LXL04_022403 | RubberDandelionOmics

Gene overview

LXL04_022403

Reference: OH-1004 Chr: Chr04 Coordinates: 149569702-149572701 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2517 bp · LXL04_022403|LXL04_022403|OH1004|cDNA

ATGGATATTGATCTTAGGCTCCCATCTGGAGACCATGAAAATGAAGAGAAAGAAGAGGCGAAAGAAATGAGCAACATGATAGATGTTGAACATAAAATACACAATGAAGAGTTTCTAACCATTAGAGACAAATCACCTCATGACAATGACATAGTCTTGAATTCACCATCACTTGATATGGTAGATTATAAAGATGACATAAACCTCGAACCAATTGCTGGCATGGAATTCATATCAAATGGTGAAGCATATTCTTTCTA...

CDS

Download CDS FASTA

2517 bp · LXL04_022403|LXL04_022403|OH1004|CDS

ATGGATATTGATCTTAGGCTCCCATCTGGAGACCATGAAAATGAAGAGAAAGAAGAGGCGAAAGAAATGAGCAACATGATAGATGTTGAACATAAAATACACAATGAAGAGTTTCTAACCATTAGAGACAAATCACCTCATGACAATGACATAGTCTTGAATTCACCATCACTTGATATGGTAGATTATAAAGATGACATAAACCTCGAACCAATTGCTGGCATGGAATTCATATCAAATGGTGAAGCATATTCTTTCTA...

Protein

Download Protein FASTA

838 aa · LXL04_022403|LXL04_022403|OH1004|PROTEIN

MDIDLRLPSGDHENEEKEEAKEMSNMIDVEHKIHNEEFLTIRDKSPHDNDIVLNSPSLDMVDYKDDINLEPIAGMEFISNGEAYSFYQEYARSMGFTTAIQNSRRSKTSREFIDAKFACSRYGTKREHDKTFNRTRGRQGTNTQDPENASGRRSGSKTDCKASMHIKRRPDGKWIIHRFEKEHNHELLPAQAVSEQTRNMYAAMARQFAEYKNVIGLKNDSSNPFDKTRTTGLESGDANTFCKFFAQMQTINSNFFYAID...

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_022403`
TK1151 ID	TkA05G464950
OH-1004 ID	LXL04_022403
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.500
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_022403

Location Chr04:149569702-149572701 (-)

Description Similar to FHY3: Protein FAR-RED ELONGATED HYPOCOTYL 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g22170`	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'.	Arabidopsis FHY3 defines a key phytochrome A signaling component directly interacting with its homologous partner FAR1.2002 · DOI: 10.1093/emboj/21.6.1339 The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway.2003 · DOI: 10.1046/j.1365-313x.2003.01741.x Arabidopsis FHY3 specifically gates phytochrome signaling to the circadian clock.2006 · DOI: 10.1105/tpc.105.037358 Transposase-derived transcription factors regulate light signaling in Arabidopsis.2007 · DOI: 10.1126/science.1146281 Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction.2008 · DOI: 10.1104/pp.108.120436 Transposase-derived proteins FHY3/FAR1 interact with PHYTOCHROME-INTERACTING FACTOR1 to regulate chlorophyll biosynthesis by modulating HEMB1 during deetiolation in Arabidopsis.2012 · DOI: 10.1105/tpc.112.097022
`At4g15090`	Transcription activator that recognizes and binds to the DNA consensus sequence 5'-CACGCGC-3'.	No verified direct reference in this release
`At1g76320`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At2g32250`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At4g19990`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_022403 · 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:0007623 circadian rhythm Biological Process

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

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

GO:0010017 red or far-red light signaling pathway Biological Process

GO:0010018 far-red light signaling pathway Biological Process

GO:0010218 response to far red light Biological Process

GO:0042753 positive regulation of circadian rhythm Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:1900056 negative regulation of leaf senescence Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G76320

ath:AT2G32250

ath:AT3G22170

ath:AT4G15090

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.

Nucleus0.960

Rank 1 · LXL04_022403 · OH-1004

Cytoplasm0.072

Rank 2 · LXL04_022403 · OH-1004

Cell membrane0.022

Rank 3 · LXL04_022403 · OH-1004

Plastid0.014

Rank 4 · LXL04_022403 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_022403 · 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.

PF03101.22FAR185-189 aa

PF21056.4ZSWIM1-3_RNaseH-like258-370 aa

PF10551.16MULE287-379 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_022403	`PF03101.22`	FAR1	85	189	1.4e-26	93.7
LXL04_022403	`PF21056.4`	ZSWIM1-3_RNaseH-like	258	370	1.1e-06	29.3
LXL04_022403	`PF10551.16`	MULE	287	379	8e-26	91.0

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
`Q9LIE5`	Arabidopsis thaliana	Protein FAR-RED ELONGATED HYPOCOTYL 3	59.294%	Swiss-Prot	strong database homology
`Q9SWG3`	Arabidopsis thaliana	Protein FAR-RED IMPAIRED RESPONSE 1	50.000%	Swiss-Prot	strong database homology
`Q6NQJ7`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 4	41.417%	Swiss-Prot	moderate database homology
`Q3EBQ3`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 2	39.142%	Swiss-Prot	moderate database homology
`Q5UBY2`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 1	38.866%	Swiss-Prot	moderate database homology

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