LXL04_029448 | RubberDandelionOmics

Gene overview

LXL04_029448

Reference: OH-1004 Chr: Chr06 Coordinates: 90844124-90845474 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1122 bp · LXL04_029448|LXL04_029448|OH1004|cDNA

ATGGGGGACGGAATTAGAAGTGGTGTCGGCGGTGGTGGGGCGGCGTCTCCATTGGAGTGTGATGTTGGGCTGGGTTTGAACAGTTGTGAGCCTTCTTACCCTTGTAAAAAGACGAGTTTGATAAACCAGCATCGGCATCACCAAGGTTCTGAAATCGGTGGCTGTTTTGGTGGTGTTTATGGTAACAATGGCGGCCAACTGTTCGTCAACCAAACTAATTCTAATAATCAGTTTGCATCTGGGATCTCTTTCAAATCGAA...

CDS

Download CDS FASTA

1122 bp · LXL04_029448|LXL04_029448|OH1004|CDS

ATGGGGGACGGAATTAGAAGTGGTGTCGGCGGTGGTGGGGCGGCGTCTCCATTGGAGTGTGATGTTGGGCTGGGTTTGAACAGTTGTGAGCCTTCTTACCCTTGTAAAAAGACGAGTTTGATAAACCAGCATCGGCATCACCAAGGTTCTGAAATCGGTGGCTGTTTTGGTGGTGTTTATGGTAACAATGGCGGCCAACTGTTCGTCAACCAAACTAATTCTAATAATCAGTTTGCATCTGGGATCTCTTTCAAATCGAA...

Protein

Download Protein FASTA

373 aa · LXL04_029448|LXL04_029448|OH1004|PROTEIN

MGDGIRSGVGGGGAASPLECDVGLGLNSCEPSYPCKKTSLINQHRHHQGSEIGGCFGGVYGNNGGQLFVNQTNSNNQFASGISFKSNTDGVMGASGKVLFTANQFQELERQTIIYKYIRASIPIPPQLLLPSSSQPNNSTFLFSFLRKQIPLLRTSTGIRFSNGSDPEPWRCRRTDGKKWRCAKDVGPNQKYCDRHAHKTRSRSRKPVDTNTNTNTNHISNNHHHPATPSSTQQTMCHEWFIKSGTTTPVTQSKRDDCLL...

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_029448`
TK1151 ID	TkA07G316460
OH-1004 ID	LXL04_029448
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.200
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_029448

Location Chr06:90844124-90845474 (-)

Description Similar to GRF5: Growth-regulating factor 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g24150`	Transcription activator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues.	No verified direct reference in this release
`At2g22840`	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
`Os06g0116200`	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
`Os04g0600900`	Transcription activator that plays a regulatory role in gibberellin-induced stem elongation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029448 · 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:0009409 response to cold Biological Process

GO:0009624 response to nematode Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0019760 glucosinolate metabolic process 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:0048364 root development Biological Process

GO:0048366 leaf development Biological Process

KEGG gene cross-reference

ath:AT2G22840

ath:AT4G24150

dosa:Os02g0701300

dosa:Os04g0600900

dosa:Os06g0116200

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

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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.

Nucleus0.978

Rank 1 · LXL04_029448 · OH-1004

Cytoplasm0.083

Rank 2 · LXL04_029448 · OH-1004

Cell membrane0.023

Rank 3 · LXL04_029448 · OH-1004

Endoplasmic reticulum0.016

Rank 4 · LXL04_029448 · OH-1004

Plastid0.012

Rank 5 · LXL04_029448 · 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.

PF08880.17QLQ100-131 aa

PF08879.16WRC167-208 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029448	`PF08880.17`	QLQ	100	131	7.5e-10	39.0
LXL04_029448	`PF08879.16`	WRC	167	208	2e-18	66.5

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SU44`	Arabidopsis thaliana	Growth-regulating factor 8	42.177%	Swiss-Prot	weak database homology
`O81001`	Arabidopsis thaliana	Growth-regulating factor 1	37.500%	Swiss-Prot	weak database homology
`Q6AWY4`	Oryza sativa subsp. japonica	Growth-regulating factor 5	45.865%	Swiss-Prot	weak database homology
`Q6ZIK5`	Oryza sativa subsp. japonica	Growth-regulating factor 4	50.450%	Swiss-Prot	weak database homology
`Q6AWY6`	Oryza sativa subsp. japonica	Growth-regulating factor 3	49.550%	Swiss-Prot	weak database homology

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