LXL04_002335 | RubberDandelionOmics

Gene overview

LXL04_002335

Reference: OH-1004 Chr: Chr01 Coordinates: 46440220-46441430 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1002 bp · LXL04_002335|LXL04_002335|OH1004|cDNA

ATGATGAGTACAGAAGCCGGTGGCGGAAGTCTACGGAGTAACAATGGCGGCCGGTATCCTTTCACCGCAAGTCAATGGCAAGAACTCGAACACCAAGCGCTCGTTTACAAATACATGATTTCCGGCATGCCGATTCCGGCCGATCTTCTTTACACGATCAAGAAGAGTCTGGAATCTTCCACGAAGCTCCTTCTTCACCACCAGCCACCTCATCCTTCAATTGGGTGGAACTGTTTTCAAATGGGTTTCGGAAGAAAGAT...

CDS

Download CDS FASTA

1002 bp · LXL04_002335|LXL04_002335|OH1004|CDS

ATGATGAGTACAGAAGCCGGTGGCGGAAGTCTACGGAGTAACAATGGCGGCCGGTATCCTTTCACCGCAAGTCAATGGCAAGAACTCGAACACCAAGCGCTCGTTTACAAATACATGATTTCCGGCATGCCGATTCCGGCCGATCTTCTTTACACGATCAAGAAGAGTCTGGAATCTTCCACGAAGCTCCTTCTTCACCACCAGCCACCTCATCCTTCAATTGGGTGGAACTGTTTTCAAATGGGTTTCGGAAGAAAGAT...

Protein

Download Protein FASTA

333 aa · LXL04_002335|LXL04_002335|OH1004|PROTEIN

MMSTEAGGGSLRSNNGGRYPFTASQWQELEHQALVYKYMISGMPIPADLLYTIKKSLESSTKLLLHHQPPHPSIGWNCFQMGFGRKIDPEPGRCRRTDGKKWRCSKEAYPDSKYCERHMHRGRNRSRKPVEVNMSTHTTTPKPPPTIITKSPNYPSPNPHPLSSYSRSMGNMGSNNNNNNNNLLSSQDHFLLESSPYRKGYGMKEVIDEHPFFSESSGTIKTSLGGDSWQLEPLAMSNSNSLAHLKQRTFNDFHQNGYLY...

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_002335`
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_002335

Location Chr01:46440220-46441430 (+)

Description Similar to GRF1: Growth-regulating factor 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13960`	Transcription activator that plays a role in the regulation of cell expansion in leaf and cotyledons tissues.	The transcription factor AtGRF5 and the transcription coactivator AN3 regulate cell proliferation in leaf primordia of Arabidopsis thaliana.2005 · DOI: 10.1111/j.1365-313x.2005.02429.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os02g0776900`	Transcription activator that plays a regulatory role in gibberellin-induced stem elongation.	No verified direct reference in this release
`UniProt: A2XA73`	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_002335 · 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:0009739 response to gibberellin Biological Process

GO:0030912 response to deep water 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:AT3G13960

dosa:Os02g0701300

dosa:Os02g0776900

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.

Nucleus0.977

Rank 1 · LXL04_002335 · OH-1004

Cytoplasm0.080

Rank 2 · LXL04_002335 · OH-1004

Cell membrane0.031

Rank 3 · LXL04_002335 · OH-1004

Endoplasmic reticulum0.022

Rank 4 · LXL04_002335 · OH-1004

Plastid0.014

Rank 5 · LXL04_002335 · 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.

PF08880.17QLQ20-53 aa

PF08879.16WRC89-131 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002335	`PF08880.17`	QLQ	20	53	1.9e-14	53.7
LXL04_002335	`PF08879.16`	WRC	89	131	1.9e-21	76.2

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
`Q8L8A6`	Arabidopsis thaliana	Growth-regulating factor 5	68.376%	Swiss-Prot	weak database homology
`Q6AWY8`	Oryza sativa subsp. japonica	Growth-regulating factor 1	37.240%	Swiss-Prot	moderate database homology
`A2XA73`	Oryza sativa subsp. indica	Growth-regulating factor 1	37.566%	Swiss-Prot	moderate database homology
`Q6AWY6`	Oryza sativa subsp. japonica	Growth-regulating factor 3	36.522%	Swiss-Prot	moderate database homology
`Q6ZIK5`	Oryza sativa subsp. japonica	Growth-regulating factor 4	36.890%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card