LXL04_014196 | RubberDandelionOmics

Gene overview

LXL04_014196

Reference: OH-1004 Chr: Chr03 Coordinates: 43417725-43421461 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1419 bp · LXL04_014196|LXL04_014196|OH1004|cDNA

ATGAGAGAAGAGAAGGATGATGAACTCGACGAAGGTTGTGAACAAAGAAGAAAAAATGGATTAAAAGGTGGTGGAGTCTTGCTCCGGAGAATCGAAAGATCGCAAGACTCAGCACAACTGGTGGAGACTAGCCGTACAACGGAGAGAGTAATGTCGAATTCGGAGGGTTCATCTACTGCAACGCCCATCTCCTCCTCTAATATTGGCTTTCAGCTGCTGAAAAAACACGGCTGGAAAGAAGGAACCGGCCTCGGTATATC...

CDS

Download CDS FASTA

1419 bp · LXL04_014196|LXL04_014196|OH1004|CDS

ATGAGAGAAGAGAAGGATGATGAACTCGACGAAGGTTGTGAACAAAGAAGAAAAAATGGATTAAAAGGTGGTGGAGTCTTGCTCCGGAGAATCGAAAGATCGCAAGACTCAGCACAACTGGTGGAGACTAGCCGTACAACGGAGAGAGTAATGTCGAATTCGGAGGGTTCATCTACTGCAACGCCCATCTCCTCCTCTAATATTGGCTTTCAGCTGCTGAAAAAACACGGCTGGAAAGAAGGAACCGGCCTCGGTATATC...

Protein

Download Protein FASTA

472 aa · LXL04_014196|LXL04_014196|OH1004|PROTEIN

MREEKDDELDEGCEQRRKNGLKGGGVLLRRIERSQDSAQLVETSRTTERVMSNSEGSSTATPISSSNIGFQLLKKHGWKEGTGLGISEQGRLEPVQAFLKKNKRGLGAAEIKKPQSTEDKKKPVSDKTNDKLSKRSKAKISKKMRKAQELEKKLQENEFQRAFFREFWPDNCFWDLLPRKRDEQKVIVSINTAINIKIKIKVFCCITKFHTSDKMDPQGHGQPQSSNMMSSVTQLSYATNPYDSTQISGTPGRVPVGGAI...

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_014196`
TK1151 ID	TkA02G448420
OH-1004 ID	LXL04_014196
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	81.500
Protein coverage (%)	TK1151 77.907 / OH-1004 27.542 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_014196

Location Chr03:43417725-43421461 (+)

Description Similar to NFYC9: Nuclear transcription factor Y subunit C-9

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g08970`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters (By similarity).	No verified direct reference in this release
`At1g54830`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`At1g56170`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`At3g48590`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0667100`	Probable transcription factor involved in the regulation of flowering time under long day (LD) conditions.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014196 · 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:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009740 gibberellic acid mediated signaling pathway Biological Process

GO:0009908 flower development Biological Process

GO:0010029 regulation of seed germination Biological Process

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

GO:0048574 long-day photoperiodism, flowering Biological Process

GO:0048579 negative regulation of long-day photoperiodism, flowering Biological Process

GO:2000306 positive regulation of photomorphogenesis Biological Process

GO:0005576 extracellular region Cellular Component

KEGG gene cross-reference

ath:AT1G08970

ath:AT1G54830

ath:AT1G56170

ath:AT3G48590

dosa:Os06g0667100

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.

Nucleus0.899

Rank 1 · LXL04_014196 · OH-1004

Cytoplasm0.236

Rank 2 · LXL04_014196 · OH-1004

Mitochondrion0.026

Rank 3 · LXL04_014196 · OH-1004

Cell membrane0.018

Rank 4 · LXL04_014196 · OH-1004

Endoplasmic reticulum0.011

Rank 5 · LXL04_014196 · 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.

PF01585.29G-patch66-108 aa

PF12656.13G-patch_266-110 aa

PF00125.31Histone304-377 aa

PF00808.30CBFD_NFYB_HMF314-377 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014196	`PF01585.29`	G-patch	66	108	3.1e-18	66.1
LXL04_014196	`PF12656.13`	G-patch_2	66	110	3.6e-06	27.6
LXL04_014196	`PF00125.31`	Histone	304	377	4e-17	63.1
LXL04_014196	`PF00808.30`	CBFD_NFYB_HMF	314	377	1.4e-16	61.2

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
`Q8L4B2`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-9	58.537%	Swiss-Prot	moderate database homology
`Q9ZVL3`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-3	56.904%	Swiss-Prot	moderate database homology
`Q8LCG7`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-2	72.993%	Swiss-Prot	weak database homology
`Q9SMP0`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-1	66.456%	Swiss-Prot	weak database homology
`Q655V5`	Oryza sativa subsp. japonica	Nuclear transcription factor Y subunit C-4	55.319%	Swiss-Prot	weak database homology

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