AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene36320

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene36320.t1 MTR_2g101770 55.446 101 43 2 1 100 1 100 5.04e-29 102
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene36320.t1 AT1G79850 37.234 94 51 3 10 100 15 103 9.30e-11 55.5

Find 26 sgRNAs with CRISPR-Local

Find 31 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TCCTAATACGTTCTTGTATT+TGG 0.030837 2.2:-1945329 None:intergenic
CCTAATACGTTCTTGTATTT+GGG 0.263359 2.2:-1945328 None:intergenic
CCCAAATACAAGAACGTATT+AGG 0.286427 2.2:+1945328 MS.gene36320:CDS
TTTGATTGATGGAAGGGATT+GGG 0.366091 2.2:-1945221 None:intergenic
TTGATGGAAGGGATTGGGGC+TGG 0.379607 2.2:-1945216 None:intergenic
TGATGGAAGGGATTGGGGCT+GGG 0.417770 2.2:-1945215 None:intergenic
CCATTGTTGCCGTTGAGAAA+TGG 0.447061 2.2:-1945144 None:intergenic
CTTTGATTGATGGAAGGGAT+TGG 0.447339 2.2:-1945222 None:intergenic
TAGGATGAAGAAGAAGTATC+AGG 0.470403 2.2:+1945347 MS.gene36320:CDS
CATAGCTTTGATTGATGGAA+GGG 0.486622 2.2:-1945227 None:intergenic
TTGATTGATGGAAGGGATTG+GGG 0.489144 2.2:-1945220 None:intergenic
GGATAGAGAGAGTGTGGATG+TGG 0.489261 2.2:-1945194 None:intergenic
ACGTTCTTGTATTTGGGATG+AGG 0.490100 2.2:-1945322 None:intergenic
TCATAGCTTTGATTGATGGA+AGG 0.545842 2.2:-1945228 None:intergenic
GGGCTGGGATAGAGAGAGTG+TGG 0.548257 2.2:-1945200 None:intergenic
CCATTTCTCAACGGCAACAA+TGG 0.562511 2.2:+1945144 MS.gene36320:CDS
AAATGGTGTTGAGAGCGTGC+TGG 0.564865 2.2:-1945127 None:intergenic
AATCAAAGCTATGAAAACAA+TGG 0.574259 2.2:+1945237 MS.gene36320:CDS
AATGGTGTTGAGAGCGTGCT+GGG 0.576801 2.2:-1945126 None:intergenic
CAACGACAAAACCGTGTCTG+TGG 0.582090 2.2:+1945282 MS.gene36320:CDS
AAAGCTATGAAAACAATGGA+AGG 0.583695 2.2:+1945241 MS.gene36320:CDS
GGCTTTGAGAGACGATGTGA+GGG 0.602003 2.2:-1945172 None:intergenic
ACGAGTAACTTCCACAGACA+CGG 0.613173 2.2:-1945293 None:intergenic
CTCTCAACACCATTTCTCAA+CGG 0.613389 2.2:+1945135 MS.gene36320:CDS
GGGCTTTGAGAGACGATGTG+AGG 0.682697 2.2:-1945173 None:intergenic
GATAGAGAGAGTGTGGATGT+GGG 0.697666 2.2:-1945193 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AATCAAAGCTATGAAAACAA+TGG + chr2.2:1945237-1945256 MS.gene36320:CDS 25.0%
AAAGCTATGAAAACAATGGA+AGG + chr2.2:1945241-1945260 MS.gene36320:CDS 30.0%
CCTAATACGTTCTTGTATTT+GGG - chr2.2:1945331-1945350 None:intergenic 30.0%
TCCTAATACGTTCTTGTATT+TGG - chr2.2:1945332-1945351 None:intergenic 30.0%
!!! GTTTTCATAGCTTTGATTGA+TGG - chr2.2:1945235-1945254 None:intergenic 30.0%
CCCAAATACAAGAACGTATT+AGG + chr2.2:1945328-1945347 MS.gene36320:CDS 35.0%
TTTGATTGATGGAAGGGATT+GGG - chr2.2:1945224-1945243 None:intergenic 35.0%
! CCTGAAAACGTTTTCAAAGT+TGG + chr2.2:1945378-1945397 MS.gene36320:CDS 35.0%
!! CATAGCTTTGATTGATGGAA+GGG - chr2.2:1945230-1945249 None:intergenic 35.0%
!! CCAACTTTGAAAACGTTTTC+AGG - chr2.2:1945381-1945400 None:intergenic 35.0%
!! TAGGATGAAGAAGAAGTATC+AGG + chr2.2:1945347-1945366 MS.gene36320:CDS 35.0%
!! TCATAGCTTTGATTGATGGA+AGG - chr2.2:1945231-1945250 None:intergenic 35.0%
CTCTCAACACCATTTCTCAA+CGG + chr2.2:1945135-1945154 MS.gene36320:CDS 40.0%
CTTTGATTGATGGAAGGGAT+TGG - chr2.2:1945225-1945244 None:intergenic 40.0%
TTGATTGATGGAAGGGATTG+GGG - chr2.2:1945223-1945242 None:intergenic 40.0%
! ACGTTCTTGTATTTGGGATG+AGG - chr2.2:1945325-1945344 None:intergenic 40.0%
ACGAGTAACTTCCACAGACA+CGG - chr2.2:1945296-1945315 None:intergenic 45.0%
CCATTGTTGCCGTTGAGAAA+TGG - chr2.2:1945147-1945166 None:intergenic 45.0%
CCATTTCTCAACGGCAACAA+TGG + chr2.2:1945144-1945163 MS.gene36320:CDS 45.0%
! GATAGAGAGAGTGTGGATGT+GGG - chr2.2:1945196-1945215 None:intergenic 45.0%
CAACGACAAAACCGTGTCTG+TGG + chr2.2:1945282-1945301 MS.gene36320:CDS 50.0%
! AAATGGTGTTGAGAGCGTGC+TGG - chr2.2:1945130-1945149 None:intergenic 50.0%
! AATGGTGTTGAGAGCGTGCT+GGG - chr2.2:1945129-1945148 None:intergenic 50.0%
! GGATAGAGAGAGTGTGGATG+TGG - chr2.2:1945197-1945216 None:intergenic 50.0%
!! AGACACGGTTTTGTCGTTGG+TGG - chr2.2:1945281-1945300 None:intergenic 50.0%
!! CACAGACACGGTTTTGTCGT+TGG - chr2.2:1945284-1945303 None:intergenic 50.0%
!! GGCTTTGAGAGACGATGTGA+GGG - chr2.2:1945175-1945194 None:intergenic 50.0%
TGATGGAAGGGATTGGGGCT+GGG - chr2.2:1945218-1945237 None:intergenic 55.0%
TTGATGGAAGGGATTGGGGC+TGG - chr2.2:1945219-1945238 None:intergenic 55.0%
!! GGGCTTTGAGAGACGATGTG+AGG - chr2.2:1945176-1945195 None:intergenic 55.0%
GGGCTGGGATAGAGAGAGTG+TGG - chr2.2:1945203-1945222 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr2.2 gene 1945108 1945422 1945108 ID=MS.gene36320
chr2.2 mRNA 1945108 1945422 1945108 ID=MS.gene36320.t1;Parent=MS.gene36320
chr2.2 exon 1945108 1945422 1945108 ID=MS.gene36320.t1.exon1;Parent=MS.gene36320.t1
chr2.2 CDS 1945108 1945422 1945108 ID=cds.MS.gene36320.t1;Parent=MS.gene36320.t1
Gene Sequence

>MS.gene36320

ATGTGGCTTCTGCAACTTCCCAGCACGCTCTCAACACCATTTCTCAACGGCAACAATGGCGTCGCCCTCACATCGTCTCTCAAAGCCCACATCCACACTCTCTCTATCCCAGCCCCAATCCCTTCCATCAATCAAAGCTATGAAAACAATGGAAGGAAAAGTTGTGTGTGCCACCAACGACAAAACCGTGTCTGTGGAAGTTACTCGTTTAGCACCTCATCCCAAATACAAGAACGTATTAGGATGAAGAAGAAGTATCAGGCTCATGATCCTGAAAACGTTTTCAAAGTTGGTGATGTTGATTCAGCTTTGTAA
Protein sequence

>MS.gene36320.t1

MWLLQLPSTLSTPFLNGNNGVALTSSLKAHIHTLSIPAPIPSINQSYENNGRKSCVCHQRQNRVCGSYSFSTSSQIQERIRMKKKYQAHDPENVFKVGDVDSAL