+22812560 MS.gene44273:CDS
CAAAATTAGAGCACTTTCTG+AGG 0.566466 5.4:+22812350 MS.gene44273:CDS
GATTGAAAGAGAATTAGAAG+AGG 0.571961 5.4:+22812242 MS.gene44273:CDS
GAGGGGAAAGAATGCAAGTG+AGG 0.574468 5.4:+22812596 MS.gene44273:CDS
AGAAGCTACTTCAATTGGTG+TGG 0.577937 5.4:+22812622 MS.gene44273:CDS
AAAAGGATAAGATAATGATG+AGG 0.592572 5.4:+22812577 MS.gene44273:CDS
TGGGAGAAGAGTTTGAGGGC+AGG 0.600710 5.4:+22812510 MS.gene44273:CDS
ATAAGGATGAGAATGGAAGG+AGG 0.636221 5.4:+22812378 MS.gene44273:CDS
CATCATGGAATGTACACCAA+AGG 0.652781 5.4:+22812040 MS.gene44273:CDS
AAGGATAAGATAATGATGAG+GGG 0.685809 5.4:+22812579 MS.gene44273:CDS
AACTAAAATTGAAATCAAGG+AGG 0.721284 5.4:+22812401 MS.gene44273:CDS

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AACAAAGAAGCAAATAAAAA+GGG + chr5.4:22812426-22812445 MS.gene44273:CDS 20.0%
!! TAACAAAGAAGCAAATAAAA+AGG + chr5.4:22812425-22812444 MS.gene44273:CDS 20.0%
!!! ACTTCTTTCAAACATTTTTT+GGG - chr5.4:22812477-22812496 None:intergenic 20.0%
!!! AGTTTTGTTGATAAAATTCT+TGG + chr5.4:22812119-22812138 MS.gene44273:intron 20.0%
! AAAAGGATAAGATAATGATG+AGG + chr5.4:22812577-22812596 MS.gene44273:CDS 25.0%
! AAAGGATAAGATAATGATGA+GGG + chr5.4:22812578-22812597 MS.gene44273:CDS 25.0%
! AACTAAAATTGAAATCAAGG+AGG + chr5.4:22812401-22812420 MS.gene44273:CDS 25.0%
! AGGAACTAAAATTGAAATCA+AGG + chr5.4:22812398-22812417 MS.gene44273:CDS 25.0%
! ATATGTTAGATCAAAGCAAA+AGG + chr5.4:22812560-22812579 MS.gene44273:CDS 25.0%
! GTCAAATAAAAATGTTCTTG+AGG + chr5.4:22812170-22812189 MS.gene44273:CDS 25.0%
!!! CACTTCTTTCAAACATTTTT+TGG - chr5.4:22812478-22812497 None:intergenic 25.0%
!!! CATTTTTTGGGTCTAAAATT+TGG - chr5.4:22812465-22812484 None:intergenic 25.0%
AAGAAGTGAAGAAGATTGAT+TGG + chr5.4:22812490-22812509 MS.gene44273:CDS 30.0%
AAGGATAAGATAATGATGAG+GGG + chr5.4:22812579-22812598 MS.gene44273:CDS 30.0%
AGAAGTGAAGAAGATTGATT+GGG + chr5.4:22812491-22812510 MS.gene44273:CDS 30.0%
AGAATTAGAAGAGGAGATTA+AGG + chr5.4:22812251-22812270 MS.gene44273:CDS 30.0%
ATTATAAGGATGAGAATGGA+AGG + chr5.4:22812375-22812394 MS.gene44273:CDS 30.0%
GATTGAAAGAGAATTAGAAG+AGG + chr5.4:22812242-22812261 MS.gene44273:CDS 30.0%
! ATGATCCTTTTACAGGAATA+GGG - chr5.4:22812542-22812561 None:intergenic 30.0%
! CTAACATATGATCCTTTTAC+AGG - chr5.4:22812549-22812568 None:intergenic 30.0%
! TATGATCCTTTTACAGGAAT+AGG - chr5.4:22812543-22812562 None:intergenic 30.0%
CAAAGGTGAAGTGAAATTCT+AGG + chr5.4:22812057-22812076 MS.gene44273:intron 35.0%
CTAGAATTTCACTTCACCTT+TGG - chr5.4:22812059-22812078 None:intergenic 35.0%
GGATAAGAAGCTACTTCAAT+TGG + chr5.4:22812617-22812636 MS.gene44273:CDS 35.0%
GGTGATTATAAGGATGAGAA+TGG + chr5.4:22812371-22812390 MS.gene44273:CDS 35.0%
TTAGAAGAGGAGATTAAGGA+AGG + chr5.4:22812255-22812274 MS.gene44273:CDS 35.0%
! CAAAATTAGAGCACTTTCTG+AGG + chr5.4:22812350-22812369 MS.gene44273:CDS 35.0%
!! CACTTTCTGAGGTGATTATA+AGG + chr5.4:22812361-22812380 MS.gene44273:CDS 35.0%
AGAAGCTACTTCAATTGGTG+TGG + chr5.4:22812622-22812641 MS.gene44273:CDS 40.0%
ATAAGGATGAGAATGGAAGG+AGG + chr5.4:22812378-22812397 MS.gene44273:CDS 40.0%
CATCATGGAATGTACACCAA+AGG + chr5.4:22812040-22812059 MS.gene44273:CDS 40.0%
TCAAGCCCTATTCCTGTAAA+AGG + chr5.4:22812534-22812553 MS.gene44273:CDS 40.0%
TGATTGGGAGAAGAGTTTGA+GGG + chr5.4:22812506-22812525 MS.gene44273:CDS 40.0%
TTGATTGGGAGAAGAGTTTG+AGG + chr5.4:22812505-22812524 MS.gene44273:CDS 40.0%
GCTACTTCAATTGGTGTGGA+AGG + chr5.4:22812626-22812645 MS.gene44273:CDS 45.0%
TTCAACTCCTCTGCTGAAAC+AGG - chr5.4:22812198-22812217 None:intergenic 45.0%
! ATCTTGCTCGTCGATTGCTT+CGG + chr5.4:22812286-22812305 MS.gene44273:CDS 45.0%
!! TCGGATTTTTCAGCAGAGGA+AGG + chr5.4:22812305-22812324 MS.gene44273:CDS 45.0%
!! TGCTTCGGATTTTTCAGCAG+AGG + chr5.4:22812301-22812320 MS.gene44273:CDS 45.0%
GAGGGGAAAGAATGCAAGTG+AGG + chr5.4:22812596-22812615 MS.gene44273:CDS 50.0%
TGAGGTTCCTGTTTCAGCAG+AGG + chr5.4:22812188-22812207 MS.gene44273:CDS 50.0%
TGGGAGAAGAGTTTGAGGGC+AGG + chr5.4:22812510-22812529 MS.gene44273:CDS 55.0%


Chromosome Type Strat End Strand Name
chr5.4 gene 22812034 22812653 22812034 ID=MS.gene44273
chr5.4 mRNA 22812034 22812653 22812034 ID=MS.gene44273.t1;Parent=MS.gene44273
chr5.4 exon 22812034 22812061 22812034 ID=MS.gene44273.t1.exon1;Parent=MS.gene44273.t1
chr5.4 CDS 22812034 22812061 22812034 ID=cds.MS.gene44273.t1;Parent=MS.gene44273.t1
chr5.4 exon 22812166 22812653 22812166 ID=MS.gene44273.t1.exon2;Parent=MS.gene44273.t1
chr5.4 CDS 22812166 22812653 22812166 ID=cds.MS.gene44273.t1;Parent=MS.gene44273.t1
Gene Sequence

>MS.gene44273

ATGGATCATCATGGAATGTACACCAAAGGTGAAGTGAAATTCTAGGTTCACTCAATTAAATTCGTTTTTTTTGTTCATTCTTCATAGTTTTGTTGATAAAATTCTTGGTGTTTTTATTTTTTATTTTTGTAGATATGTCAAATAAAAATGTTCTTGAGGTTCCTGTTTCAGCAGAGGAGTTGAAGATACGAAGTGAGCTTGCAATGATGATTGAAAGAGAATTAGAAGAGGAGATTAAGGAAGGTTTATACAATCTTGCTCGTCGATTGCTTCGGATTTTTCAGCAGAGGAAGGAGAGAGATGCAAAAGTAGATAACAAAATTAGAGCACTTTCTGAGGTGATTATAAGGATGAGAATGGAAGGAGGAACTAAAATTGAAATCAAGGAGGTTAACAAAGAAGCAAATAAAAAGGGTTGTGCTTTTACACCAAATTTTAGACCCAAAAAATGTTTGAAAGAAGTGAAGAAGATTGATTGGGAGAAGAGTTTGAGGGCAGGTTCAAGCCCTATTCCTGTAAAAGGATCATATGTTAGATCAAAGCAAAAGGATAAGATAATGATGAGGGGAAAGAATGCAAGTGAGGATAAGAAGCTACTTCAATTGGTGTGGAAGGTTTAA
Protein sequence

>MS.gene44273.t1

MDHHGMYTKDMSNKNVLEVPVSAEELKIRSELAMMIERELEEEIKEGLYNLARRLLRIFQQRKERDAKVDNKIRALSEVIIRMRMEGGTKIEIKEVNKEANKKGCAFTPNFRPKKCLKEVKKIDWEKSLRAGSSPIPVKGSYVRSKQKDKIMMRGKNASEDKKLLQLVWKV