AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene09040

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09040.t1 MTR_8g080380 91.398 93 8 0 1 93 92 184 1.05e-60 183
MS.gene09040.t1 MTR_3g085510 77.419 93 21 0 1 93 1 93 3.48e-50 153
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene09040.t1 AT4G40042 77.215 79 18 0 1 79 1 79 3.42e-42 133
MS.gene09040.t1 AT2G22425 72.043 93 25 1 1 93 1 92 6.01e-42 132
MS.gene09040.t1 AT2G22425 72.043 93 25 1 1 93 1 92 6.01e-42 132

Find 28 sgRNAs with CRISPR-Local

Find 27 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GCATTTGCTGTGATTGCATT+TGG 0.297854 4.2:+14587147 MS.gene09040:CDS
GCCCCATTCACAGATGGTTC+TGG 0.371797 4.2:-14587324 None:intergenic
CATATGTGAGGATCATTGTT+TGG 0.377646 4.2:-14587194 None:intergenic
TTCACAGATGGTTCTGGCTT+AGG 0.396810 4.2:-14587318 None:intergenic
CTTTGCTTGATTAGATGGAT+TGG 0.415898 4.2:+14587079 None:intergenic
ATGGTTGAAGAAGGGCCAAT+TGG 0.421141 4.2:-14587253 None:intergenic
AGCCAGAACCATCTGTGAAT+GGG 0.423930 4.2:+14587322 MS.gene09040:CDS
CTCGGGTCCAACCACTTAAG+AGG 0.441788 4.2:-14587279 None:intergenic
TCAACCATCACCCTCTTAAG+TGG 0.455788 4.2:+14587268 MS.gene09040:CDS
CATTAGTCACTATTCCCAAT+TGG 0.473943 4.2:+14587238 MS.gene09040:CDS
TTTGCTTGATTAGATGGATT+GGG 0.484747 4.2:+14587080 None:intergenic
TGGTTGAAGAAGGGCCAATT+GGG 0.491266 4.2:-14587252 None:intergenic
AAGCCAGAACCATCTGTGAA+TGG 0.495835 4.2:+14587321 MS.gene09040:CDS
GCTGTGATTGCATTTGGAGC+TGG 0.523448 4.2:+14587153 MS.gene09040:CDS
AAGAGGGTGATGGTTGAAGA+AGG 0.527062 4.2:-14587262 None:intergenic
TTTGTAGCCCCATTCACAGA+TGG 0.528383 4.2:-14587330 None:intergenic
ACAATGATCCTCACATATGC+TGG 0.532761 4.2:+14587198 MS.gene09040:CDS
CCATCACCCTCTTAAGTGGT+TGG 0.557168 4.2:+14587272 MS.gene09040:CDS
ATTTGGAGCTGGATATCTCA+CGG 0.563264 4.2:+14587164 MS.gene09040:CDS
CTTGATTAGATGGATTGGGA+AGG 0.597000 4.2:+14587084 None:intergenic
TCGGGTCCAACCACTTAAGA+GGG 0.612466 4.2:-14587278 None:intergenic
GCCAGAACCATCTGTGAATG+GGG 0.614435 4.2:+14587323 MS.gene09040:CDS
AGAGGGTGATGGTTGAAGAA+GGG 0.639069 4.2:-14587261 None:intergenic
CCAACCACTTAAGAGGGTGA+TGG 0.648150 4.2:-14587272 None:intergenic
GTGGTTGGACCCGAGCGAAG+CGG 0.659606 4.2:+14587287 MS.gene09040:CDS
CAACACCACCAGCATATGTG+AGG 0.672885 4.2:-14587206 None:intergenic
ATGATCCTCACATATGCTGG+TGG 0.731619 4.2:+14587201 MS.gene09040:CDS
ATTGGGAATAGTGACTAATG+TGG 0.776405 4.2:-14587235 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
ATTGGGAATAGTGACTAATG+TGG - chr4.2:14587238-14587257 None:intergenic 35.0%
CATATGTGAGGATCATTGTT+TGG - chr4.2:14587197-14587216 None:intergenic 35.0%
CATTAGTCACTATTCCCAAT+TGG + chr4.2:14587238-14587257 MS.gene09040:CDS 35.0%
ACAATGATCCTCACATATGC+TGG + chr4.2:14587198-14587217 MS.gene09040:CDS 40.0%
! ATTTGGAGCTGGATATCTCA+CGG + chr4.2:14587164-14587183 MS.gene09040:CDS 40.0%
!! GCATTTGCTGTGATTGCATT+TGG + chr4.2:14587147-14587166 MS.gene09040:CDS 40.0%
AAGCCAGAACCATCTGTGAA+TGG + chr4.2:14587321-14587340 MS.gene09040:CDS 45.0%
AGCCAGAACCATCTGTGAAT+GGG + chr4.2:14587322-14587341 MS.gene09040:CDS 45.0%
ATGATCCTCACATATGCTGG+TGG + chr4.2:14587201-14587220 MS.gene09040:CDS 45.0%
ATGGTTGAAGAAGGGCCAAT+TGG - chr4.2:14587256-14587275 None:intergenic 45.0%
TCAACCATCACCCTCTTAAG+TGG + chr4.2:14587268-14587287 MS.gene09040:CDS 45.0%
TGGTTGAAGAAGGGCCAATT+GGG - chr4.2:14587255-14587274 None:intergenic 45.0%
TTTGTAGCCCCATTCACAGA+TGG - chr4.2:14587333-14587352 None:intergenic 45.0%
! AAGAGGGTGATGGTTGAAGA+AGG - chr4.2:14587265-14587284 None:intergenic 45.0%
! AGAGGGTGATGGTTGAAGAA+GGG - chr4.2:14587264-14587283 None:intergenic 45.0%
!! TTCACAGATGGTTCTGGCTT+AGG - chr4.2:14587321-14587340 None:intergenic 45.0%
CAACACCACCAGCATATGTG+AGG - chr4.2:14587209-14587228 None:intergenic 50.0%
CCAACCACTTAAGAGGGTGA+TGG - chr4.2:14587275-14587294 None:intergenic 50.0%
CCATCACCCTCTTAAGTGGT+TGG + chr4.2:14587272-14587291 MS.gene09040:CDS 50.0%
GCCAGAACCATCTGTGAATG+GGG + chr4.2:14587323-14587342 MS.gene09040:CDS 50.0%
TCGGGTCCAACCACTTAAGA+GGG - chr4.2:14587281-14587300 None:intergenic 50.0%
! GCTGTGATTGCATTTGGAGC+TGG + chr4.2:14587153-14587172 MS.gene09040:CDS 50.0%
CTCGGGTCCAACCACTTAAG+AGG - chr4.2:14587282-14587301 None:intergenic 55.0%
GCCCCATTCACAGATGGTTC+TGG - chr4.2:14587327-14587346 None:intergenic 55.0%
! GATGCTTTTCCGCTTCGCTC+GGG - chr4.2:14587299-14587318 None:intergenic 55.0%
! GGATGCTTTTCCGCTTCGCT+CGG - chr4.2:14587300-14587319 None:intergenic 55.0%
GTGGTTGGACCCGAGCGAAG+CGG + chr4.2:14587287-14587306 MS.gene09040:CDS 65.0%


Chromosome Type Strat End Strand Name
chr4.2 gene 14587093 14587374 14587093 ID=MS.gene09040
chr4.2 mRNA 14587093 14587374 14587093 ID=MS.gene09040.t1;Parent=MS.gene09040
chr4.2 exon 14587093 14587374 14587093 ID=MS.gene09040.t1.exon1;Parent=MS.gene09040.t1
chr4.2 CDS 14587093 14587374 14587093 ID=cds.MS.gene09040.t1;Parent=MS.gene09040.t1
Gene Sequence

>MS.gene09040

ATGGATTGGGAAGGACAAAAGCTAGCAGAGCAGCTGATGCAGATAATGCTGCTTGCATTTGCTGTGATTGCATTTGGAGCTGGATATCTCACGGCTTCTTTCCAAACAATGATCCTCACATATGCTGGTGGTGTTGTTCTCACCACATTAGTCACTATTCCCAATTGGCCCTTCTTCAACCATCACCCTCTTAAGTGGTTGGACCCGAGCGAAGCGGAAAAGCATCCTAAGCCAGAACCATCTGTGAATGGGGCTACAAAGAAAAAATCCGTTAAAAAGTAG
Protein sequence

>MS.gene09040.t1

MDWEGQKLAEQLMQIMLLAFAVIAFGAGYLTASFQTMILTYAGGVVLTTLVTIPNWPFFNHHPLKWLDPSEAEKHPKPEPSVNGATKKKSVKK