TkA01G495950 | RubberDandelionOmics

Gene overview

TkA01G495950

Reference: TK1151 Chr: Chr01 Coordinates: 124116646-124121267 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3151 bp · TkA01G495950|TK1151|cDNA

CTGTTTTAGTAAAATGCTAGAAAAGAAGGGTAATAGCTACAAAATCGTGAGGAACCACAAGTATAACCCGAACCTAGAAAAACGCTCATCAGTCATAACCCTCCCTCCTACCTTTTTGATCGATAACAAATCCCAAATTTCCTCTGTTTCAAATTCCACATGTTTACCTTCATGCATTACAGACTCCAGTTCCTCGTTCTAAAAAACTAATTCGAGATTTCTTGCTTAGAATCTAGCAATTGTTCCTGACAGGTTTTTGC...

CDS

Download CDS FASTA

2223 bp · TkA01G495950|TK1151|CDS

ATGGGTAGACCGCCCAGTAATGGAGGCCCTTCTTTCCGCTTTAACCCGGCCGAGATTGCGGAGATGGAAGCCATCTTGCAAGCACACAAAACCCAAATGCCTGCACGTGAGGTTCTTGTTGCCTTAGCCGAAAAGTTCAGCAACTCTGAAGAACGAAAGGGAAAGATTGAAGTTCAAATGAAACAAGTATGGAATTGGTTCCAAAATAGACGATATGCAATCAGGGCTAAAGCAGGAAAATCACCAGGGAAGTTAATAAA...

Protein

Download Protein FASTA

740 aa · TkA01G495950|TK1151|PROTEIN

MGRPPSNGGPSFRFNPAEIAEMEAILQAHKTQMPAREVLVALAEKFSNSEERKGKIEVQMKQVWNWFQNRRYAIRAKAGKSPGKLINITQVNRDDNPTMAKGIPQPTLPHAASAATVRFMPQAQQHPTVPTVRTFPQAPQNTMSFSVQNAGRVTDNSQMEYEAKSARDGAWYDVSTFLSHRSLDSGDPEVMVRFAGFGAEEDEWVNVRKNVRQRSLPCEASECVAVLPADLILCFQEGKEQALYFDAHVLDAQRRRHDVR...

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	`TkA01G495950`
TK1151 ID	TkA01G495950
OH-1004 ID	LXL04_001948
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	92.200
Protein coverage (%)	TK1151 99.595 / OH-1004 98.797 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 TkA01G495950

Location Chr01:124116646-124121267 (-)

Description Similar to SHH2: Protein SAWADEE HOMEODOMAIN HOMOLOG 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g18380`	May play a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM.	No verified direct reference in this release
`At1g15215`	Involved in RNA-directed DNA methylation (RdDM).	SHH1, a homeodomain protein required for DNA methylation, as well as RDR2, RDM4, and chromatin remodeling factors, associate with RNA polymerase IV.2011 · DOI: 10.1371/journal.pgen.1002195 An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing.2011 · DOI: 10.1038/cr.2011.173 Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.2013 · DOI: 10.1038/nature12178 DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.2013 · DOI: 10.1073/pnas.1300585110

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001948 · 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:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0007155 cell adhesion Biological Process

GO:0007339 binding of sperm to zona pellucida Biological Process

GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:2000359 regulation of binding of sperm to zona pellucida Biological Process

GO:0005615 extracellular space Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0031012 extracellular matrix Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

KEGG gene cross-reference

ath:AT1G15215

ath:AT3G18380

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.

Nucleus0.874

Rank 1 · TkA01G495950 · TK1151

Cytoplasm0.180

Rank 2 · TkA01G495950 · TK1151

Cell membrane0.042

Rank 3 · TkA01G495950 · TK1151

Endoplasmic reticulum0.031

Rank 4 · TkA01G495950 · TK1151

Mitochondrion0.020

Rank 5 · TkA01G495950 · 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.

PF00046Homeodomain13-73 aa

PF23604Ig_TRAPPC1048-75 aa

PF16719SAWADEE158-285 aa

PF30489Ropporin_N413-433 aa

PF23604Ig_TRAPPC10421-452 aa

PF23604Ig_TRAPPC10467-516 aa

PF30489Ropporin_N535-544 aa

PF30489Ropporin_N557-566 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G495950	`PF00046`	Homeodomain	13	73	0.0012	19.3
TkA01G495950	`PF23604`	Ig_TRAPPC10	48	75	8.2	7.2
TkA01G495950	`PF16719`	SAWADEE	158	285	2.9e-44	150.9
TkA01G495950	`PF30489`	Ropporin_N	413	433	9.9	7.0
TkA01G495950	`PF23604`	Ig_TRAPPC10	421	452	8.2	7.2
TkA01G495950	`PF23604`	Ig_TRAPPC10	467	516	8.2	7.2
TkA01G495950	`PF30489`	Ropporin_N	535	544	9.9	7.0
TkA01G495950	`PF30489`	Ropporin_N	557	566	9.9	7.0
TkA01G495950	`PF23604`	Ig_TRAPPC10	604	643	8.2	7.2
TkA01G495950	`PF30489`	Ropporin_N	612	621	9.9	7.0

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
`Q8RWJ7`	Arabidopsis thaliana	sp\|Q8RWJ7\|SHH2_ARATH Protein SAWADEE HOMEODOMAIN HOMOLOG 2	64.100%	Swiss-Prot	Low
`Q9XI47`	Arabidopsis thaliana	sp\|Q9XI47\|SHH1_ARATH Protein SAWADEE HOMEODOMAIN HOMOLOG 1	38.300%	Swiss-Prot	Low

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