LXL04_000873 | RubberDandelionOmics

Gene overview

LXL04_000873

Reference: OH-1004 Chr: Chr01 Coordinates: 16000880-16009297 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1143 bp · LXL04_000873|LXL04_000873|OH1004|cDNA

ATGAATCATATTGTTCCTGACTTCCAAGCGGACGAGGATTACTTAATTACGGAGTTGCCTAAGAAATCGATAATTATCTGGACCGAGTTTTGCAGGGTTGGAGATGAAGATGTGATGGAGCTACTATGGAAAAATGGTGAAGTGGTGATGCAGAGCCAAAATCAGAGATCCGCCGGGAATAAGAAGCCAGAAACGAGGCCGCCGTTGGCCAGTAGAGAGATCCGATCCTCCGTTGCAGATGAAGAAACGGGACCTTCTGA...

CDS

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1143 bp · LXL04_000873|LXL04_000873|OH1004|CDS

ATGAATCATATTGTTCCTGACTTCCAAGCGGACGAGGATTACTTAATTACGGAGTTGCCTAAGAAATCGATAATTATCTGGACCGAGTTTTGCAGGGTTGGAGATGAAGATGTGATGGAGCTACTATGGAAAAATGGTGAAGTGGTGATGCAGAGCCAAAATCAGAGATCCGCCGGGAATAAGAAGCCAGAAACGAGGCCGCCGTTGGCCAGTAGAGAGATCCGATCCTCCGTTGCAGATGAAGAAACGGGACCTTCTGA...

Protein

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380 aa · LXL04_000873|LXL04_000873|OH1004|PROTEIN

MNHIVPDFQADEDYLITELPKKSIIIWTEFCRVGDEDVMELLWKNGEVVMQSQNQRSAGNKKPETRPPLASREIRSSVADEETGPSDLFMQEDEMASWLHYPVDDNTLESYLYSNDLLYPTPPSSAPLTTDSRSLPPPPPPSVMIPSPRPPIPPVRREVELGQPKYPNFLHFSRLNKGRTPESGPSNSNMLPGALKPSTVVASNETSGAEAPESRASRVSDKPTPVSATTNIGYGGVGAAGRSSAGREIETCEPSVTSTP...

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_000873`
TK1151 ID	TkA04G023960
OH-1004 ID	LXL04_000873
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	63.200
Protein coverage (%)	TK1151 69.403 / OH-1004 99.211 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_000873

Location Chr01:16000880-16009297 (-)

Description Similar to PIF1: Transcription factor PIF1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g20180`	Transcription activator.	SOMNUS, a CCCH-type zinc finger protein in Arabidopsis, negatively regulates light-dependent seed germination downstream of PIL5.2008 · DOI: 10.1105/tpc.108.058859
`At4g28790`	Transcription factor bHLH23.	No verified direct reference in this release
`At4g28800`	Putative transcription factor bHLH056.	No verified direct reference in this release
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`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_000873 · 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:0006783 heme biosynthetic process 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:0009686 gibberellin biosynthetic process Biological Process

GO:0009704 de-etiolation Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009733 response to auxin Biological Process

KEGG gene cross-reference

ath:AT1G09530

ath:AT2G20180

ath:AT4G28790

dosa:Os03g0782500

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_000873 · OH-1004

Cytoplasm0.098

Rank 2 · LXL04_000873 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_000873 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_000873 · OH-1004

Plastid0.009

Rank 5 · LXL04_000873 · 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.

PF00010.32HLH326-373 aa

PF23173.3bHLH_SAC51331-375 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000873	`PF00010.32`	HLH	326	373	6.6e-14	52.2
LXL04_000873	`PF23173.3`	bHLH_SAC51	331	375	1.2e-08	35.4

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
`Q8GZM7`	Arabidopsis thaliana	Transcription factor PIF1	43.038%	Swiss-Prot	moderate database homology
`Q9SVU6`	Arabidopsis thaliana	Transcription factor bHLH23	35.598%	Swiss-Prot	moderate database homology
`Q9SVU7`	Arabidopsis thaliana	Putative transcription factor bHLH056	34.555%	Swiss-Prot	moderate database homology
`O80536`	Arabidopsis thaliana	Transcription factor PIF3	62.931%	Swiss-Prot	weak database homology
`Q10CH5`	Oryza sativa subsp. japonica	Transcription factor PHYTOCHROME INTERACTING FACTOR-LIKE 13	65.686%	Swiss-Prot	weak database homology

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