LXL04_030101 | RubberDandelionOmics

Gene overview

LXL04_030101

Reference: OH-1004 Chr: Chr06 Coordinates: 108191975-108199896 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5460 bp · LXL04_030101|LXL04_030101|OH1004|cDNA

ATGGATTCTGATGCTGGTAATACATCTCAAGATGGGAGGGCCACTGATGACCGTGATGAAGATAACCATGATGAATATGAAGATGCTCTAAAATCTCAACTGgcagatgatgatgatgagtaTGAAGATGCTCGTGATGGCAATCGTCTTTTGGAATTCATGTTTGGAAATATCGATGGGTCTGGTGATCTTGACATTGATTACCTTGATGAGGATGCAAAGGAGCATCTTGCTGCATTAGCTGACAAACTTGGTTCATC...

CDS

Download CDS FASTA

5460 bp · LXL04_030101|LXL04_030101|OH1004|CDS

ATGGATTCTGATGCTGGTAATACATCTCAAGATGGGAGGGCCACTGATGACCGTGATGAAGATAACCATGATGAATATGAAGATGCTCTAAAATCTCAACTGGCAGATGATGATGATGAGTATGAAGATGCTCGTGATGGCAATCGTCTTTTGGAATTCATGTTTGGAAATATCGATGGGTCTGGTGATCTTGACATTGATTACCTTGATGAGGATGCAAAGGAGCATCTTGCTGCATTAGCTGACAAACTTGGTTCATC...

Protein

Download Protein FASTA

1819 aa · LXL04_030101|LXL04_030101|OH1004|PROTEIN

MDSDAGNTSQDGRATDDRDEDNHDEYEDALKSQLADDDDEYEDARDGNRLLEFMFGNIDGSGDLDIDYLDEDAKEHLAALADKLGSSLTDIHLSVKTSQKSSDATEQDYDVKDENAVDYEDIDEQYEGPEVQALTEEDYLLPKSDYVSTTVPPVAPSSIFDDDNYDEDEEEEEGEGLQKEQDPVLDNNVDQVDQTQTTTSLPEDDNTNAAVEIEISDPDVVELPKEDTDISEEPLEAKSSTPLPVLCVEDGNVILRFSEI...

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_030101`
TK1151 ID	TkA07G375620
OH-1004 ID	LXL04_030101
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
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

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Basic Information and Functional Annotation

Gene ID LXL04_030101

Location Chr06:108191975-108199896 (-)

Description Similar to TAF1: Transcription initiation factor TFIID subunit 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g32750`	TAFs are components of the transcription factor IID (TFIID) complex that is essential for mediating regulation of RNA polymerase transcription.	No verified direct reference in this release
`At3g19040`	TAFs are components of the transcription factor IID (TFIID) complex that is essential for mediating regulation of RNA polymerase transcription.	Arabidopsis HAF2 gene encoding TATA-binding protein (TBP)-associated factor TAF1, is required to integrate light signals to regulate gene expression and growth.2005 · DOI: 10.1074/jbc.m409000200 Arabidopsis GCN5, HD1, and TAF1/HAF2 interact to regulate histone acetylation required for light-responsive gene expression.2006 · DOI: 10.1105/tpc.106.043489

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0645700`	Largest component and core scaffold of the TFIID basal transcription factor complex.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030101 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009294 DNA-mediated transformation Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0051123 RNA polymerase II preinitiation complex assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005669 transcription factor TFIID complex Cellular Component

GO:0004402 histone acetyltransferase activity Molecular Function

GO:0016251 RNA polymerase II general transcription initiation factor activity Molecular Function

GO:0017025 TBP-class protein binding Molecular Function

KEGG gene cross-reference

ath:AT1G32750

ath:AT3G19040

ddi:DDB_G0292242

osa:9266475

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.

Nucleus0.952

Rank 1 · LXL04_030101 · OH-1004

Cytoplasm0.133

Rank 2 · LXL04_030101 · OH-1004

Cell membrane0.018

Rank 3 · LXL04_030101 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_030101 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_030101 · 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.

PF09247.17TBP-binding38-85 aa

PF12157.14DUF3591533-1097 aa

PF11976.15Rad60-SLD616-686 aa

PF00240.30ubiquitin618-688 aa

PF00439.31Bromodomain1710-1784 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_030101	`PF09247.17`	TBP-binding	38	85	1.9e-09	38.4
LXL04_030101	`PF12157.14`	DUF3591	533	1097	6.9e-120	401.5
LXL04_030101	`PF11976.15`	Rad60-SLD	616	686	3.3e-08	33.9
LXL04_030101	`PF00240.30`	ubiquitin	618	688	5.8e-12	45.9
LXL04_030101	`PF00439.31`	Bromodomain	1710	1784	1.3e-18	67.5

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
`Q8LRK9`	Arabidopsis thaliana	Transcription initiation factor TFIID subunit 1	50.077%	Swiss-Prot	strong database homology
`Q6PUA2`	Arabidopsis thaliana	Transcription initiation factor TFIID subunit 1b	44.806%	Swiss-Prot	moderate database homology
`Q67W65`	Oryza sativa subsp. japonica	Transcription initiation factor TFIID subunit 1	49.758%	Swiss-Prot	moderate database homology

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