LXL04_001236 | RubberDandelionOmics

Gene overview

LXL04_001236

Reference: OH-1004 Chr: Chr01 Coordinates: 22601816-22608777 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2052 bp · LXL04_001236|LXL04_001236|OH1004|cDNA

ATGGGCGGTGTTGTCTCGGAAATCAAGGAAGCGTCATCGAGGAAGAACAGCGAGTCTGCAATCTCAGCGGAAGAACAACGAGTCTATGATCTCATGTACAATTTTGGAAGGGAGGCAACAGTAGTGTTGCCACTTAAAAGTGATTCTTCTCTTGGTTACCTCCATTTTTCGCAAGCCTTTCGCCGTCTTCTACTATTACCCAACAAGTCTCCCTTTTCTCCATATACTTTCACCAATTTCGAGAAATTGACAACCAGTCA...

CDS

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2052 bp · LXL04_001236|LXL04_001236|OH1004|CDS

ATGGGCGGTGTTGTCTCGGAAATCAAGGAAGCGTCATCGAGGAAGAACAGCGAGTCTGCAATCTCAGCGGAAGAACAACGAGTCTATGATCTCATGTACAATTTTGGAAGGGAGGCAACAGTAGTGTTGCCACTTAAAAGTGATTCTTCTCTTGGTTACCTCCATTTTTCGCAAGCCTTTCGCCGTCTTCTACTATTACCCAACAAGTCTCCCTTTTCTCCATATACTTTCACCAATTTCGAGAAATTGACAACCAGTCA...

Protein

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683 aa · LXL04_001236|LXL04_001236|OH1004|PROTEIN

MGGVVSEIKEASSRKNSESAISAEEQRVYDLMYNFGREATVVLPLKSDSSLGYLHFSQAFRRLLLLPNKSPFSPYTFTNFEKLTTSQTWKATGSSRSILKLTPISIIGLFYRGVCFIEWVAAFIVEFYGSVNGKNESSQQKSTDISYIPNDEFVELVWEKGQIMMQGQSSKVRKTPVSSNFLFHTPKVQEKEVLLDVPMQELDDDMVPWLNYPIDDYCSDLLPEISGVTGNDHNTFNALDKRSSYNHSNKDSHPPNVPRS...

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_001236`
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_001236

Location Chr01:22601816-22608777 (-)

Description Similar to PIF3: Transcription factor PIF3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g09530`	Transcription factor acting in the phytochrome signaling pathway.	PHYTOCHROME INTERACTING FACTOR3 associates with the histone deacetylase HDA15 in repression of chlorophyll biosynthesis and photosynthesis in etiolated Arabidopsis seedlings.2013 · DOI: 10.1105/tpc.113.109710 Coordinated Regulation of Hypocotyl Cell Elongation by Light and Ethylene through a Microtubule Destabilizing Protein.2018 · DOI: 10.1104/pp.17.01109 Submergence stress-induced hypocotyl elongation through ethylene signaling-mediated regulation of cortical microtubules in Arabidopsis.2020 · DOI: 10.1093/jxb/erz453 PHYTOCHROME INTERACTING FACTOR8 Inhibits Phytochrome A-Mediated Far-Red Light Responses in Arabidopsis.2020 · DOI: 10.1105/tpc.19.00515
`At2g46970`	Transcription factor.	Identification of primary target genes of phytochrome signaling. Early transcriptional control during shade avoidance responses in Arabidopsis.2006 · DOI: 10.1104/pp.105.076331

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0286100`	Transcription factor that may act as negative regulator of phyB-dependent light signal transduction.	Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.2007 · DOI: 10.1271/bbb.60643
`Os05g0139100`	Atypical bHLH transcription factor that acts as a negative regulator of grain size.	No verified direct reference in this release
`Os03g0782500`	Transcription factor that may act as negative regulator of phyB-dependent light signal transduction.	Characterization of a set of phytochrome-interacting factor-like bHLH proteins in Oryza sativa.2007 · DOI: 10.1271/bbb.60643 Rice phytochrome-interacting factor-like protein OsPIL1 functions as a key regulator of internode elongation and induces a morphological response to drought stress.2012 · DOI: 10.1073/pnas.1207324109

Functional annotation source

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Functional annotation source: OH1004 · LXL04_001236 · 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:0007165 signal transduction Biological Process

GO:0009408 response to heat Biological Process

GO:0009409 response to cold Biological Process

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

GO:0009639 response to red or far red light Biological Process

GO:0009641 shade avoidance Biological Process

GO:0009704 de-etiolation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

GO:0009737 response to abscisic acid Biological Process

KEGG gene cross-reference

ath:AT1G09530

ath:AT2G46970

dosa:Os01g0286100

dosa:Os03g0782500

dosa:Os05g0139100

osa:4327916

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.

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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.

Nucleus0.973

Rank 1 · LXL04_001236 · OH-1004

Cytoplasm0.091

Rank 2 · LXL04_001236 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_001236 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_001236 · OH-1004

Plastid0.010

Rank 5 · LXL04_001236 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF00010.32HLH454-501 aa

PF23173.3bHLH_SAC51459-503 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001236	`PF00010.32`	HLH	454	501	4.7e-14	52.6
LXL04_001236	`PF23173.3`	bHLH_SAC51	459	503	1e-07	32.4

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
`O80536`	Arabidopsis thaliana	Transcription factor PIF3	39.871%	Swiss-Prot	moderate database homology
`Q8L5W8`	Arabidopsis thaliana	Transcription factor PIL1	39.676%	Swiss-Prot	weak database homology
`Q0JNI9`	Oryza sativa subsp. japonica	Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 15	34.455%	Swiss-Prot	moderate database homology
`Q6AT90`	Oryza sativa subsp. japonica	Transcription factor APG	62.698%	Swiss-Prot	weak database homology
`Q10CH5`	Oryza sativa subsp. japonica	Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13	41.841%	Swiss-Prot	weak database homology

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