TkA01G401660 | RubberDandelionOmics

Gene overview

TkA01G401660

Reference: TK1151 Chr: Chr01 Coordinates: 100340910-100347434 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3638 bp · TkA01G401660|TK1151|cDNA

TAACAGTGGGCTCACCGCCAACTTCGGCCCCAAATCTGTTCTATAAATCAAATGCATACACGTCTCCACTCTCGAAGTTTTACTCGTGTATCAATCGTGATATGTTAACGTTTTTTCTAGGGTTAACGTTTCACTGTAATCTTTGTCTATCTTCTCTATGACTCTATCTATGGATTAGGGCACGTATCGCTCCTCAAATTCAACTCAATCCGCTTCATTTCCCTTTCAGTTGCTTTGCTGTATAATTAGCATAACTGGAT...

CDS

Download CDS FASTA

2649 bp · TkA01G401660|TK1151|CDS

ATGAGCAGCATTGCATCTCAGCCATTATCAACACCTCTCCAAATGGAACCACCTGTATCCAATCAAGACTCATCACTCAACAACATGGGCCCACAGAAGCCATTACTTCCTTCAAAACGAAAAGCTGCATCCGAATCCTTTTCCAACAACCCTTTATCCTCAATCCCAAACAAACGTGGTGTACTTCATATGGATGTAATCTCAAGTCCAAGTCCAAATTCAAATTCAAATTCACCACTTTCTGTTAACAGGAAACAAAC...

Protein

Download Protein FASTA

882 aa · TkA01G401660|TK1151|PROTEIN

MSSIASQPLSTPLQMEPPVSNQDSSLNNMGPQKPLLPSKRKAASESFSNNPLSSIPNKRGVLHMDVISSPSPNSNSNSPLSVNRKQTQVPSSQPNKRMIRNESMSSNKTVSPRVQMSKSKTAPMEVSPKVQSESYVRAKMRDTLSAALSVGIQTKDEEPSKNASHEESGNAGPTADVAKPQYNYVMPETDDTFFVKDELLQGNGLSWAWDMEVVDEKSNPGQQSQTTETGTDNVNDTEEVVKESPQELAIKIEAELFKLF...

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	`TkA01G401660`
TK1151 ID	TkA01G401660
OH-1004 ID	LXL04_005669
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.600
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G401660

Location Chr01:100340910-100347434 (+)

Description Similar to PHF3: PHD finger protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g38560`	Necessary for efficient RNA polymerase II transcription elongation past template-encoded arresting sites (Probable).	Transcript elongation factor TFIIS is involved in arabidopsis seed dormancy.2009 · DOI: 10.1016/j.jmb.2008.12.066 Identification of the Arabidopsis REDUCED DORMANCY 2 gene uncovers a role for the polymerase associated factor 1 complex in seed dormancy.2011 · DOI: 10.1371/journal.pone.0022241

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005669 · 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:0006351 DNA-templated transcription Biological Process

GO:0006368 transcription elongation by RNA polymerase II Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0030154 cell differentiation Biological Process

GO:0141006 transposable element silencing by piRNA-mediated heterochromatin formation Biological Process

GO:0141196 transposable element silencing by piRNA-mediated DNA methylation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005694 chromosome Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005819 spindle Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

cel:CELE_T24H10.1

hsa:11083

hsa:23469

hsa:90853

mmu:23856

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.

Nucleus0.942

Rank 1 · TkA01G401660 · TK1151

Cytoplasm0.106

Rank 2 · TkA01G401660 · TK1151

Cell membrane0.048

Rank 3 · TkA01G401660 · TK1151

Endoplasmic reticulum0.041

Rank 4 · TkA01G401660 · TK1151

Plastid0.015

Rank 5 · TkA01G401660 · 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.

PF07500TFIIS_M135-159 aa

PF07500TFIIS_M239-323 aa

PF15335CAAP1294-327 aa

PF07744SPOC498-643 aa

PF07500TFIIS_M559-583 aa

PF07500TFIIS_M611-624 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G401660	`PF07500`	TFIIS_M	135	159	1e-28	100.7
TkA01G401660	`PF07500`	TFIIS_M	239	323	1e-28	100.7
TkA01G401660	`PF15335`	CAAP1	294	327	0.35	12.1
TkA01G401660	`PF07744`	SPOC	498	643	6.5e-24	85.3
TkA01G401660	`PF07500`	TFIIS_M	559	583	1e-28	100.7
TkA01G401660	`PF07500`	TFIIS_M	611	624	1e-28	100.7

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
`Q9ZVH8`	Arabidopsis thaliana	sp\|Q9ZVH8\|RDO2_ARATH Transcription elongation factor TFIIS	41.100%	Swiss-Prot	Low

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