AlfalfaGEDB Alfalfa Gene Editing Database

M. sativa cultivar XinJiangDaYe / MS.gene060917


Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060917.t1 MTR_3g106310 100.000 51 0 0 1 51 1 51 3.35e-32 105
MS.gene060917.t1 MTR_1g013070 100.000 51 0 0 1 51 1 51 3.35e-32 105
Query id Subject id identity % alignment length mismatches gap openings q. start q. end s. start s. end e-value bit score
MS.gene060917.t1 AT4G31985 90.196 51 5 0 1 51 1 51 1.80e-29 98.2
MS.gene060917.t1 AT3G02190 88.235 51 6 0 1 51 1 51 4.22e-28 94.7
MS.gene060917.t1 AT2G25210 90.909 44 4 0 8 51 1 44 6.32e-24 84.0

Find 14 sgRNAs with CRISPR-Local

Find 19 sgRNAs with CRISPR-GE


CRISPR-Local

CRISPR-Local
sgRNA_sequence on_target_score Position Region
GTTCTCATACGGATCCAATA+AGG 0.402869 1.2:+8602120 None:intergenic
AGAACAGACCCATCCCTTAT+TGG 0.418161 1.2:-8602134 MS.gene060917:CDS
CACTGGCGTCGTACCAAGCT+TGG 0.445699 1.2:-8601967 MS.gene060917:CDS
TTCTCATACGGATCCAATAA+GGG 0.468482 1.2:+8602121 None:intergenic
AATTAACCTGATGGTGTTGT+CGG 0.494295 1.2:+8602098 None:intergenic
TGAGAACCGACAACACCATC+AGG 0.505441 1.2:-8602104 MS.gene060917:intron
CGTACCAAGCTTGGATTCTG+AGG 0.522895 1.2:-8601958 None:intergenic
TGGTGTTGTCGGTTCTCATA+CGG 0.540409 1.2:+8602109 None:intergenic
ACAATGCTAAGCGTCGTCAC+TGG 0.548403 1.2:-8601984 MS.gene060917:CDS
AAAACCTCAGAATCCAAGCT+TGG 0.552557 1.2:+8601954 None:intergenic
AGAAGCTCGCGAAGAAGATG+AGG 0.578712 1.2:-8602158 MS.gene060917:CDS
CATACGGATCCAATAAGGGA+TGG 0.584103 1.2:+8602125 None:intergenic
ATGACGAATGTCTTGTGTGA+AGG 0.588940 1.2:+8602186 None:intergenic
ATACGGATCCAATAAGGGAT+GGG 0.595390 1.2:+8602126 None:intergenic

CRISPR-GE

badsite warning sgRNA_sequence Strand Position Region GC_content
!!! ATGTTATTTCATTTGATTTT+AGG - chr1.2:8602241-8602260 MS.gene060917:intron 15.0%
! ATAGATAGAAATTAACCTGA+TGG + chr1.2:8602163-8602182 None:intergenic 25.0%
AGAATAGTGAAATTAGGAGT+GGG + chr1.2:8601999-8602018 None:intergenic 30.0%
GAATCGAGAATAGTGAAATT+AGG + chr1.2:8602005-8602024 None:intergenic 30.0%
GAGAATAGTGAAATTAGGAG+TGG + chr1.2:8602000-8602019 None:intergenic 35.0%
TGAAATTAGGAGTGGGAATT+TGG + chr1.2:8601992-8602011 None:intergenic 35.0%
TTAACAGTACAACGTTGTTG+TGG + chr1.2:8602191-8602210 None:intergenic 35.0%
TTCTCATACGGATCCAATAA+GGG + chr1.2:8602131-8602150 None:intergenic 35.0%
!! AATTAACCTGATGGTGTTGT+CGG + chr1.2:8602154-8602173 None:intergenic 35.0%
ATACGGATCCAATAAGGGAT+GGG + chr1.2:8602126-8602145 None:intergenic 40.0%
ATGACGAATGTCTTGTGTGA+AGG + chr1.2:8602066-8602085 None:intergenic 40.0%
GTTCTCATACGGATCCAATA+AGG + chr1.2:8602132-8602151 None:intergenic 40.0%
AGAACAGACCCATCCCTTAT+TGG - chr1.2:8602115-8602134 MS.gene060917:CDS 45.0%
CATACGGATCCAATAAGGGA+TGG + chr1.2:8602127-8602146 None:intergenic 45.0%
!! TGGTGTTGTCGGTTCTCATA+CGG + chr1.2:8602143-8602162 None:intergenic 45.0%
AGAAGCTCGCGAAGAAGATG+AGG - chr1.2:8602091-8602110 MS.gene060917:intron 50.0%
TGAGAACCGACAACACCATC+AGG - chr1.2:8602145-8602164 MS.gene060917:CDS 50.0%
! ACAATGCTAAGCGTCGTCAC+TGG - chr1.2:8602265-8602284 MS.gene060917:intron 50.0%
CACTGGCGTCGTACCAAGCT+TGG - chr1.2:8602282-8602301 MS.gene060917:intron 60.0%


Chromosome Type Strat End Strand Name
chr1.2 gene 8601960 8602311 8601960 ID=MS.gene060917
chr1.2 mRNA 8601960 8602311 8601960 ID=MS.gene060917.t1;Parent=MS.gene060917
chr1.2 exon 8602309 8602311 8602309 ID=MS.gene060917.t1.exon1;Parent=MS.gene060917.t1
chr1.2 CDS 8602309 8602311 8602309 ID=cds.MS.gene060917.t1;Parent=MS.gene060917.t1
chr1.2 exon 8602105 8602208 8602105 ID=MS.gene060917.t1.exon2;Parent=MS.gene060917.t1
chr1.2 CDS 8602105 8602208 8602105 ID=cds.MS.gene060917.t1;Parent=MS.gene060917.t1
chr1.2 exon 8601960 8602008 8601960 ID=MS.gene060917.t1.exon3;Parent=MS.gene060917.t1
chr1.2 CDS 8601960 8602008 8601960 ID=cds.MS.gene060917.t1;Parent=MS.gene060917.t1
Gene Sequence

>MS.gene060917

ATGGTAAATCAAATCGAAACTCTTTATCACCAAATTCCCACTCCTAATTTCACTATTCTCGATTCAATTTCTGATTTAACGTTTTTGATTAATCTAATTTCAGCCTTCACACAAGACATTCGTCATCAAGAAGAAGCTCGCGAAGAAGATGAGGCAGAACAGACCCATCCCTTATTGGATCCGTATGAGAACCGACAACACCATCAGGTTAATTTCTATCTATCTCAACCACAACAACGTTGTACTGTTAATCGTGTTAAATCATGTTTTGTTTCTTATGTATGTTATTTCATTTGATTTTAGGTACAATGCTAAGCGTCGTCACTGGCGTCGTACCAAGCTTGGATTCTGA

Protein sequence

>MS.gene060917.t1

MPSHKTFVIKKKLAKKMRQNRPIPYWIRMRTDNTIRYNAKRRHWRRTKLGF