TkA07G423770 | RubberDandelionOmics

Gene overview

TkA07G423770

Reference: TK1151 Chr: Chr07 Coordinates: 107182625-107187399 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1776 bp · TkA07G423770|TK1151|cDNA

GGTACCGGTCATCTTCCCCCATTGTTCATCTTCCGCCTCTATCCTCCCTGTTTCTTCTTCACGTGAACCTCTCATCTGGTTCTTTCTTCACCGCCTCAACCCACGCATTAATCTTCTTTCCATTCATCATTAAATCAAGAAGCCAACACATCTCTGTAATCTCTGTACTCAAATCGACTCCAACAAGATTTACCTCCGTCATGGGCTGATATCAAGATCAAATCAATTAGAAGATGGGATCAAAATAACCCAATTAGAGC...

CDS

Download CDS FASTA

585 bp · TkA07G423770|TK1151|CDS

ATGGCGTCGTATGGAGGGACGACACAAAAGTGTAAGGCTTGTGAGAAGACTGTTTACTTGGTGGATGAACTGACTGTTGATAATAAAGTTTATCATAGGGCTTGTTTCAGATGCCACCATTGCAAGAGCACCCTCAAGTTGAGTAATTACAGCTCTTTTGAAGGAGTGTTATATTGTCAACCTCATTTTGATCAGCTCTTCAAATTAACCGGAAGTTTGGATAAGAGTTTTGAAGGTACCCCCAAAACGGTTCGAGTTGA...

Protein

Download Protein FASTA

194 aa · TkA07G423770|TK1151|PROTEIN

MASYGGTTQKCKACEKTVYLVDELTVDNKVYHRACFRCHHCKSTLKLSNYSSFEGVLYCQPHFDQLFKLTGSLDKSFEGTPKTVRVDRSSDHGQSNTRVSSMFGGTQDKCITCKKTVYPLEKVGVDGDAYHKACFKCSYGGCHISPSNYVAHEHQLYCKHHAAQLFMAKGNFSQFDKQHEPDNNNGVTENTTEV

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	`TkA07G423770`
TK1151 ID	TkA07G423770
OH-1004 ID	LXL04_030697
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.000
Protein coverage (%)	TK1151 100.000 / OH-1004 27.209 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 TkA07G423770

Location Chr07:107182625-107187399 (+)

Description Similar to PCMP-H61: Pentatricopeptide repeat-containing protein At5g66520

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_030697 · 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:0006397 mRNA processing Biological Process

GO:0009451 RNA modification Biological Process

GO:0016554 cytidine to uridine editing Biological Process

GO:0031425 chloroplast RNA processing Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:1900865 chloroplast RNA modification Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT2G20540

ath:AT4G37380

ath:AT5G40405

ath:AT5G59200

ath:AT5G66520

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.

Cytoplasm0.761

Rank 1 · TkA07G423770 · TK1151

Nucleus0.223

Rank 2 · TkA07G423770 · TK1151

Cell membrane0.078

Rank 3 · TkA07G423770 · TK1151

Golgi apparatus0.043

Rank 4 · TkA07G423770 · TK1151

Mitochondrion0.036

Rank 5 · TkA07G423770 · 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.

PF29858GP46_beta6-23 aa

PF17121zf-C3HC4_510-38 aa

PF17848Zn_ribbon_ACC10-19 aa

PF00412LIM11-66 aa

PF03966Trm112p11-22 aa

PF08782c-SKI_SMAD_bind33-45 aa

PF29858GP46_beta35-40 aa

PF17848Zn_ribbon_ACC36-45 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G423770	`PF29858`	GP46_beta	6	23	0.16	12.8
TkA07G423770	`PF17121`	zf-C3HC4_5	10	38	3.3	8.4
TkA07G423770	`PF17848`	Zn_ribbon_ACC	10	19	7.7	7.6
TkA07G423770	`PF00412`	LIM	11	66	2.1e-20	73.5
TkA07G423770	`PF03966`	Trm112p	11	22	4.1	8.1
TkA07G423770	`PF08782`	c-SKI_SMAD_bind	33	45	4.2	8.3
TkA07G423770	`PF29858`	GP46_beta	35	40	0.16	12.8
TkA07G423770	`PF17848`	Zn_ribbon_ACC	36	45	7.7	7.6
TkA07G423770	`PF03966`	Trm112p	38	59	4.1	8.1
TkA07G423770	`PF08782`	c-SKI_SMAD_bind	99	115	4.2	8.3
TkA07G423770	`PF29858`	GP46_beta	105	115	0.16	12.8
TkA07G423770	`PF17121`	zf-C3HC4_5	108	137	3.3	8.4
TkA07G423770	`PF17848`	Zn_ribbon_ACC	109	118	7.7	7.6
TkA07G423770	`PF00412`	LIM	110	164	2.1e-20	73.5
TkA07G423770	`PF03966`	Trm112p	110	159	4.1	8.1
TkA07G423770	`PF08782`	c-SKI_SMAD_bind	132	158	4.2	8.3

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
`Q94JX5`	Arabidopsis thaliana	sp\|Q94JX5\|WLIM1_ARATH LIM domain-containing protein WLIM1	68.600%	Swiss-Prot	High
`O04193`	Arabidopsis thaliana	sp\|O04193\|WLI2A_ARATH LIM domain-containing protein WLIM2a	58.300%	Swiss-Prot	High
`Q9M047`	Arabidopsis thaliana	sp\|Q9M047\|WLI2B_ARATH LIM domain-containing protein WLIM2b	58.500%	Swiss-Prot	High
`O80839`	Arabidopsis thaliana	sp\|O80839\|PLI2A_ARATH LIM domain-containing protein PLIM2a	52.300%	Swiss-Prot	High

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