AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene25942


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25942.t1 MTR_3g078130 100.000 73 0 0 1 73 1 73 4.87e-44 136
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene25942.t1 AT1G64750 76.712 73 16 1 1 72 1 73 3.24e-11 53.5
MS.gene25942.t1 AT1G64750 76.712 73 16 1 1 72 1 73 3.24e-11 53.5

Find 17 sgRNAs with CRISPR-Local

Find 59 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
CTCAACAATGGGAGGATGAT+TGG 0.329365 3.2:-69036937 MS.gene25942:CDS
TCAACAATGGGAGGATGATT+GGG 0.443446 3.2:-69036936 MS.gene25942:CDS
ATTTCTCTGTTCAGCTGAGA+AGG 0.461195 3.2:-69036892 MS.gene25942:CDS
TGTTCAGCTGAGAAGGGAGT+TGG 0.494913 3.2:-69036885 MS.gene25942:CDS
GAAAGAAGTAACTCAACAAT+GGG 0.498445 3.2:-69036948 MS.gene25942:CDS
GAAGAGTTTGAAATCAATGA+AGG 0.502774 3.2:-69037974 MS.gene25942:intron
GAGTGGGATGACATGGAGGA+AGG 0.532354 3.2:-69036971 MS.gene25942:CDS
TTTCTCTGTTCAGCTGAGAA+GGG 0.558420 3.2:-69036891 MS.gene25942:CDS
AGCCTTTGCTTCAGTCGCCA+TGG 0.560336 3.2:+69038045 None:intergenic
GGAAAGAAGTAACTCAACAA+TGG 0.565472 3.2:-69036949 MS.gene25942:CDS
ATCCATGGCGACTGAAGCAA+AGG 0.576258 3.2:-69038047 None:intergenic
ACTTGCAGAGTGGGATGACA+TGG 0.578383 3.2:-69036978 MS.gene25942:intron
AGTGGGATGACATGGAGGAA+GGG 0.591985 3.2:-69036970 MS.gene25942:CDS
TGAAGCAAAGGCTGTGACCG+AGG 0.600680 3.2:-69038035 MS.gene25942:CDS
TAGATCGATCTTGACATCCT+CGG 0.618819 3.2:+69038018 None:intergenic
AGAAGTAACTCAACAATGGG+AGG 0.631574 3.2:-69036945 MS.gene25942:CDS
TGCAGAGTGGGATGACATGG+AGG 0.657206 3.2:-69036975 MS.gene25942:intron

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!! AAGTTTCAAATTACATGATT+GGG + chr3.2:69037413-69037432 None:intergenic 20.0%
!! TAAGTTTCAAATTACATGAT+TGG + chr3.2:69037414-69037433 None:intergenic 20.0%
! AACATCACTGAAAATTTCTT+AGG + chr3.2:69037034-69037053 None:intergenic 25.0%
! ATTGGCATTTGTATGTTAAT+TGG - chr3.2:69037787-69037806 MS.gene25942:intron 25.0%
! ATTTCATACACGAAATAAAG+TGG + chr3.2:69037454-69037473 None:intergenic 25.0%
! CTTATACATAAGCACTTATT+TGG - chr3.2:69037334-69037353 MS.gene25942:intron 25.0%
! GTTTGGCATTCAATTAATTA+CGG - chr3.2:69037157-69037176 MS.gene25942:intron 25.0%
! TTTGGCATTCAATTAATTAC+GGG - chr3.2:69037158-69037177 MS.gene25942:intron 25.0%
!! ATTATCTTTGCTTCTGTTTT+AGG - chr3.2:69036988-69037007 MS.gene25942:intron 25.0%
!! TGTTAATCCTATTTCTCATT+AGG - chr3.2:69037701-69037720 MS.gene25942:intron 25.0%
!!! TGAATCTCATTTAGTTTGAT+TGG - chr3.2:69037769-69037788 MS.gene25942:intron 25.0%
AAGCAAAGATAATTGCATCA+GGG + chr3.2:69036981-69037000 None:intergenic 30.0%
ACAGCACTTATATACTAGAT+AGG + chr3.2:69037201-69037220 None:intergenic 30.0%
CAAATTACATGATTGGGTTA+TGG + chr3.2:69037407-69037426 None:intergenic 30.0%
GAAAGAAGTAACTCAACAAT+GGG - chr3.2:69037957-69037976 MS.gene25942:intron 30.0%
GCTGCATCATTTATATAATC+AGG + chr3.2:69037556-69037575 None:intergenic 30.0%
TTTCTTGACGACTTGAAATT+AGG - chr3.2:69037829-69037848 MS.gene25942:intron 30.0%
! GAACATTTGTTAGACTGTTT+GGG - chr3.2:69037238-69037257 MS.gene25942:intron 30.0%
! GAAGAGTTTGAAATCAATGA+AGG - chr3.2:69036931-69036950 MS.gene25942:CDS 30.0%
! TCTAGTATATAAGTGCTGTT+TGG - chr3.2:69037202-69037221 MS.gene25942:intron 30.0%
! TGAACATTTGTTAGACTGTT+TGG - chr3.2:69037237-69037256 MS.gene25942:intron 30.0%
AGATTAGATTGTGAGTGCAA+TGG + chr3.2:69037871-69037890 None:intergenic 35.0%
ATACACGAAATAAAGTGGTG+AGG + chr3.2:69037449-69037468 None:intergenic 35.0%
ATCCTAATTCGTTTCTTCCA+CGG + chr3.2:69037097-69037116 None:intergenic 35.0%
ATTAGGCATGAACACTTCTA+GGG - chr3.2:69037718-69037737 MS.gene25942:intron 35.0%
GAAGCAAAGATAATTGCATC+AGG + chr3.2:69036982-69037001 None:intergenic 35.0%
GGAAAGAAGTAACTCAACAA+TGG - chr3.2:69037956-69037975 MS.gene25942:intron 35.0%
GTTCATGCCTAATGAGAAAT+AGG + chr3.2:69037711-69037730 None:intergenic 35.0%
TAATTGCATCAGGGAAGAAA+CGG + chr3.2:69036972-69036991 None:intergenic 35.0%
TTACATGATTGGGTTATGGT+TGG + chr3.2:69037403-69037422 None:intergenic 35.0%
TTCAAGTCGTCAAGAAAAGT+TGG + chr3.2:69037826-69037845 None:intergenic 35.0%
! GACTTGAAATTAGGAGGTTT+TGG - chr3.2:69037838-69037857 MS.gene25942:intron 35.0%
! TGTTTTACAACTTGCAGAGT+GGG - chr3.2:69037918-69037937 MS.gene25942:intron 35.0%
!! ACTTCTAGGGCGAAAATTAT+AGG - chr3.2:69037731-69037750 MS.gene25942:intron 35.0%
!! TATTCATTAGTTTGCTTCCG+TGG - chr3.2:69037077-69037096 MS.gene25942:intron 35.0%
!! TTGTTTTACAACTTGCAGAG+TGG - chr3.2:69037917-69037936 MS.gene25942:intron 35.0%
AATTGCATCAGGGAAGAAAC+GGG + chr3.2:69036971-69036990 None:intergenic 40.0%
AGAAGTAACTCAACAATGGG+AGG - chr3.2:69037960-69037979 MS.gene25942:intron 40.0%
AGACTGTTTGGGAGAACTTA+TGG - chr3.2:69037249-69037268 MS.gene25942:intron 40.0%
ATTTCTCTGTTCAGCTGAGA+AGG - chr3.2:69038013-69038032 MS.gene25942:CDS 40.0%
CATTAGGCATGAACACTTCT+AGG - chr3.2:69037717-69037736 MS.gene25942:intron 40.0%
CTTGACGACTTGAAATTAGG+AGG - chr3.2:69037832-69037851 MS.gene25942:intron 40.0%
GGCATTCAATTAATTACGGG+AGG - chr3.2:69037161-69037180 MS.gene25942:intron 40.0%
GTCGTCAAGAAAAGTTGGAT+AGG + chr3.2:69037821-69037840 None:intergenic 40.0%
TAGATCGATCTTGACATCCT+CGG + chr3.2:69036890-69036909 None:intergenic 40.0%
TCAACAATGGGAGGATGATT+GGG - chr3.2:69037969-69037988 MS.gene25942:intron 40.0%
TGAGCTAGACTTTGTGTGTT+TGG - chr3.2:69037140-69037159 MS.gene25942:intron 40.0%
TTCCGTGGAAGAAACGAATT+AGG - chr3.2:69037092-69037111 MS.gene25942:intron 40.0%
TTTCTCTGTTCAGCTGAGAA+GGG - chr3.2:69038014-69038033 MS.gene25942:CDS 40.0%
ATGCCACTACTCTCTTCTCA+TGG - chr3.2:69037677-69037696 MS.gene25942:intron 45.0%
CTCAACAATGGGAGGATGAT+TGG - chr3.2:69037968-69037987 MS.gene25942:intron 45.0%
TGCCACTACTCTCTTCTCAT+GGG - chr3.2:69037678-69037697 MS.gene25942:intron 45.0%
ACTTGCAGAGTGGGATGACA+TGG - chr3.2:69037927-69037946 MS.gene25942:intron 50.0%
AGTGGGATGACATGGAGGAA+GGG - chr3.2:69037935-69037954 MS.gene25942:intron 50.0%
CACCCATGAGAAGAGAGTAG+TGG + chr3.2:69037683-69037702 None:intergenic 50.0%
TGTTCAGCTGAGAAGGGAGT+TGG - chr3.2:69038020-69038039 MS.gene25942:CDS 50.0%
GAGTGGGATGACATGGAGGA+AGG - chr3.2:69037934-69037953 MS.gene25942:intron 55.0%
TGAAGCAAAGGCTGTGACCG+AGG - chr3.2:69036870-69036889 MS.gene25942:CDS 55.0%
TGCAGAGTGGGATGACATGG+AGG - chr3.2:69037930-69037949 MS.gene25942:intron 55.0%


Chromosome Type Strat End Strand Name
chr3.2 gene 69036862 69038065 69036862 ID=MS.gene25942
chr3.2 mRNA 69036862 69038065 69036862 ID=MS.gene25942.t1;Parent=MS.gene25942
chr3.2 exon 69037975 69038065 69037975 ID=MS.gene25942.t1.exon1;Parent=MS.gene25942.t1
chr3.2 CDS 69037975 69038065 69037975 ID=cds.MS.gene25942.t1;Parent=MS.gene25942.t1
chr3.2 exon 69036862 69036992 69036862 ID=MS.gene25942.t1.exon2;Parent=MS.gene25942.t1
chr3.2 CDS 69036862 69036992 69036862 ID=cds.MS.gene25942.t1;Parent=MS.gene25942.t1
Gene Sequence

>MS.gene25942

ATGGCGACTGAAGCAAAGGCTGTGACCGAGGATGTCAAGATCGATCTATTCGAAGACGATGATGAGTTCGAAGAGTTTGAAATCAATGAAGGTATGAATCAGTAATCCCGTTTCTTCCCTGATGCAATTATCTTTGCTTCTGTTTTAGGTTTACATTTAGTTAAGTGCTCCTAAGAAATTTTCAGTGATGTTATCATCAAATGATTTATAAGTTATATTCATTAGTTTGCTTCCGTGGAAGAAACGAATTAGGATTTCATCGCGTATTGTTGCACATTTGAGCTAGACTTTGTGTGTTTGGCATTCAATTAATTACGGGAGGTTATGAAAATTTAACCTATCTAGTATATAAGTGCTGTTTGGATTTGAGTAACATGAACATTTGTTAGACTGTTTGGGAGAACTTATGGAAACAACTTATAACTTATATGAAAATAGTTTGAATTTATTTTATGCTTTGTTATAAAAATTGCTTATACATAAGCACTTATTTGGTAAGCGCTTGTGCTATAAGCACTTAATTAATTAAGCTGTATGTCCAACCATAACCCAATCATGTAATTTGAAACTTATTTGATACTTCACCTCACCACTTTATTTCGTGTATGAAATAATATGATATTTAAATATACATATCTACTATTAAATCATATATACTTGCAAATGTCTAAACTTTTATATACATTATTGTCCTGATTATATAAATGATGCAGCATTTAGATTTGCTAGATTCACGTTGTACACAGCGTTAATGAAGATGTAAGTTTGCTAATTTTTTGTGCGTGTGTCTCACAGTGCATGCAAACTGTAATTTTATGCCACTACTCTCTTCTCATGGGTGTTAATCCTATTTCTCATTAGGCATGAACACTTCTAGGGCGAAAATTATAGGACTTATTTAATTGCTTGAATCTCATTTAGTTTGATTGGCATTTGTATGTTAATTGGCTTCACTGCCTATCCAACTTTTCTTGACGACTTGAAATTAGGAGGTTTTGGATTTCTGCCATTGCACTCACAATCTAATCTTGCTAACTATTTCTTTTTGCGCTTCTTTGTTTTACAACTTGCAGAGTGGGATGACATGGAGGAAGGGAAAGAAGTAACTCAACAATGGGAGGATGATTGGGATGATGATGATGTTAGCGATGATTTCTCTGTTCAGCTGAGAAGGGAGTTGGAGAAGACTACTGATAAGAATTAA

Protein sequence

>MS.gene25942.t1

MATEAKAVTEDVKIDLFEDDDEFEEFEINEEWDDMEEGKEVTQQWEDDWDDDDVSDDFSVQLRRELEKTTDKN