TkA07G004860 | RubberDandelionOmics

Gene overview

TkA07G004860

Reference: TK1151 Chr: Chr07 Coordinates: 1341180-1343307 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

916 bp · TkA07G004860|TK1151|cDNA

TCTTTCTAAAATTATTTGGCATGGATATATAAGTGTTTGCCTGTTTGGTAACCCATTTTTGTTGGGTTGCTTTCTTCTTGTTAAGTTTTTCCGAAAGCAAACCGAAGAACAATACAAAAAAAGCAAAGAAAATGTCATTCACAGGAACGTTAGACAAATGCAAAGCTTGTGATAAAACGGTCTATTTCGTTGATTTATTGACTGCAGATGGAATCACGTATCATAAATCGTGTTTCAAATGTACCCACTGCAAAGGAACG...

CDS

Download CDS FASTA

705 bp · TkA07G004860|TK1151|CDS

ATGTCATTCACAGGAACGTTAGACAAATGCAAAGCTTGTGATAAAACGGTCTATTTCGTTGATTTATTGACTGCAGATGGAATCACGTATCATAAATCGTGTTTCAAATGTACCCACTGCAAAGGAACGCTTGTGATGAGCAACTACTCCTCCATGGATGGAGTCCTCTATTGCAGGACTCATTTTGAACAACTTTTCAAGGAATCAGGGAACTTCAGCAAGAACTTTCAACAATCAAAAGCGGAAAAAGATTCACATCC...

Protein

Download Protein FASTA

234 aa · TkA07G004860|TK1151|PROTEIN

MSFTGTLDKCKACDKTVYFVDLLTADGITYHKSCFKCTHCKGTLVMSNYSSMDGVLYCRTHFEQLFKESGNFSKNFQQSKAEKDSHPKAPPSKLSSMFSGTIDKCRACNKTVYPLEKVTMEGEPYHKLCFKCAHGGCPLTHASYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANQKHNASASEEHHEQPPAEEGEPTDDTPSEPPPEAEQPHEEEKEEEKENEKEKDKEEEES

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	`TkA07G004860`
TK1151 ID	TkA07G004860
OH-1004 ID	LXL04_029626
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	59.900
Protein coverage (%)	TK1151 77.778 / OH-1004 90.863 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 TkA07G004860

Location Chr07:1341180-1343307 (-)

Description Similar to PLIM2C: LIM domain-containing protein PLIM2c

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`At2g45800`	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
`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
`At2g39900`	Binds to actin filaments and promotes cross-linking into thick bundles.	No verified direct reference in this release
`At3g61230`	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_029626 · 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:0005634 nucleus Cellular Component

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:AT2G39900

ath:AT2G45800

ath:AT3G55770

ath:AT3G61230

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.

Cytoplasm0.701

Rank 1 · TkA07G004860 · TK1151

Nucleus0.254

Rank 2 · TkA07G004860 · TK1151

Cell membrane0.126

Rank 3 · TkA07G004860 · TK1151

Golgi apparatus0.087

Rank 4 · TkA07G004860 · TK1151

Endoplasmic reticulum0.047

Rank 5 · TkA07G004860 · 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.

PF13926DUF42116-17 aa

PF25454zf-C3HC4_IRF-2BP1_29-39 aa

PF17848Zn_ribbon_ACC9-18 aa

PF00020TNFR_c69-14 aa

PF12172zf-ChsH29-18 aa

PF00412LIM10-66 aa

PF03966Trm112p10-20 aa

PF00020TNFR_c630-46 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G004860	`PF13926`	DUF4211	6	17	0.067	14.0
TkA07G004860	`PF25454`	zf-C3HC4_IRF-2BP1_2	9	39	0.26	12.3
TkA07G004860	`PF17848`	Zn_ribbon_ACC	9	18	0.32	12.0
TkA07G004860	`PF00020`	TNFR_c6	9	14	0.56	11.4
TkA07G004860	`PF12172`	zf-ChsH2	9	18	1.9	9.0
TkA07G004860	`PF00412`	LIM	10	66	7.8e-24	84.4
TkA07G004860	`PF03966`	Trm112p	10	20	0.0045	17.6
TkA07G004860	`PF00020`	TNFR_c6	30	46	0.56	11.4
TkA07G004860	`PF17848`	Zn_ribbon_ACC	35	41	0.32	12.0
TkA07G004860	`PF03966`	Trm112p	36	59	0.0045	17.6
TkA07G004860	`PF12172`	zf-ChsH2	37	42	1.9	9.0
TkA07G004860	`PF13926`	DUF4211	96	127	0.067	14.0
TkA07G004860	`PF12172`	zf-ChsH2	103	114	1.9	9.0
TkA07G004860	`PF25454`	zf-C3HC4_IRF-2BP1_2	104	134	0.26	12.3
TkA07G004860	`PF17848`	Zn_ribbon_ACC	104	113	0.32	12.0
TkA07G004860	`PF00020`	TNFR_c6	104	109	0.56	11.4

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q1ECF5`	Arabidopsis thaliana	sp\|Q1ECF5\|PLI2B_ARATH LIM domain-containing protein PLIM2b	74.600%	Swiss-Prot	High
`O80839`	Arabidopsis thaliana	sp\|O80839\|PLI2A_ARATH LIM domain-containing protein PLIM2a	77.100%	Swiss-Prot	High
`Q9M047`	Arabidopsis thaliana	sp\|Q9M047\|WLI2B_ARATH LIM domain-containing protein WLIM2b	64.300%	Swiss-Prot	High
`O04193`	Arabidopsis thaliana	sp\|O04193\|WLI2A_ARATH LIM domain-containing protein WLIM2a	64.000%	Swiss-Prot	High
`Q500W4`	Arabidopsis thaliana	sp\|Q500W4\|PLI2C_ARATH LIM domain-containing protein PLIM2c	63.300%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card