LXL04_014191 | RubberDandelionOmics

Gene overview

LXL04_014191

Reference: OH-1004 Chr: Chr03 Coordinates: 43382797-43390889 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1635 bp · LXL04_014191|LXL04_014191|OH1004|cDNA

atgcatgcaaggaaggatgctaagagaaggaagacaatttggatggtttgtgataagatgcaagttcaaggaccattttggatgttttggaagatcaaggacttgcatggcacattaagatgcacatacacatgcatgcatggacatagaagcttctttgtaatgctgtcaagtgcaagaaaccgacttaatcaattaagattgaggataagatgcaaggtggaaagcaaaagaggaagaaaacaaagaaaacacggttt...

CDS

Download CDS FASTA

1635 bp · LXL04_014191|LXL04_014191|OH1004|CDS

ATGCATGCAAGGAAGGATGCTAAGAGAAGGAAGACAATTTGGATGGTTTGTGATAAGATGCAAGTTCAAGGACCATTTTGGATGTTTTGGAAGATCAAGGACTTGCATGGCACATTAAGATGCACATACACATGCATGCATGGACATAGAAGCTTCTTTGTAATGCTGTCAAGTGCAAGAAACCGACTTAATCAATTAAGATTGAGGATAAGATGCAAGGTGGAAAGCAAAAGAGGAAGAAAACAAAGAAAACACGGTTT...

Protein

Download Protein FASTA

544 aa · LXL04_014191|LXL04_014191|OH1004|PROTEIN

MHARKDAKRRKTIWMVCDKMQVQGPFWMFWKIKDLHGTLRCTYTCMHGHRSFFVMLSSARNRLNQLRLRIRCKVESKRGRKQRKHGFTRYATAHRPRAAARLVKASTSASRRIKLTFRHAKRDEKNKDAALKNAYVLMGRHELELVVNFFFHGGDIASSINVCAKTLKDEQLVLVICRLLEGTTGMQLLGDGVKGWCFIISSEILWHHNEGSGSVLEEIVEALCRHVSDDSPMIRRLCLRGLSRCPWKLCPPFKLPGPVD...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_014191`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_014191

Location Chr03:43382797-43390889 (+)

Description Similar to IDM2: Increased DNA methylation 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g54840`	Prevents DNA hypermethylation and transcriptional silencing of transgenes and of some endogenous genes.	REPRESSOR OF SILENCING5 Encodes a Member of the Small Heat Shock Protein Family and Is Required for DNA Demethylation in Arabidopsis.2014 · DOI: 10.1105/tpc.114.126730 Regulation of active DNA demethylation by an α-crystallin domain protein in Arabidopsis.2014 · DOI: 10.1016/j.molcel.2014.06.008
`At2g36810`	Involved in inflorescence stems gravitropism, by modulating vacuolar membrane (VMs) dynamics in gravity-sensing cells (e.g. endodermal cells) during the amyloplast sedimentation process.	A unique HEAT repeat-containing protein SHOOT GRAVITROPISM6 is involved in vacuolar membrane dynamics in gravity-sensing cells of Arabidopsis inflorescence stem.2014 · DOI: 10.1093/pcp/pcu020 Mutations in the SGR4, SGR5 and SGR6 loci of Arabidopsis thaliana alter the shoot gravitropism.1997 · DOI: 10.1093/oxfordjournals.pcp.a029201
`At1g20870`	Acts as an anti-silencing factor that prevents DNA hypermethylation and gene repression.	The methyl-CpG-binding protein MBD7 facilitates active DNA demethylation to limit DNA hyper-methylation and transcriptional gene silencing.2015 · DOI: 10.1016/j.molcel.2015.01.009

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014191 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0007035 vacuolar acidification Biological Process

GO:0009630 gravitropism Biological Process

GO:0009660 amyloplast organization Biological Process

GO:0009959 negative gravitropism Biological Process

GO:0032880 regulation of protein localization Biological Process

GO:0070070 proton-transporting V-type ATPase complex assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009705 plant-type vacuole membrane Cellular Component

KEGG gene cross-reference

ath:AT1G20870

ath:AT1G54840

ath:AT2G36810

hsa:1657

mmu:240283

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.802

Rank 1 · LXL04_014191 · OH-1004

Cytoplasm0.211

Rank 2 · LXL04_014191 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_014191 · OH-1004

Mitochondrion0.037

Rank 4 · LXL04_014191 · OH-1004

Endoplasmic reticulum0.037

Rank 5 · LXL04_014191 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF12234.14Rav1p_C122-188 aa

PF31004.1IDM_C252-280 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014191	`PF12234.14`	Rav1p_C	122	188	5e-13	49.0
LXL04_014191	`PF31004.1`	IDM_C	252	280	5.1e-10	39.8

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q8RWL4`	Arabidopsis thaliana	Increased DNA methylation 2	62.222%	Swiss-Prot	weak database homology
`F4IP13`	Arabidopsis thaliana	Protein SHOOT GRAVITROPISM 6	64.444%	Swiss-Prot	weak database homology
`Q9SYQ0`	Arabidopsis thaliana	Increased DNA methylation 3	27.347%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card