LXL04_037978 | RubberDandelionOmics

Gene overview

LXL04_037978

Reference: OH-1004 Chr: Chr09 Coordinates: 27260770-27267767 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3570 bp · LXL04_037978|LXL04_037978|OH1004|cDNA

ATGTCATCAAGATCAACTAGCAGGACCCATTGTTCCAGGAGCAGTTCATCAAGATTGAAACGCGATGCTCGAGTGATCTCACAAACCCCAATTGACGCAAAGCTTCATGGAGATTTCGAAGACTCCGAACGACAATTTGACTACTCTACTTCCGTCGACGTCAACGCATCAACGTCAACCAGCAATGTCCCGTCATCGACTGTATCAGCGTACCTTCAAAAAATGCAAAGAGGAACTCTAATCCAGCCTTTCGGTTGCAT...

CDS

Download CDS FASTA

3570 bp · LXL04_037978|LXL04_037978|OH1004|CDS

ATGTCATCAAGATCAACTAGCAGGACCCATTGTTCCAGGAGCAGTTCATCAAGATTGAAACGCGATGCTCGAGTGATCTCACAAACCCCAATTGACGCAAAGCTTCATGGAGATTTCGAAGACTCCGAACGACAATTTGACTACTCTACTTCCGTCGACGTCAACGCATCAACGTCAACCAGCAATGTCCCGTCATCGACTGTATCAGCGTACCTTCAAAAAATGCAAAGAGGAACTCTAATCCAGCCTTTCGGTTGCAT...

Protein

Download Protein FASTA

1189 aa · LXL04_037978|LXL04_037978|OH1004|PROTEIN

MSSRSTSRTHCSRSSSSRLKRDARVISQTPIDAKLHGDFEDSERQFDYSTSVDVNASTSTSNVPSSTVSAYLQKMQRGTLIQPFGCMIAIDEQTLTVLAYSENALEMLDLAPHAVPNIEQQEALTFGTDVRTLFRSSSASALQKAVNFPEINLLNPILVHCRSSGKPFYAILHRNDVGLIIDLEPVNPADVPVTAAGALKSYKLAAKAISRLQSLQSGNITRMCDVLVREVSELTGYDRVMVYKFHEDEHGEVIAECRKP...

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_037978`
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_037978

Location Chr09:27260770-27267767 (-)

Description Similar to PHYC: Phytochrome C

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g35840`	Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0752100`	Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.	No verified direct reference in this release
`UniProt: A2XM23`	Regulatory photoreceptor which exists in two forms that are reversibly interconvertible by light: the Pr form that absorbs maximally in the red region of the spectrum and the Pfr form that absorbs maximally in the far-red region.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037978 · 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:0009584 detection of visible light Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009637 response to blue light Biological Process

GO:0017006 protein-tetrapyrrole linkage Biological Process

GO:0005634 nucleus Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0000155 phosphorelay sensor kinase activity Molecular Function

GO:0009881 photoreceptor activity Molecular Function

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT5G35840

dosa:Os03g0752100

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.

Cytoplasm0.335

Rank 1 · LXL04_037978 · OH-1004

Nucleus0.248

Rank 2 · LXL04_037978 · OH-1004

Cell membrane0.183

Rank 3 · LXL04_037978 · OH-1004

Endoplasmic reticulum0.137

Rank 4 · LXL04_037978 · OH-1004

Golgi apparatus0.118

Rank 5 · LXL04_037978 · 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.

PF08446.18PAS_270-186 aa

PF01590.33GAF221-412 aa

PF00360.27PHY426-600 aa

PF00989.32PAS638-751 aa

PF08448.17PAS_4645-755 aa

PF00989.32PAS768-890 aa

PF02518.32HATPase_c1054-1164 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037978	`PF08446.18`	PAS_2	70	186	2.1e-37	128.8
LXL04_037978	`PF01590.33`	GAF	221	412	5.5e-15	56.8
LXL04_037978	`PF00360.27`	PHY	426	600	1e-56	191.9
LXL04_037978	`PF00989.32`	PAS	638	751	2e-34	118.7
LXL04_037978	`PF08448.17`	PAS_4	645	755	1.4e-07	32.4
LXL04_037978	`PF00989.32`	PAS	768	890	2e-34	118.7
LXL04_037978	`PF02518.32`	HATPase_c	1054	1164	2.3e-14	54.5

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
`P14714`	Arabidopsis thaliana	Phytochrome C	57.524%	Swiss-Prot	strong database homology
`Q10CQ8`	Oryza sativa subsp. japonica	Phytochrome C	62.137%	Swiss-Prot	strong database homology
`A2XM23`	Oryza sativa subsp. indica	Phytochrome C	62.051%	Swiss-Prot	strong database homology

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