TkA04G113060 | RubberDandelionOmics

Gene overview

TkA04G113060

Reference: TK1151 Chr: Chr04 Coordinates: 29364360-29365054 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

471 bp · TkA04G113060|TK1151|cDNA

TGTTTGAAGACGACTAACAACAAAAAGTACGATGTTGACCTGGTTTCCTTTACTTCACACCCCATAAGTATTATATACTCCTCTAAAAACAGATGGGATGAATCTTTACGGCTTCTTTCTTTGCATGACAACAAATATTTGCGCTACTTTAAAGGTCATCATGAGTGGGCTGTCTCTCTTAGTCTATGTGCCCCAACAGATTGTTTCATTTTGGGCTCTCTTGATAGAATCTTTATTCTTTGGGATCAAAGTATTGATAA...

CDS

Download CDS FASTA

471 bp · TkA04G113060|TK1151|CDS

TGTTTGAAGACGACTAACAACAAAAAGTACGATGTTGACCTGGTTTCCTTTACTTCACACCCCATAAGTATTATATACTCCTCTAAAAACAGATGGGATGAATCTTTACGGCTTCTTTCTTTGCATGACAACAAATATTTGCGCTACTTTAAAGGTCATCATGAGTGGGCTGTCTCTCTTAGTCTATGTGCCCCAACAGATTGTTTCATTTTGGGCTCTCTTGATAGAATCTTTATTCTTTGGGATCAAAGTATTGATAA...

Protein

Download Protein FASTA

156 aa · TkA04G113060|TK1151|PROTEIN

CLKTTNNKKYDVDLVSFTSHPISIIYSSKNRWDESLRLLSLHDNKYLRYFKGHHEWAVSLSLCAPTDCFILGSLDRIFILWDQSIDKWQGHLWVKGKPASAYTDQGLVFVVAFGGSIRMVDSYNYKKVSCTLYISICRYVCMYVWFMCLIPFVAHL

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	`TkA04G113060`
TK1151 ID	TkA04G113060
OH-1004 ID	LXL04_013818
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	58.700
Protein coverage (%)	TK1151 81.410 / OH-1004 39.143 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

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Basic Information and Functional Annotation

Gene ID TkA04G113060

Location Chr04:29364360-29365054 (-)

Description Similar to APRF1: Protein ANTHESIS POMOTING FACTOR 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g14530`	Component of a chromatin regulatory complex involved in regulating chromatin structure in the nucleus (By similarity).	APRF1 promotes flowering under long days in Arabidopsis thaliana.2016 · DOI: 10.1016/j.plantsci.2016.09.015

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013818 · 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:0001111 RNA polymerase II promoter clearance Biological Process

GO:0006353 DNA-templated transcription termination Biological Process

GO:0009908 flower development Biological Process

GO:0010467 gene expression Biological Process

GO:0032785 negative regulation of DNA-templated transcription, elongation Biological Process

GO:0032968 positive regulation of transcription elongation by RNA polymerase II Biological Process

GO:0048510 regulation of timing of transition from vegetative to reproductive phase Biological Process

GO:0048586 regulation of long-day photoperiodism, flowering Biological Process

GO:0071027 nuclear RNA surveillance Biological Process

GO:0110064 lncRNA catabolic process Biological Process

GO:0140744 negative regulation of lncRNA transcription Biological Process

GO:0000781 chromosome, telomeric region Cellular Component

KEGG gene cross-reference

ath:AT5G14530

mmu:77305

xla:494657

xla:735072

xtr:448141

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.

Nucleus0.515

Rank 1 · TkA04G113060 · TK1151

Cytoplasm0.361

Rank 2 · TkA04G113060 · TK1151

Endoplasmic reticulum0.066

Rank 3 · TkA04G113060 · TK1151

Mitochondrion0.053

Rank 4 · TkA04G113060 · TK1151

Cell membrane0.045

Rank 5 · TkA04G113060 · 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.

PF25175Beta-prop_WDR53-126 aa

PF25174Beta-prop_THOC34-83 aa

PF24814WD40_Prp199-84 aa

PF00400WD4016-32 aa

PF20426NBCH_WD4030-84 aa

PF25173Beta-prop_WDR3_1st32-83 aa

PF23381Beta-prop_IFT122_1st33-85 aa

PF00400WD4045-82 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G113060	`PF25175`	Beta-prop_WDR5	3	126	3.5e-05	23.9
TkA04G113060	`PF25174`	Beta-prop_THOC3	4	83	0.00063	19.5
TkA04G113060	`PF24814`	WD40_Prp19	9	84	0.26	11.1
TkA04G113060	`PF00400`	WD40	16	32	0.01	17.1
TkA04G113060	`PF20426`	NBCH_WD40	30	84	0.019	14.6
TkA04G113060	`PF25173`	Beta-prop_WDR3_1st	32	83	0.054	13.9
TkA04G113060	`PF23381`	Beta-prop_IFT122_1st	33	85	0.024	14.7
TkA04G113060	`PF00400`	WD40	45	82	0.01	17.1
TkA04G113060	`PF25174`	Beta-prop_THOC3	111	140	0.00063	19.5

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
`Q9LYK6`	Arabidopsis thaliana	sp\|Q9LYK6\|APRF1_ARATH Protein ANTHESIS PROMOTING FACTOR 1	48.500%	Swiss-Prot	Medium

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