AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene63140

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene63140.t1 MTR_2g062330 90.000 120 11 1 3 122 23 141 6.47e-74 216
MS.gene63140.t1 MTR_2g012700 84.426 122 19 0 1 122 1 122 1.68e-72 212
MS.gene63140.t1 MTR_0010s0310 42.857 91 50 1 22 110 150 240 3.56e-16 72.0
MS.gene63140.t1 MTR_7g117590 32.308 130 69 4 7 119 44 171 3.91e-16 70.5
MS.gene63140.t1 MTR_7g117585 32.000 100 66 1 18 115 42 141 8.94e-15 66.6
MS.gene63140.t1 MTR_3g008190 27.835 97 70 0 24 120 6 102 1.50e-13 62.0
MS.gene63140.t1 MTR_5g071410 38.202 89 54 1 27 115 177 264 2.01e-13 65.1
MS.gene63140.t1 MTR_5g078270 36.264 91 56 1 22 110 208 298 1.67e-11 59.7
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score

Find 24 sgRNAs with CRISPR-Local

Find 28 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TAAGGTTATTGCTTCTATTT+TGG 0.132946 8.1:-43549663 MS.gene63140:CDS
GAAGTCAATGGTACTGAATT+AGG 0.159497 8.1:-43549722 MS.gene63140:CDS
TGTATGCTACCGTCGTTAAC+TGG 0.211996 8.1:-43549303 MS.gene63140:CDS
AAAATATCGATGTCCATTAT+TGG 0.234776 8.1:-43549691 MS.gene63140:CDS
TACCGGTTTCTTCATCAAAA+AGG 0.272684 8.1:+43549470 None:intergenic
TAACCTTATGCTTCCAATAA+TGG 0.277357 8.1:+43549678 None:intergenic
ATCAAAGTCATAAGATTTAC+CGG 0.326757 8.1:+43549453 None:intergenic
CCTCGATGTGTTGCGGAGAA+TGG 0.338723 8.1:-43549520 MS.gene63140:CDS
TTTGGATGGAAACAATGTTT+TGG 0.356448 8.1:-43549645 MS.gene63140:intron
TAAGGAAACATGAATGAGAT+TGG 0.380138 8.1:-43549749 None:intergenic
GTACAACTTTGTTCTTGAAA+AGG 0.417029 8.1:-43549380 MS.gene63140:CDS
AAGTCAATGGTACTGAATTA+GGG 0.437113 8.1:-43549721 MS.gene63140:CDS
TGTCCATTATTGGAAGCATA+AGG 0.460083 8.1:-43549681 MS.gene63140:CDS
CGGTCAATAATCCTCCTAAT+CGG 0.465785 8.1:-43549327 MS.gene63140:CDS
ACGGTAGCATACATCCGATT+AGG 0.477261 8.1:+43549313 None:intergenic
CTTGAAAAGGACCTAAAAGT+TGG 0.486000 8.1:-43549367 MS.gene63140:CDS
AGAAATACATAGGGAGAGAA+TGG 0.518052 8.1:-43549402 MS.gene63140:CDS
GTATGCTACCGTCGTTAACT+GGG 0.522932 8.1:-43549302 MS.gene63140:CDS
AACATGCATCAGAAATACAT+AGG 0.535430 8.1:-43549412 MS.gene63140:CDS
GAGATTGGAGTTGAAGTCAA+TGG 0.575541 8.1:-43549734 MS.gene63140:CDS
ACATGCATCAGAAATACATA+GGG 0.587826 8.1:-43549411 MS.gene63140:CDS
GTAGCATACATCCGATTAGG+AGG 0.600441 8.1:+43549316 None:intergenic
CCATTCTCCGCAACACATCG+AGG 0.699602 8.1:+43549520 None:intergenic
GAATCAGTCCCAGTTAACGA+CGG 0.733495 8.1:+43549294 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! AAAATATCGATGTCCATTAT+TGG - chr8.1:43549346-43549365 MS.gene63140:CDS 25.0%
! ATCAAAGTCATAAGATTTAC+CGG + chr8.1:43549587-43549606 None:intergenic 25.0%
!! TAAGGTTATTGCTTCTATTT+TGG - chr8.1:43549374-43549393 MS.gene63140:CDS 25.0%
AACATGCATCAGAAATACAT+AGG - chr8.1:43549625-43549644 MS.gene63140:intron 30.0%
ACATGCATCAGAAATACATA+GGG - chr8.1:43549626-43549645 MS.gene63140:intron 30.0%
GTACAACTTTGTTCTTGAAA+AGG - chr8.1:43549657-43549676 MS.gene63140:CDS 30.0%
TAACCTTATGCTTCCAATAA+TGG + chr8.1:43549362-43549381 None:intergenic 30.0%
! AAATAACGTCACCAACTTTT+AGG + chr8.1:43549684-43549703 None:intergenic 30.0%
! AAGTCAATGGTACTGAATTA+GGG - chr8.1:43549316-43549335 MS.gene63140:CDS 30.0%
! TTTGGATGGAAACAATGTTT+TGG - chr8.1:43549392-43549411 MS.gene63140:CDS 30.0%
!! GTTATTGCTTCTATTTTGGA+TGG - chr8.1:43549378-43549397 MS.gene63140:CDS 30.0%
AGAAATACATAGGGAGAGAA+TGG - chr8.1:43549635-43549654 MS.gene63140:intron 35.0%
CTTGAAAAGGACCTAAAAGT+TGG - chr8.1:43549670-43549689 MS.gene63140:CDS 35.0%
! CTCCTTTTTGATGAAGAAAC+CGG - chr8.1:43549565-43549584 MS.gene63140:intron 35.0%
! GAAGTCAATGGTACTGAATT+AGG - chr8.1:43549315-43549334 MS.gene63140:CDS 35.0%
! TGTCCATTATTGGAAGCATA+AGG - chr8.1:43549356-43549375 MS.gene63140:CDS 35.0%
!! TACCGGTTTCTTCATCAAAA+AGG + chr8.1:43549570-43549589 None:intergenic 35.0%
!! TGGTGACGTTATTTTGTTCA+CGG - chr8.1:43549690-43549709 MS.gene63140:CDS 35.0%
!!! GGAAACAATGTTTTGGTTAG+TGG - chr8.1:43549399-43549418 MS.gene63140:CDS 35.0%
CGGTCAATAATCCTCCTAAT+CGG - chr8.1:43549710-43549729 MS.gene63140:CDS 40.0%
GAGATTGGAGTTGAAGTCAA+TGG - chr8.1:43549303-43549322 MS.gene63140:CDS 40.0%
ACGGTAGCATACATCCGATT+AGG + chr8.1:43549727-43549746 None:intergenic 45.0%
GTAGCATACATCCGATTAGG+AGG + chr8.1:43549724-43549743 None:intergenic 45.0%
GTATGCTACCGTCGTTAACT+GGG - chr8.1:43549735-43549754 MS.gene63140:CDS 45.0%
TGTATGCTACCGTCGTTAAC+TGG - chr8.1:43549734-43549753 MS.gene63140:CDS 45.0%
! GCATTTTCCTCGATGTGTTG+CGG - chr8.1:43549510-43549529 MS.gene63140:CDS 45.0%
CCATTCTCCGCAACACATCG+AGG + chr8.1:43549520-43549539 None:intergenic 55.0%
CCTCGATGTGTTGCGGAGAA+TGG - chr8.1:43549517-43549536 MS.gene63140:CDS 55.0%


Chromosome Type Strat End Strand Name
chr8.1 gene 43549297 43549762 43549297 ID=MS.gene63140
chr8.1 mRNA 43549297 43549762 43549297 ID=MS.gene63140.t1;Parent=MS.gene63140
chr8.1 exon 43549646 43549762 43549646 ID=MS.gene63140.t1.exon1;Parent=MS.gene63140.t1
chr8.1 CDS 43549646 43549762 43549646 ID=cds.MS.gene63140.t1;Parent=MS.gene63140.t1
chr8.1 exon 43549297 43549548 43549297 ID=MS.gene63140.t1.exon2;Parent=MS.gene63140.t1
chr8.1 CDS 43549297 43549548 43549297 ID=cds.MS.gene63140.t1;Parent=MS.gene63140.t1
Gene Sequence

>MS.gene63140

ATGAATGAGATTGGAGTTGAAGTCAATGGTACTGAATTAGGGAATGTTCAAAATATCGATGTCCATTATTGGAAGCATAAGGTTATTGCTTCTATTTTGGATGGAAACAATGTTTTGGTTAGTGGCATTTACGAAGCTTTTTTGTTGTTTTCATATTGTTAAGTTGTTGTTGATTAATTTTAATTTGTACGATTTCTTTACAAATCTATTGTAGCATTTTCCTCGATGTGTTGCGGAGAATGGTTTGTTTATCAATCAATCTAAAATTCTCCTTTTTGATGAAGAAACCGGTAAATCTTATGACTTTGATGTTCACACTACGTCAAAAAACATGCATCAGAAATACATAGGGAGAGAATGGTACAACTTTGTTCTTGAAAAGGACCTAAAAGTTGGTGACGTTATTTTGTTCACGGTCAATAATCCTCCTAATCGGATGTATGCTACCGTCGTTAACTGGGACTGA
Protein sequence

>MS.gene63140.t1

MNEIGVEVNGTELGNVQNIDVHYWKHKVIASILDGNNVLHFPRCVAENGLFINQSKILLFDEETGKSYDFDVHTTSKNMHQKYIGREWYNFVLEKDLKVGDVILFTVNNPPNRMYATVVNWD