LXL04_005850 | RubberDandelionOmics

Gene overview

LXL04_005850

Reference: OH-1004 Chr: Chr01 Coordinates: 174502174-174502716 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

477 bp · LXL04_005850|LXL04_005850|OH1004|cDNA

ATGAATGGTGTAGAAGGGTCGTCGTCAGCAGACTCATCATTTCTTGACCAAAATGCGAATAATTACATGAGTACTTCTGTTCTCGCTAGAAATGGCGTCAATGGGTTCACCTTTATGCAGATGGAAGAACTCAAATTACAAGCTCTAATATACAAATACATGGAAGCTGGATTGCCTGTTCCTTCCAATCTCCTCCTCCCCATTTGGAACTCTGTTCTCGCTTCTTTCGCAGGGTCGGGATACGATCGGAGTTTGTACGA...

CDS

Download CDS FASTA

477 bp · LXL04_005850|LXL04_005850|OH1004|CDS

ATGAATGGTGTAGAAGGGTCGTCGTCAGCAGACTCATCATTTCTTGACCAAAATGCGAATAATTACATGAGTACTTCTGTTCTCGCTAGAAATGGCGTCAATGGGTTCACCTTTATGCAGATGGAAGAACTCAAATTACAAGCTCTAATATACAAATACATGGAAGCTGGATTGCCTGTTCCTTCCAATCTCCTCCTCCCCATTTGGAACTCTGTTCTCGCTTCTTTCGCAGGGTCGGGATACGATCGGAGTTTGTACGA...

Protein

Download Protein FASTA

158 aa · LXL04_005850|LXL04_005850|OH1004|PROTEIN

MNGVEGSSSADSSFLDQNANNYMSTSVLARNGVNGFTFMQMEELKLQALIYKYMEAGLPVPSNLLLPIWNSVLASFAGSGYDRSLYDNYKNSMEAEPGRCKRTDGKKWRCSKEVVMGYKYCDKHLHRGRSSRSRKDVEVHDSIIAGAGATTNATHKNL

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_005850`
TK1151 ID	TkA01G012640
OH-1004 ID	LXL04_005850
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.100
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
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_005850

Location Chr01:174502174-174502716 (+)

Description Similar to GRF12: Growth-regulating factor 12

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g52910`	Transcription activator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0574500`	Transcription activator that plays a regulatory role in gibberellin-induced stem elongation.	No verified direct reference in this release
`Os02g0678800`	Transcription activator that plays a regulatory role in gibberellin-induced stem elongation.	No verified direct reference in this release
`Os04g0600900`	Transcription activator that plays a regulatory role in gibberellin-induced stem elongation.	No verified direct reference in this release
`Os02g0701300`	Transcription activator that plays a role in the regulation of meristematic function in leaves, stems and inflorescences.	Interaction between the GROWTH-REGULATING FACTOR and KNOTTED1-LIKE HOMEOBOX families of transcription factors.2014 · DOI: 10.1104/pp.113.222836 A Rare Allele of GS2 Enhances Grain Size and Grain Yield in Rice.2015 · DOI: 10.1016/j.molp.2015.07.002 OsGRF4 controls grain shape, panicle length and seed shattering in rice.2016 · DOI: 10.1111/jipb.12473 The OsmiR396c-OsGRF4-OsGIF1 regulatory module determines grain size and yield in rice.2016 · DOI: 10.1111/pbi.12569 Control of grain size and rice yield by GL2-mediated brassinosteroid responses.2015 · DOI: 10.1038/nplants.2015.195 Regulation of OsGRF4 by OsmiR396 controls grain size and yield in rice.2015 · DOI: 10.1038/nplants.2015.203

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005850 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0008283 cell population proliferation Biological Process

GO:0032502 developmental process Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0048316 seed development Biological Process

GO:0048366 leaf development Biological Process

GO:0005634 nucleus Cellular Component

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT3G52910

dosa:Os02g0678800

dosa:Os02g0701300

dosa:Os04g0574500

dosa:Os04g0600900

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.

Nucleus0.964

Rank 1 · LXL04_005850 · OH-1004

Cytoplasm0.095

Rank 2 · LXL04_005850 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_005850 · OH-1004

Endoplasmic reticulum0.017

Rank 4 · LXL04_005850 · OH-1004

Plastid0.015

Rank 5 · LXL04_005850 · 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.

PF08880.17QLQ36-69 aa

PF08879.16WRC95-135 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005850	`PF08880.17`	QLQ	36	69	6.1e-14	52.1
LXL04_005850	`PF08879.16`	WRC	95	135	4.6e-19	68.6

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
`Q8L8A7`	Arabidopsis thaliana	Growth-regulating factor 4	52.174%	Swiss-Prot	moderate database homology
`Q6AWX7`	Oryza sativa subsp. japonica	Growth-regulating factor 12	52.991%	Swiss-Prot	moderate database homology
`Q6EPP9`	Oryza sativa subsp. japonica	Growth-regulating factor 10	55.856%	Swiss-Prot	moderate database homology
`Q6AWY6`	Oryza sativa subsp. japonica	Growth-regulating factor 3	55.556%	Swiss-Prot	moderate database homology
`Q6ZIK5`	Oryza sativa subsp. japonica	Growth-regulating factor 4	54.630%	Swiss-Prot	moderate database homology

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