AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene04368

Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04368.t1 MTR_3g061130 99.537 216 1 0 1 216 1 216 1.28e-160 442
MS.gene04368.t1 MTR_5g088410 60.930 215 51 5 3 216 6 188 1.08e-75 226
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene04368.t1 AT3G13230 75.472 212 52 0 3 214 4 215 7.02e-123 347
MS.gene04368.t1 AT3G13230 75.472 212 52 0 3 214 4 215 7.02e-123 347

Find 50 sgRNAs with CRISPR-Local

Find 54 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
TTCTCTTTGTTACCTAATTA+TGG 0.104484 3.4:+56878192 MS.gene04368:CDS
AGATCCCAGAATGTGAATTT+TGG 0.238915 3.4:-56878143 None:intergenic
CTGCTGGTGATCCCATAATT+AGG 0.273715 3.4:-56878204 None:intergenic
TGATACCAAAATTCACATTC+TGG 0.283493 3.4:+56878138 MS.gene04368:CDS
AGTTGAGAGCCGTTACTTCT+AGG 0.295245 3.4:+56878242 MS.gene04368:CDS
TGCTATTGCTATTCTGCGTT+TGG 0.312006 3.4:+56877967 MS.gene04368:CDS
TCTCTTTGTTACCTAATTAT+GGG 0.325990 3.4:+56878193 MS.gene04368:CDS
TTTGTCCATGCTTTCATGTT+GGG 0.347801 3.4:+56877929 MS.gene04368:CDS
GGCTCAAACTTTGGCTTTGG+AGG 0.352039 3.4:-56877686 None:intergenic
AGAGGCTCAAACTTTGGCTT+TGG 0.356673 3.4:-56877689 None:intergenic
ATACACCTCTCAAGAAAGTT+TGG 0.369468 3.4:+56877777 MS.gene04368:CDS
GATCACTTGTCCCGTGCTAT+TGG 0.373903 3.4:+56878043 MS.gene04368:CDS
CGTGCTATTGGAAGATTATC+TGG 0.376662 3.4:+56878055 MS.gene04368:CDS
TGCATTCTCAATTGTAAACT+TGG 0.386651 3.4:-56878092 None:intergenic
GGTTTCAGAGGCTCAAACTT+TGG 0.395402 3.4:-56877695 None:intergenic
TGTTGAATCCTTTGAGATCA+AGG 0.405447 3.4:+56878000 MS.gene04368:CDS
TTCGACCCTTCAAATTCATT+CGG 0.417898 3.4:-56877844 None:intergenic
CACAATGGCATCATCTTCAA+TGG 0.462021 3.4:+56877628 None:intergenic
ATTGGAAGATTATCTGGAAA+AGG 0.469137 3.4:+56878061 MS.gene04368:CDS
TTGCAAACATCAAGATTGCT+AGG 0.471818 3.4:+56878167 MS.gene04368:CDS
GGCAAAACTTTCTGTTCAGA+TGG 0.482890 3.4:-56877665 None:intergenic
AGAAGTAACGGCTCTCAACT+TGG 0.482912 3.4:-56878239 None:intergenic
TGACATCCGAATGAATTTGA+AGG 0.495230 3.4:+56877838 MS.gene04368:CDS
TTGGAATATACCTTTCCTGC+TGG 0.496163 3.4:-56878220 None:intergenic
CGAAACTGAACCGCAGCACC+AGG 0.498813 3.4:-56877728 None:intergenic
GATACCAAAATTCACATTCT+GGG 0.511425 3.4:+56878139 MS.gene04368:CDS
CTGAAACCTCATGAGATGCC+TGG 0.516679 3.4:+56877710 MS.gene04368:CDS
TGCAAACATCAAGATTGCTA+GGG 0.524357 3.4:+56878168 MS.gene04368:CDS
AAGGATGTTAAGACACTTCG+AGG 0.530319 3.4:+56878019 MS.gene04368:CDS
CTAATTATGGGATCACCAGC+AGG 0.540701 3.4:+56878205 MS.gene04368:CDS
TATGGGATCACCAGCAGGAA+AGG 0.547596 3.4:+56878210 MS.gene04368:CDS
CAGATAATCTTCCAATAGCA+CGG 0.551311 3.4:-56878054 None:intergenic
CTTAACATCCTTGATCTCAA+AGG 0.557482 3.4:-56878008 None:intergenic
GACATCCGAATGAATTTGAA+GGG 0.559638 3.4:+56877839 MS.gene04368:CDS
ACCTCTCAAGAAAGTTTGGA+TGG 0.563023 3.4:+56877781 MS.gene04368:CDS
TCATGAGATGCCTGGTGCTG+CGG 0.567566 3.4:+56877718 MS.gene04368:CDS
TCCATCCAAACTTTCTTGAG+AGG 0.572045 3.4:-56877782 None:intergenic
GGAAGATTATCTGGAAAAGG+TGG 0.573573 3.4:+56878064 MS.gene04368:CDS
TTCTGCCATCCTAGAAGTAA+CGG 0.576020 3.4:-56878251 None:intergenic
GAGAGCCGTTACTTCTAGGA+TGG 0.578516 3.4:+56878246 MS.gene04368:CDS
TTACTTCTAGGATGGCAGAA+AGG 0.584575 3.4:+56878254 MS.gene04368:CDS
GCAAAACTTTCTGTTCAGAT+GGG 0.590899 3.4:-56877664 None:intergenic
AGATAATCTTCCAATAGCAC+GGG 0.591480 3.4:-56878053 None:intergenic
CAAAACCCAACATGAAAGCA+TGG 0.601082 3.4:-56877934 None:intergenic
TGCTGCGGTTCAGTTTCGCA+AGG 0.601400 3.4:+56877733 MS.gene04368:CDS
GGCATCTCATGAGGTTTCAG+AGG 0.608176 3.4:-56877707 None:intergenic
GCAGCACCAGGCATCTCATG+AGG 0.646562 3.4:-56877716 None:intergenic
TTGAGAGGTGTATAACGATG+TGG 0.685518 3.4:-56877767 None:intergenic
GAAAAGTTGAGTTGAAGACA+AGG 0.702510 3.4:+56877864 MS.gene04368:CDS
AGAGGTGTATAACGATGTGG+TGG 0.702702 3.4:-56877764 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
! TCTCTTTGTTACCTAATTAT+GGG + chr3.4:56878193-56878212 MS.gene04368:CDS 25.0%
! TTCTCTTTGTTACCTAATTA+TGG + chr3.4:56878192-56878211 MS.gene04368:CDS 25.0%
!! AATTTTCATCTGCTCAAATA+CGG - chr3.4:56877819-56877838 None:intergenic 25.0%
ATTGGAAGATTATCTGGAAA+AGG + chr3.4:56878061-56878080 MS.gene04368:CDS 30.0%
GATACCAAAATTCACATTCT+GGG + chr3.4:56878139-56878158 MS.gene04368:CDS 30.0%
TGATACCAAAATTCACATTC+TGG + chr3.4:56878138-56878157 MS.gene04368:CDS 30.0%
TGCATTCTCAATTGTAAACT+TGG - chr3.4:56878095-56878114 None:intergenic 30.0%
! ATTTTCATCTGCTCAAATAC+GGG - chr3.4:56877818-56877837 None:intergenic 30.0%
AGATAATCTTCCAATAGCAC+GGG - chr3.4:56878056-56878075 None:intergenic 35.0%
ATACACCTCTCAAGAAAGTT+TGG + chr3.4:56877777-56877796 MS.gene04368:CDS 35.0%
CAGATAATCTTCCAATAGCA+CGG - chr3.4:56878057-56878076 None:intergenic 35.0%
CTTAACATCCTTGATCTCAA+AGG - chr3.4:56878011-56878030 None:intergenic 35.0%
GACATCCGAATGAATTTGAA+GGG + chr3.4:56877839-56877858 MS.gene04368:CDS 35.0%
GCAAAACTTTCTGTTCAGAT+GGG - chr3.4:56877667-56877686 None:intergenic 35.0%
TGACATCCGAATGAATTTGA+AGG + chr3.4:56877838-56877857 MS.gene04368:CDS 35.0%
TGCAAACATCAAGATTGCTA+GGG + chr3.4:56878168-56878187 MS.gene04368:CDS 35.0%
TTCGACCCTTCAAATTCATT+CGG - chr3.4:56877847-56877866 None:intergenic 35.0%
TTGCAAACATCAAGATTGCT+AGG + chr3.4:56878167-56878186 MS.gene04368:CDS 35.0%
TTTGTCCATGCTTTCATGTT+GGG + chr3.4:56877929-56877948 MS.gene04368:CDS 35.0%
! AGATCCCAGAATGTGAATTT+TGG - chr3.4:56878146-56878165 None:intergenic 35.0%
! CAAAATCAGCACATTTTTGC+AGG - chr3.4:56877913-56877932 None:intergenic 35.0%
! TTTTGTCCATGCTTTCATGT+TGG + chr3.4:56877928-56877947 MS.gene04368:CDS 35.0%
!! GAAAAGTTGAGTTGAAGACA+AGG + chr3.4:56877864-56877883 MS.gene04368:CDS 35.0%
!! TGTTGAATCCTTTGAGATCA+AGG + chr3.4:56878000-56878019 MS.gene04368:CDS 35.0%
AAGGATGTTAAGACACTTCG+AGG + chr3.4:56878019-56878038 MS.gene04368:CDS 40.0%
ACCTCTCAAGAAAGTTTGGA+TGG + chr3.4:56877781-56877800 MS.gene04368:CDS 40.0%
CAAAACCCAACATGAAAGCA+TGG - chr3.4:56877937-56877956 None:intergenic 40.0%
GGAAGATTATCTGGAAAAGG+TGG + chr3.4:56878064-56878083 MS.gene04368:CDS 40.0%
GGCAAAACTTTCTGTTCAGA+TGG - chr3.4:56877668-56877687 None:intergenic 40.0%
TCCATCCAAACTTTCTTGAG+AGG - chr3.4:56877785-56877804 None:intergenic 40.0%
TTCTGCCATCCTAGAAGTAA+CGG - chr3.4:56878254-56878273 None:intergenic 40.0%
TTGGAATATACCTTTCCTGC+TGG - chr3.4:56878223-56878242 None:intergenic 40.0%
! CGTGCTATTGGAAGATTATC+TGG + chr3.4:56878055-56878074 MS.gene04368:CDS 40.0%
! TGCTATTGCTATTCTGCGTT+TGG + chr3.4:56877967-56877986 MS.gene04368:CDS 40.0%
! TTGAGAGGTGTATAACGATG+TGG - chr3.4:56877770-56877789 None:intergenic 40.0%
! TTTTGCAGGTTACTGATGTC+AGG - chr3.4:56877899-56877918 None:intergenic 40.0%
!! TTACTTCTAGGATGGCAGAA+AGG + chr3.4:56878254-56878273 MS.gene04368:CDS 40.0%
AGAAGTAACGGCTCTCAACT+TGG - chr3.4:56878242-56878261 None:intergenic 45.0%
AGTTGAGAGCCGTTACTTCT+AGG + chr3.4:56878242-56878261 MS.gene04368:CDS 45.0%
CTAATTATGGGATCACCAGC+AGG + chr3.4:56878205-56878224 MS.gene04368:CDS 45.0%
CTGCTGGTGATCCCATAATT+AGG - chr3.4:56878207-56878226 None:intergenic 45.0%
GGTTTCAGAGGCTCAAACTT+TGG - chr3.4:56877698-56877717 None:intergenic 45.0%
! AGAGGCTCAAACTTTGGCTT+TGG - chr3.4:56877692-56877711 None:intergenic 45.0%
! AGAGGTGTATAACGATGTGG+TGG - chr3.4:56877767-56877786 None:intergenic 45.0%
CTGAAACCTCATGAGATGCC+TGG + chr3.4:56877710-56877729 MS.gene04368:CDS 50.0%
GATCACTTGTCCCGTGCTAT+TGG + chr3.4:56878043-56878062 MS.gene04368:CDS 50.0%
GGCATCTCATGAGGTTTCAG+AGG - chr3.4:56877710-56877729 None:intergenic 50.0%
TATGGGATCACCAGCAGGAA+AGG + chr3.4:56878210-56878229 MS.gene04368:CDS 50.0%
! GAGAGCCGTTACTTCTAGGA+TGG + chr3.4:56878246-56878265 MS.gene04368:CDS 50.0%
!! GGCTCAAACTTTGGCTTTGG+AGG - chr3.4:56877689-56877708 None:intergenic 50.0%
TGCTGCGGTTCAGTTTCGCA+AGG + chr3.4:56877733-56877752 MS.gene04368:CDS 55.0%
! TCATGAGATGCCTGGTGCTG+CGG + chr3.4:56877718-56877737 MS.gene04368:CDS 55.0%
CGAAACTGAACCGCAGCACC+AGG - chr3.4:56877731-56877750 None:intergenic 60.0%
GCAGCACCAGGCATCTCATG+AGG - chr3.4:56877719-56877738 None:intergenic 60.0%


Chromosome Type Strat End Strand Name
chr3.4 gene 56877632 56878282 56877632 ID=MS.gene04368
chr3.4 mRNA 56877632 56878282 56877632 ID=MS.gene04368.t1;Parent=MS.gene04368
chr3.4 exon 56877632 56878282 56877632 ID=MS.gene04368.t1.exon1;Parent=MS.gene04368.t1
chr3.4 CDS 56877632 56878282 56877632 ID=cds.MS.gene04368.t1;Parent=MS.gene04368.t1
Gene Sequence

>MS.gene04368

ATGGCATCATCTTCAATGGAAGTTGACAATGTCCCATCTGAACAGAAAGTTTTGCCTCCAAAGCCAAAGTTTGAGCCTCTGAAACCTCATGAGATGCCTGGTGCTGCGGTTCAGTTTCGCAAGGTATCAGTTCCACCACATCGTTATACACCTCTCAAGAAAGTTTGGATGGACATCTACACTCCCGTATTTGAGCAGATGAAAATTGACATCCGAATGAATTTGAAGGGTCGAAAAGTTGAGTTGAAGACAAGGCATGATACACCTGACATCAGTAACCTGCAAAAATGTGCTGATTTTGTCCATGCTTTCATGTTGGGTTTTGATGTCATAGATGCTATTGCTATTCTGCGTTTGGATGAGCTCTATGTTGAATCCTTTGAGATCAAGGATGTTAAGACACTTCGAGGTGATCACTTGTCCCGTGCTATTGGAAGATTATCTGGAAAAGGTGGTAAAACCAAGTTTACAATTGAGAATGCATCAAAGACAAGAATCGTGATTGCTGATACCAAAATTCACATTCTGGGATCTTTTGCAAACATCAAGATTGCTAGGGATTCTCTTTGTTACCTAATTATGGGATCACCAGCAGGAAAGGTATATTCCAAGTTGAGAGCCGTTACTTCTAGGATGGCAGAAAGGTTTTGA
Protein sequence

>MS.gene04368.t1

MASSSMEVDNVPSEQKVLPPKPKFEPLKPHEMPGAAVQFRKVSVPPHRYTPLKKVWMDIYTPVFEQMKIDIRMNLKGRKVELKTRHDTPDISNLQKCADFVHAFMLGFDVIDAIAILRLDELYVESFEIKDVKTLRGDHLSRAIGRLSGKGGKTKFTIENASKTRIVIADTKIHILGSFANIKIARDSLCYLIMGSPAGKVYSKLRAVTSRMAERF