TkA01G617500 | RubberDandelionOmics

Gene overview

TkA01G617500

Reference: TK1151 Chr: Chr01 Coordinates: 155830160-155833133 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1501 bp · TkA01G617500|TK1151|cDNA

TAGACAATTTGGAGATAGAAAATATTACTAAAACAATTAATATCGCATAAACACCGCATAATCCCCAGAGAAGGCTATCTTGTCCTTTCGAGTTTTCTCCGTTACTTCACCTTCGGCGGCTCCCCACCAATCTTAGATTGCAAACTCAAAATCGCAGAAAGAAATCATATGATCTGAACCTTCATCCACCAAATCTCCAAATCCCACATAAAATTTGTCCACAAAAAGACTTAAAATCCGAAAGATATGGCAGATGCATA...

CDS

Download CDS FASTA

351 bp · TkA01G617500|TK1151|CDS

ATGGGCCAGTCTGTTGAAATGGGGACTATTCATGCTGGTGATTTTATGAGGCGTTTTTGTTCCAATCTTGGTATGACTAATCAGACTGTTAAAGCTGCCCAAGAATCTGTCCAAAAGTCGGAGGAGTTTGATATAAGGAGAAGTCCAATCTCTATAGCTGCAGCTGTTATTTATATAGTAACTCAACTTTCTGATGATAAGAAACCCCTCAAAGACGTGGCACTTGCAACTGGAGTTGCAGAAGGTACAATAAGAAACTC...

Protein

Download Protein FASTA

116 aa · TkA01G617500|TK1151|PROTEIN

MGQSVEMGTIHAGDFMRRFCSNLGMTNQTVKAAQESVQKSEEFDIRRSPISIAAAVIYIVTQLSDDKKPLKDVALATGVAEGTIRNSYKDLYPHLVKIIPTWYAQEDEILRNLCSP

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	`TkA01G617500`
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	TK1151 / GWHBCHF00000000

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G617500

Location Chr01:155830160-155833133 (+)

Description Similar to TFIIB2: Transcription initiation factor IIB-2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At3g29380`	Plant-specific TFIIB-related protein involved in the regulation of endosperm proliferation during the syncytial phase of endosperm development.	No verified direct reference in this release

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. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

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.

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.

Nucleus0.868

Rank 1 · TkA01G617500 · TK1151

Cytoplasm0.208

Rank 2 · TkA01G617500 · TK1151

Cell membrane0.032

Rank 3 · TkA01G617500 · TK1151

Endoplasmic reticulum0.025

Rank 4 · TkA01G617500 · TK1151

Mitochondrion0.019

Rank 5 · TkA01G617500 · TK1151

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.

PF00382TFIIB7-93 aa

PF13542HTH_Tnp_ISL357-90 aa

PF15075SPMAP1-like78-109 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G617500	`PF00382`	TFIIB	7	93	2.4e-14	53.9
TkA01G617500	`PF13542`	HTH_Tnp_ISL3	57	90	0.013	15.7
TkA01G617500	`PF15075`	SPMAP1-like	78	109	0.28	12.3

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
`Q9SS44`	Arabidopsis thaliana	sp\|Q9SS44\|TF2B2_ARATH Transcription initiation factor IIB-2	87.000%	Swiss-Prot	High
`P48512`	Arabidopsis thaliana	sp\|P48512\|TF2B1_ARATH Transcription initiation factor IIB-1	80.900%	Swiss-Prot	High
`Q9LIA6`	Arabidopsis thaliana	sp\|Q9LIA6\|PBRP2_ARATH Plant-specific TFIIB-related protein 2	42.300%	Swiss-Prot	Medium
`Q8W0W3`	Oryza sativa subsp. japonica	sp\|Q8W0W3\|TF2B_ORYSJ Transcription initiation factor IIB	78.400%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card