LXL04_000359 | RubberDandelionOmics

Gene overview

LXL04_000359

Reference: OH-1004 Chr: Chr01 Coordinates: 6589973-6592432 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

939 bp · LXL04_000359|LXL04_000359|OH1004|cDNA

ATGGCAGATGCATATTGCTCCGACTGCAGGAAGAGCACCGAGGTCGTGTTCGACCACTCGGCCGGAGACACCGTCTGTTCCGAGTGTGGGCTCGTCCTTGAGTCCCATTCCATCGACGAGACATCTGAGTGGCGTACCTTCGCCAACGAGTCAGGTGATAACGATCCCGTCCGTGTCGGTGGCCCCACCAATGTCCTTCTCAACGATGGCGGCTTGTCAACCGTGATTTCCAAACCTAATGGCGTCACCAGCGATTTTCT...

CDS

Download CDS FASTA

939 bp · LXL04_000359|LXL04_000359|OH1004|CDS

ATGGCAGATGCATATTGCTCCGACTGCAGGAAGAGCACCGAGGTCGTGTTCGACCACTCGGCCGGAGACACCGTCTGTTCCGAGTGTGGGCTCGTCCTTGAGTCCCATTCCATCGACGAGACATCTGAGTGGCGTACCTTCGCCAACGAGTCAGGTGATAACGATCCCGTCCGTGTCGGTGGCCCCACCAATGTCCTTCTCAACGATGGCGGCTTGTCAACCGTGATTTCCAAACCTAATGGCGTCACCAGCGATTTTCT...

Protein

Download Protein FASTA

312 aa · LXL04_000359|LXL04_000359|OH1004|PROTEIN

MADAYCSDCRKSTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNVLLNDGGLSTVISKPNGVTSDFLSSSLGRWQNRGSNPDRSLIMAFKTIATMSDRLGLVATIKDRANEIFKKVEDQKSSRGRNQDAILAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLELEMGQSVEMGTIHAGDFMRRFCSNLGMTNQTVKAAQESVQKSEEFDIRRSPISIAAAVIYIVTQL...

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_000359`
TK1151 ID	TkA01G617500
OH-1004 ID	LXL04_000359
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	96.600
Protein coverage (%)	TK1151 100.000 / OH-1004 36.859 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_000359

Location Chr01:6589973-6592432 (-)

Description Similar to TFIIB2: Transcription initiation factor IIB-2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g10330`	General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.	No verified direct reference in this release
`At2g41630`	General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II (By similarity).	The Arabidopsis general transcription factor TFIIB1 (AtTFIIB1) is required for pollen tube growth and endosperm development.2013 · DOI: 10.1093/jxb/ert078

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0534800`	General factor that plays a major role in the activation of eukaryotic genes transcribed by RNA polymerase II.	Rice TATA binding protein interacts functionally with transcription factor IIB and the RF2a bZIP transcriptional activator in an enhanced plant in vitro transcription system.2002 · DOI: 10.1105/tpc.010364

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000359 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001174 transcriptional start site selection at RNA polymerase II promoter Biological Process

GO:0006352 DNA-templated transcription initiation Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0009960 endosperm development Biological Process

GO:0010183 pollen tube guidance Biological Process

GO:0042789 mRNA transcription by RNA polymerase II Biological Process

GO:0051123 RNA polymerase II preinitiation complex assembly Biological Process

GO:0070897 transcription preinitiation complex assembly Biological Process

GO:0080092 regulation of pollen tube growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0097550 transcription preinitiation complex Cellular Component

KEGG gene cross-reference

ath:AT2G41630

ath:AT3G10330

dme:Dmel_CG5193

gmx:548070

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.

Nucleus0.946

Rank 1 · LXL04_000359 · OH-1004

Cytoplasm0.141

Rank 2 · LXL04_000359 · OH-1004

Cell membrane0.027

Rank 3 · LXL04_000359 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_000359 · OH-1004

Mitochondrion0.010

Rank 5 · LXL04_000359 · 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.

PF08271.18Zn_Ribbon_TF5-47 aa

PF00382.25TFIIB102-185 aa

PF00382.25TFIIB204-290 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000359	`PF08271.18`	Zn_Ribbon_TF	5	47	6e-15	55.2
LXL04_000359	`PF00382.25`	TFIIB	102	185	1.5e-37	128.2
LXL04_000359	`PF00382.25`	TFIIB	204	290	1.5e-37	128.2

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
`Q9SS44`	Arabidopsis thaliana	Transcription initiation factor IIB-2	90.385%	Swiss-Prot	strong database homology
`P48512`	Arabidopsis thaliana	Transcription initiation factor IIB-1	82.051%	Swiss-Prot	strong database homology
`Q8W0W3`	Oryza sativa subsp. japonica	Transcription initiation factor IIB	84.295%	Swiss-Prot	strong database homology

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