TkA04G331900 | RubberDandelionOmics

Gene overview

TkA04G331900

Reference: TK1151 Chr: Chr04 Coordinates: 83714133-83715777 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

420 bp · TkA04G331900|TK1151|cDNA

ATGAAAGCAAATGCATGGCATCATTGTGCAGATGATGTTTCCTTACTTGCTGCTCTTATAGGGTTGGTAGAAAAATCTCACAATGCTGATCTTCATTGTGTTGATTGGAATCCGATTGATGAAAATTTCATTTTAACTGGAGAATGTGCAGAAAAACTCCAACTTCTGAGTACACTAGATGAACGGGAAAGCAGATTACAAGAAATCCCAGACGTCCATTCAGATTTTAAAATGAATCCACATTACGAATCAGATGACAC...

CDS

Download CDS FASTA

420 bp · TkA04G331900|TK1151|CDS

ATGAAAGCAAATGCATGGCATCATTGTGCAGATGATGTTTCCTTACTTGCTGCTCTTATAGGGTTGGTAGAAAAATCTCACAATGCTGATCTTCATTGTGTTGATTGGAATCCGATTGATGAAAATTTCATTTTAACTGGAGAATGTGCAGAAAAACTCCAACTTCTGAGTACACTAGATGAACGGGAAAGCAGATTACAAGAAATCCCAGACGTCCATTCAGATTTTAAAATGAATCCACATTACGAATCAGATGACAC...

Protein

Download Protein FASTA

139 aa · TkA04G331900|TK1151|PROTEIN

MKANAWHHCADDVSLLAALIGLVEKSHNADLHCVDWNPIDENFILTGECAEKLQLLSTLDERESRLQEIPDVHSDFKMNPHYESDDTEEYFNKEHGDHMESKYSEVKVKKSRSPKKRGMQMEASTSDLSIKVAESCRLQ

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	`TkA04G331900`
TK1151 ID	TkA04G331900
OH-1004 ID	LXL04_037616
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 97.842 / OH-1004 69.036 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 TkA04G331900

Location Chr04:83714133-83715777 (+)

Description Similar to MSI4: WD-40 repeat-containing protein MSI4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g19520`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA.	Regulation of flowering time by FVE, a retinoblastoma-associated protein.2004 · DOI: 10.1038/ng1295 A genetic link between cold responses and flowering time through FVE in Arabidopsis thaliana.2004 · DOI: 10.1038/ng1298
`At4g29730`	Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA (By similarity).	Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time.2018 · DOI: 10.1111/jipb.12630
`UniProt: Q9SIV5`	Plays a central role in integrating RNA silencing and chromatin signals in 21 nt siRNA-dependent DNA methylation on cytosine pathway leading to transcriptional gene silencing of specific sequences.	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_037616 · 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:0006281 DNA repair Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009908 flower development Biological Process

GO:0010224 response to UV-B Biological Process

GO:0010629 negative regulation of gene expression Biological Process

GO:0030154 cell differentiation Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

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

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

KEGG gene cross-reference

ath:AT2G16485

ath:AT2G19520

ath:AT4G29730

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.

Nucleus0.669

Rank 1 · TkA04G331900 · TK1151

Cytoplasm0.322

Rank 2 · TkA04G331900 · TK1151

Cell membrane0.061

Rank 3 · TkA04G331900 · TK1151

Mitochondrion0.052

Rank 4 · TkA04G331900 · TK1151

Endoplasmic reticulum0.034

Rank 5 · TkA04G331900 · 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.

PF23775Beta-prop_RIG_2nd22-66 aa

PF25980NERD_plant48-65 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G331900	`PF23775`	Beta-prop_RIG_2nd	22	66	0.16	12.1
TkA04G331900	`PF25980`	NERD_plant	48	65	0.037	14.5

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
`O22607`	Arabidopsis thaliana	sp\|O22607\|MSI4_ARATH WD-40 repeat-containing protein MSI4	63.600%	Swiss-Prot	Low
`Q9SU78`	Arabidopsis thaliana	sp\|Q9SU78\|MSI5_ARATH WD-40 repeat-containing protein MSI5	80.000%	Swiss-Prot	Low
`Q9SIV5`	Arabidopsis thaliana	sp\|Q9SIV5\|C3H19_ARATH Zinc finger CCCH domain-containing protein 19	59.500%	Swiss-Prot	Low

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