TkA01G530340 | RubberDandelionOmics

Gene overview

TkA01G530340

Reference: TK1151 Chr: Chr01 Coordinates: 133110879-133112506 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

832 bp · TkA01G530340|TK1151|cDNA

CGAAATTTTGACCGAGTTCTTTTTCTCACGACAAGAGAAAAAGAACTCGTTCGATAAAAATGGCCGGAGGATTCGTAGCAACAACACAAAAATGTGCAGTTTGTGACAAAACTGTATATTTGGTTGATCGGCTAGAAGCCAACAAACGGATTTATCACAAAGCCTGTTTCCGATGCCATCATTGCAACCGTACCCTCAAACTTAGCAACTTCAATTCCTTCGACGGAGTCGTGTACTGCAAGCCTCACTTTGATCAACTC...

CDS

Download CDS FASTA

594 bp · TkA01G530340|TK1151|CDS

ATGGCCGGAGGATTCGTAGCAACAACACAAAAATGTGCAGTTTGTGACAAAACTGTATATTTGGTTGATCGGCTAGAAGCCAACAAACGGATTTATCACAAAGCCTGTTTCCGATGCCATCATTGCAACCGTACCCTCAAACTTAGCAACTTCAATTCCTTCGACGGAGTCGTGTACTGCAAGCCTCACTTTGATCAACTCTTCAAGAGAACCGGCAGCTTAGAAAAAAGCTTTGATGGAACACCAAAGTTCAAGACAGA...

Protein

Download Protein FASTA

197 aa · TkA01G530340|TK1151|PROTEIN

MAGGFVATTQKCAVCDKTVYLVDRLEANKRIYHKACFRCHHCNRTLKLSNFNSFDGVVYCKPHFDQLFKRTGSLEKSFDGTPKFKTERSFNSENAAKLSNFFGGTREKCIGCSKTVYPTERVTVNGSAYHRACFKCCHGGCTISPSNYIAHESRLYCKHHHIQLFKSKGNYSQLEINGEESTSESTSDSIPASAPAS

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	`TkA01G530340`
TK1151 ID	TkA01G530340
OH-1004 ID	LXL04_001503
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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 TkA01G530340

Location Chr01:133110879-133112506 (+)

Description Similar to SF3: Pollen-specific protein SF3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g10200`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960
`At2g39900`	Binds to actin filaments and promotes cross-linking into thick bundles.	No verified direct reference in this release
`At3g55770`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960
`At1g01780`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001503 · 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:0051017 actin filament bundle assembly Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005856 cytoskeleton Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0051015 actin filament binding Molecular Function

KEGG gene cross-reference

ath:AT1G10200

ath:AT2G39900

ath:AT3G55770

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.

Cytoplasm0.764

Rank 1 · TkA01G530340 · TK1151

Nucleus0.213

Rank 2 · TkA01G530340 · TK1151

Cell membrane0.077

Rank 3 · TkA01G530340 · TK1151

Golgi apparatus0.047

Rank 4 · TkA01G530340 · TK1151

Mitochondrion0.033

Rank 5 · TkA01G530340 · 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.

PF17121zf-C3HC4_510-39 aa

PF00412LIM12-67 aa

PF14495Cytochrom_C55019-47 aa

PF21936Pcf11_C25-37 aa

PF13442Cytochrome_CBB326-43 aa

PF00412LIM109-165 aa

PF17121zf-C3HC4_5118-137 aa

PF21936Pcf11_C122-135 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G530340	`PF17121`	zf-C3HC4_5	10	39	2.0	9.1
TkA01G530340	`PF00412`	LIM	12	67	9.7e-22	77.7
TkA01G530340	`PF14495`	Cytochrom_C550	19	47	2.4	8.6
TkA01G530340	`PF21936`	Pcf11_C	25	37	4.2	8.1
TkA01G530340	`PF13442`	Cytochrome_CBB3	26	43	0.66	11.1
TkA01G530340	`PF00412`	LIM	109	165	9.7e-22	77.7
TkA01G530340	`PF17121`	zf-C3HC4_5	118	137	2.0	9.1
TkA01G530340	`PF21936`	Pcf11_C	122	135	4.2	8.1
TkA01G530340	`PF14495`	Cytochrom_C550	126	145	2.4	8.6
TkA01G530340	`PF13442`	Cytochrome_CBB3	128	139	0.66	11.1

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
`Q94JX5`	Arabidopsis thaliana	sp\|Q94JX5\|WLIM1_ARATH LIM domain-containing protein WLIM1	71.000%	Swiss-Prot	High
`O04193`	Arabidopsis thaliana	sp\|O04193\|WLI2A_ARATH LIM domain-containing protein WLIM2a	54.700%	Swiss-Prot	High
`Q9M047`	Arabidopsis thaliana	sp\|Q9M047\|WLI2B_ARATH LIM domain-containing protein WLIM2b	53.200%	Swiss-Prot	High
`Q1ECF5`	Arabidopsis thaliana	sp\|Q1ECF5\|PLI2B_ARATH LIM domain-containing protein PLIM2b	50.000%	Swiss-Prot	High

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