TkA03G016310 | RubberDandelionOmics

Gene overview

TkA03G016310

Reference: TK1151 Chr: Chr03 Coordinates: 4214070-4218648 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1847 bp · TkA03G016310|TK1151|cDNA

CTCACCAAACTCATCAACCTCTGGACCTCCTTCCTTGAACCACTCCTAGGTCTCCCTGTCCACGTCACCGCCACTCTCCACGACTCGGAACCACCACCCCAGAAGGGCGTTTCCGTAATTTCTGAAGATGATGATGGGGTTCAATCGGAGAAAGGGAAAGGGACTAGACCGAGTAATAATGTTGATGAAAATGGTCGGGAACTGAAGTTGAATGTCGATGAAGCTCAACCTACTGTGTCACAGCCCACAGACACCACAAG...

CDS

Download CDS FASTA

1605 bp · TkA03G016310|TK1151|CDS

CTCACCAAACTCATCAACCTCTGGACCTCCTTCCTTGAACCACTCCTAGGTCTCCCTGTCCACGTCACCGCCACTCTCCACGACTCGGAACCACCACCCCAGAAGGGCGTTTCCGTAATTTCTGAAGATGATGATGGGGTTCAATCGGAGAAAGGGAAAGGGACTAGACCGAGTAATAATGTTGATGAAAATGGTCGGGAACTGAAGTTGAATGTCGATGAAGCTCAACCTACTGTGTCACAGCCCACAGACACCACAAG...

Protein

Download Protein FASTA

534 aa · TkA03G016310|TK1151|PROTEIN

LTKLINLWTSFLEPLLGLPVHVTATLHDSEPPPQKGVSVISEDDDGVQSEKGKGTRPSNNVDENGRELKLNVDEAQPTVSQPTDTTRSITTTTTNVITNGPSIDPSKPEKEEGELSPTHDSDFSSYNQDNQTTNKQETELEPEDNNNNEEEEEEEDDDEEEDDDEEESEDVSGGGDDVSGDCSREEEEEEEEEKPESEGEVEGNDRVEDLNLHLPLPLQLQQSEHFLRTVKPLAKCVNVSSSSSNGGGKNEARVFYGNDS...

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	`TkA03G016310`
TK1151 ID	TkA03G016310
OH-1004 ID	LXL04_006191
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.800
Protein coverage (%)	TK1151 100.000 / OH-1004 41.647 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 TkA03G016310

Location Chr03:4214070-4218648 (-)

Description Similar to SNL2: Paired amphipathic helix protein Sin3-like 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g15020`	Acts as a transcriptional repressor.	No verified direct reference in this release
`At3g01320`	Acts as a transcriptional repressor.	PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors.2010 · DOI: 10.1016/j.jmb.2009.11.065
`At1g70060`	Acts as a transcriptional repressor.	No verified direct reference in this release
`At1g24190`	Acts as a transcriptional repressor.	Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses.2005 · DOI: 10.1105/tpc.105.033043
`At1g10450`	Acts as a transcriptional repressor.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006191 · 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:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0000118 histone deacetylase complex Cellular Component

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0070822 Sin3-type complex Cellular Component

GO:0003714 transcription corepressor activity Molecular Function

KEGG gene cross-reference

ath:AT1G70060

ath:AT3G01320

ath:AT5G15020

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.

Nucleus0.933

Rank 1 · TkA03G016310 · TK1151

Cytoplasm0.154

Rank 2 · TkA03G016310 · TK1151

Cell membrane0.026

Rank 3 · TkA03G016310 · TK1151

Mitochondrion0.016

Rank 4 · TkA03G016310 · TK1151

Golgi apparatus0.012

Rank 5 · TkA03G016310 · 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.

PF09184PPP4R250-191 aa

PF09507CDC2780-196 aa

PF09073BUD22108-200 aa

PF04147Nop14121-218 aa

PF21730Vma22_CCDC115125-224 aa

PF16879Sin3a_C126-166 aa

PF02724CDC45135-198 aa

PF05327RRN3141-209 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G016310	`PF09184`	PPP4R2	50	191	2.0	8.6
TkA03G016310	`PF09507`	CDC27	80	196	0.14	12.3
TkA03G016310	`PF09073`	BUD22	108	200	2.0	8.4
TkA03G016310	`PF04147`	Nop14	121	218	0.1	11.5
TkA03G016310	`PF21730`	Vma22_CCDC115	125	224	1.3	10.1
TkA03G016310	`PF16879`	Sin3a_C	126	166	3.4e-44	152.2
TkA03G016310	`PF02724`	CDC45	135	198	0.066	12.2
TkA03G016310	`PF05327`	RRN3	141	209	1.5	7.9
TkA03G016310	`PF04931`	DNA_pol_phi	142	216	0.24	10.2
TkA03G016310	`PF09184`	PPP4R2	231	253	2.0	8.6
TkA03G016310	`PF16879`	Sin3a_C	255	501	3.4e-44	152.2

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LFQ3`	Arabidopsis thaliana	sp\|Q9LFQ3\|SNL2_ARATH Paired amphipathic helix protein Sin3-like 2	48.400%	Swiss-Prot	Medium
`Q9SRH9`	Arabidopsis thaliana	sp\|Q9SRH9\|SNL1_ARATH Paired amphipathic helix protein Sin3-like 1	54.900%	Swiss-Prot	Medium
`O04539`	Arabidopsis thaliana	sp\|O04539\|SNL4_ARATH Paired amphipathic helix protein Sin3-like 4	51.700%	Swiss-Prot	Medium
`O48686`	Arabidopsis thaliana	sp\|O48686\|SNL3_ARATH Paired amphipathic helix protein Sin3-like 3	55.300%	Swiss-Prot	Medium
`Q9XIK6`	Arabidopsis thaliana	sp\|Q9XIK6\|SNL6_ARATH Paired amphipathic helix protein Sin3-like 6	48.700%	Swiss-Prot	Medium

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