TkA04G274290 | RubberDandelionOmics

Gene overview

TkA04G274290

Reference: TK1151 Chr: Chr04 Coordinates: 69285904-69289135 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1437 bp · TkA04G274290|TK1151|cDNA

ATGAAACTGTTGCATCAACCACATTCGGGATCAAATCAGGTGCTACTCAGACCACCCATTCATCTGCACCTTCGCCTTCTATTCCCTAATTTGGATGAAAGTGTTCTTAACCCAAAAAGCGGTTTATTTCCCGGACCTGATTCTAAAGCTGCTGATGTTGTTGCTAATCCTGAAGATGAAGAGAAGGAGCTAGAACATTGTTCTTTACAAGAAAAACTTGACAATGAGCTCAAAGAACTGGACAAATCTTCAAAACAAGA...

CDS

Download CDS FASTA

1437 bp · TkA04G274290|TK1151|CDS

ATGAAACTGTTGCATCAACCACATTCGGGATCAAATCAGGTGCTACTCAGACCACCCATTCATCTGCACCTTCGCCTTCTATTCCCTAATTTGGATGAAAGTGTTCTTAACCCAAAAAGCGGTTTATTTCCCGGACCTGATTCTAAAGCTGCTGATGTTGTTGCTAATCCTGAAGATGAAGAGAAGGAGCTAGAACATTGTTCTTTACAAGAAAAACTTGACAATGAGCTCAAAGAACTGGACAAATCTTCAAAACAAGA...

Protein

Download Protein FASTA

478 aa · TkA04G274290|TK1151|PROTEIN

MKLLHQPHSGSNQVLLRPPIHLHLRLLFPNLDESVLNPKSGLFPGPDSKAADVVANPEDEEKELEHCSLQEKLDNELKELDKSSKQERISILSCITQKPKFSIGYPSVSSQQLWKCTGYVPKKFNSQYREFPCVIHSVNQKKDDLNVVKDQNRKKMPKMDSQPHGDEGTGGGGGGGSPQKLTTNNALSYLKLVKDMFHDQREKYKMFLDVMKDFKAQRETGEIGPLAPHADRDLESGEINEDDKTTMKLQKDHKRVSENR...

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	`TkA04G274290`
TK1151 ID	TkA04G274290
OH-1004 ID	LXL04_034909
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	97.900
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 TkA04G274290

Location Chr04:69285904-69289135 (+)

Description Similar to SNL4: Paired amphipathic helix protein Sin3-like 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At5g15020`	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
`At1g59890`	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_034909 · 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:0009737 response to abscisic acid 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:AT1G24190

ath:AT1G59890

ath:AT1G70060

ath:AT3G01320

ath:AT5G15020

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.

Nucleus0.904

Rank 1 · TkA04G274290 · TK1151

Cytoplasm0.151

Rank 2 · TkA04G274290 · TK1151

Cell membrane0.046

Rank 3 · TkA04G274290 · TK1151

Endoplasmic reticulum0.031

Rank 4 · TkA04G274290 · TK1151

Mitochondrion0.017

Rank 5 · TkA04G274290 · TK1151

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.

PF06156YabA59-85 aa

PF02671PAH202-218 aa

PF06156YabA240-291 aa

PF13083KH_KhpA-B378-397 aa

PF07650KH_2380-407 aa

PF00013KH_1383-410 aa

PF00249Myb_DNA-binding443-460 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G274290	`PF06156`	YabA	59	85	1.8	9.9
TkA04G274290	`PF02671`	PAH	202	218	0.0029	18.0
TkA04G274290	`PF06156`	YabA	240	291	1.8	9.9
TkA04G274290	`PF13083`	KH_KhpA-B	378	397	0.24	12.1
TkA04G274290	`PF07650`	KH_2	380	407	0.042	14.4
TkA04G274290	`PF00013`	KH_1	383	410	0.00013	22.3
TkA04G274290	`PF00249`	Myb_DNA-binding	443	460	0.0014	19.4

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
`Q9SRH9`	Arabidopsis thaliana	sp\|Q9SRH9\|SNL1_ARATH Paired amphipathic helix protein Sin3-like 1	73.900%	Swiss-Prot	Low
`O04539`	Arabidopsis thaliana	sp\|O04539\|SNL4_ARATH Paired amphipathic helix protein Sin3-like 4	73.800%	Swiss-Prot	Low
`Q9LFQ3`	Arabidopsis thaliana	sp\|Q9LFQ3\|SNL2_ARATH Paired amphipathic helix protein Sin3-like 2	75.000%	Swiss-Prot	Low
`O48686`	Arabidopsis thaliana	sp\|O48686\|SNL3_ARATH Paired amphipathic helix protein Sin3-like 3	71.400%	Swiss-Prot	Low
`Q9XIE1`	Arabidopsis thaliana	sp\|Q9XIE1\|SNL5_ARATH Paired amphipathic helix protein Sin3-like 5	73.700%	Swiss-Prot	Low

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