LXL04_029627 | RubberDandelionOmics

Gene overview

LXL04_029627

Reference: OH-1004 Chr: Chr06 Coordinates: 95719779-95720141 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

363 bp · LXL04_029627|LXL04_029627|OH1004|cDNA

ATGAGGCAAGCCGGTGCATATTCAGGGATTTTATCAGGTGGAGGGGTATCAGGGCGAACTGGGCCCCATTTGTTGCCATTGGCAAGAATCAAGAAGATCATGAAGAAGTCAAGTGTAGATGTGAAGATGATTTCGGGAGAGGCCCCTCTTGTGTTTTCAAAAGCTTGTGAGCTTTTCATTGAGGAATTGACCAAAAGATCTTGGAATACGACCATTCAAGGAAAGAGAAGAACCCTACACAAAGAAGATGTTGCATCTGC...

CDS

Download CDS FASTA

363 bp · LXL04_029627|LXL04_029627|OH1004|CDS

ATGAGGCAAGCCGGTGCATATTCAGGGATTTTATCAGGTGGAGGGGTATCAGGGCGAACTGGGCCCCATTTGTTGCCATTGGCAAGAATCAAGAAGATCATGAAGAAGTCAAGTGTAGATGTGAAGATGATTTCGGGAGAGGCCCCTCTTGTGTTTTCAAAAGCTTGTGAGCTTTTCATTGAGGAATTGACCAAAAGATCTTGGAATACGACCATTCAAGGAAAGAGAAGAACCCTACACAAAGAAGATGTTGCATCTGC...

Protein

Download Protein FASTA

120 aa · LXL04_029627|LXL04_029627|OH1004|PROTEIN

MRQAGAYSGILSGGGVSGRTGPHLLPLARIKKIMKKSSVDVKMISGEAPLVFSKACELFIEELTKRSWNTTIQGKRRTLHKEDVASAVATTDVFDFLIDLVHPNASGDVDLDEEHVLEKK

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_029627`
TK1151 ID	TkA07G331080
OH-1004 ID	LXL04_029627
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_029627

Location Chr06:95719779-95720141 (-)

Description Similar to NFYC3: Nuclear transcription factor Y subunit C-3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g54830`	Stimulates the transcription of various genes by recognizing and binding to a CCAAT motif in promoters.	No verified direct reference in this release
`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
`At1g56170`	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
`Os03g0251350`	Probable transcription factor involved in the regulation of flowering time under long day (LD) conditions.	No verified direct reference in this release
`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_029627 · 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

dosa:Os03g0251350

dosa:Os06g0667100

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.

Nucleus0.920

Rank 1 · LXL04_029627 · OH-1004

Cytoplasm0.183

Rank 2 · LXL04_029627 · OH-1004

Mitochondrion0.020

Rank 3 · LXL04_029627 · OH-1004

Cell membrane0.016

Rank 4 · LXL04_029627 · OH-1004

Endoplasmic reticulum0.012

Rank 5 · LXL04_029627 · 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.

PF00125.31Histone23-88 aa

PF00808.30CBFD_NFYB_HMF25-88 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029627	`PF00125.31`	Histone	23	88	7.8e-15	55.8
LXL04_029627	`PF00808.30`	CBFD_NFYB_HMF	25	88	3e-17	63.3

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
`Q9ZVL3`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-3	67.089%	Swiss-Prot	moderate database homology
`Q8L4B2`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-9	67.089%	Swiss-Prot	moderate database homology
`Q8LCG7`	Arabidopsis thaliana	Nuclear transcription factor Y subunit C-2	63.291%	Swiss-Prot	moderate database homology
`A6BLW4`	Oryza sativa subsp. japonica	Nuclear transcription factor Y subunit C-2	67.089%	Swiss-Prot	moderate database homology
`Q655V5`	Oryza sativa subsp. japonica	Nuclear transcription factor Y subunit C-4	58.511%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card