LXL04_025075 | RubberDandelionOmics

Gene overview

LXL04_025075

Reference: OH-1004 Chr: Chr05 Coordinates: 105446186-105449868 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2145 bp · LXL04_025075|LXL04_025075|OH1004|cDNA

ATGGAAGAAATCGATTTCAATTTCAATGGAAGAATCGATGAAGAAATCAATGGAAGCAATCGATTTCTCAATAGGGCGACGACGGAAGAACAGCGACGACGTAGGggagaagaaggaagaacagCGGCGGAAGAACAGAGGACGGAAGGAGAAAGGATTTTGGCGAGAGAGGAAGAAGACGCAATGGAGAAGACGACGACCCTGTTCTTTCGTTGTAACTATATACAAGAAATAAATAATAAACCTAACACTATCACCGG...

CDS

Download CDS FASTA

2145 bp · LXL04_025075|LXL04_025075|OH1004|CDS

ATGGAAGAAATCGATTTCAATTTCAATGGAAGAATCGATGAAGAAATCAATGGAAGCAATCGATTTCTCAATAGGGCGACGACGGAAGAACAGCGACGACGTAGGGGAGAAGAAGGAAGAACAGCGGCGGAAGAACAGAGGACGGAAGGAGAAAGGATTTTGGCGAGAGAGGAAGAAGACGCAATGGAGAAGACGACGACCCTGTTCTTTCGTTGTAACTATATACAAGAAATAAATAATAAACCTAACACTATCACCGG...

Protein

Download Protein FASTA

714 aa · LXL04_025075|LXL04_025075|OH1004|PROTEIN

MEEIDFNFNGRIDEEINGSNRFLNRATTEEQRRRRGEEGRTAAEEQRTEGERILAREEEDAMEKTTTLFFRCNYIQEINNKPNTITGDNQELPEYRRPPPDHLRQPSEKQKRTKEEEKTETVVFLFTTTVTASTPASDEPPLLPTDKPLPLTNHRDVDKPPEKHKQTTGKNRNESEADSEEVVALTDSEWNHRRKLPETARTCRKMQETSSNPRKPPETAGEIAGEISADATYKTNKYNMAFVEIVGVTSTNKTFSIAFA...

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_025075`
TK1151 ID	TkA06G082540
OH-1004 ID	LXL04_025075
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	79.100
Protein coverage (%)	TK1151 65.839 / OH-1004 18.768 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_025075

Location Chr05:105446186-105449868 (-)

Description Similar to FRS5: Protein FAR1-RELATED SEQUENCE 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g38180`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`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
`At3g06250`	Putative transcription activator involved in regulating light control of development.	No verified direct reference in this release
`At5g18960`	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

View annotation sources

Functional annotation source: OH1004 · LXL04_025075 · 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:0006633 fatty acid biosynthetic process Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009403 toxin biosynthetic process Biological Process

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

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

GO:0010218 response to far red light Biological Process

GO:0032259 methylation 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

KEGG gene cross-reference

ath:AT3G06250

ath:AT3G22170

ath:AT4G38180

ath:AT5G18960

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.

Nucleus0.664

Rank 1 · LXL04_025075 · OH-1004

Cytoplasm0.291

Rank 2 · LXL04_025075 · OH-1004

Cell membrane0.057

Rank 3 · LXL04_025075 · OH-1004

Mitochondrion0.047

Rank 4 · LXL04_025075 · OH-1004

Endoplasmic reticulum0.034

Rank 5 · LXL04_025075 · 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.

PF10551.16MULE228-321 aa

PF21056.4ZSWIM1-3_RNaseH-like228-310 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025075	`PF10551.16`	MULE	228	321	2.8e-27	95.6
LXL04_025075	`PF21056.4`	ZSWIM1-3_RNaseH-like	228	310	1.1e-07	32.6

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
`Q9SZL8`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 5	30.088%	Swiss-Prot	weak database homology
`Q9LIE5`	Arabidopsis thaliana	Protein FAR-RED ELONGATED HYPOCOTYL 3	27.193%	Swiss-Prot	weak database homology
`Q9M8J3`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 7	23.881%	Swiss-Prot	weak database homology
`Q3E7I5`	Arabidopsis thaliana	Protein FAR1-RELATED SEQUENCE 12	25.962%	Swiss-Prot	weak database homology

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