TkA01G539710 | RubberDandelionOmics

Gene overview

TkA01G539710

Reference: TK1151 Chr: Chr01 Coordinates: 135342099-135345315 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2704 bp · TkA01G539710|TK1151|cDNA

AAAAAACATTCTGAAATCGCCAAGTGGTTTTATGAAGTCTTTTTTTTGCTTATTTTTCAGTCTCTCTCACTATATATGTGTATTCTAGAGAGAGAAAGTAATGAAGAGAGATGAGTGAGAGTCTGTTCCTCTCTCCAGCTTTTATGGCGTGAGACCTTACCAGTAAGCCAGTGTGTACACTACCATCACCTATACATACATTATGTTGTATAAAATCCTTCATCTTTGCATGCTTCACCAAACTCATTCCCAAAGATCGA...

CDS

Download CDS FASTA

1872 bp · TkA01G539710|TK1151|CDS

ATGATGGTTGAGAGAGTTGGGATAATTAAGAACATGGAGGATCAAGAACTTGAAATGTTGTTGGGTGAGATCCCTCATGCAACATCATCAGTTTCGCTTCACCATCATCGCCCATCTTATGCGAATGGCCATCATCATCATCACCATCACCATCATCATGTTGTCAATGGTAATACTCTCGGTAACCCCTCTTTTGTAACTCCGACGACGAATAGGATGATGTATGGTATGTTTGATGATGATTCATCATCTAATTATAG...

Protein

Download Protein FASTA

623 aa · TkA01G539710|TK1151|PROTEIN

MMVERVGIIKNMEDQELEMLLGEIPHATSSVSLHHHRPSYANGHHHHHHHHHHVVNGNTLGNPSFVTPTTNRMMYGMFDDDSSSNYSRNTYTQPATAFPSMFVNGYSSSDTSPPSSSSTIPTLHDPIPNPHIGTRNPEENLIDELGRLYINQDRIDSSKFGASDDYLAINPHFPRTPITPDTEIHPAFFGFQQNYGVVPSTQSSNFDRNETNYCYQWGIPAQIGKTSPKSKGNTNHGSHRFHHMAAGGSPNIRITCGGPG...

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	`TkA01G539710`
TK1151 ID	TkA01G539710
OH-1004 ID	LXL04_001406
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
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

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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 TkA01G539710

Location Chr01:135342099-135345315 (+)

Description Similar to APUM7: Putative pumilio homolog 7, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g78160`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At1g22240`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At5g56510`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At4g08840`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	No verified direct reference in this release
`At1g35730`	Sequence-specific RNA-binding protein that regulates translation and mRNA stability by binding the 3'-UTR of target mRNAs.	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_001406 · 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:0006417 regulation of translation Biological Process

GO:0010608 post-transcriptional regulation of gene expression Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G22240

ath:AT1G78160

ath:AT4G08840

ath:AT5G56510

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.

Cytoplasm0.596

Rank 1 · TkA01G539710 · TK1151

Nucleus0.402

Rank 2 · TkA01G539710 · TK1151

Cell membrane0.129

Rank 3 · TkA01G539710 · TK1151

Endoplasmic reticulum0.042

Rank 4 · TkA01G539710 · TK1151

Lysosome / Vacuole0.036

Rank 5 · TkA01G539710 · 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.

PF00806PUF9-24 aa

PF22493PUF_NOP9301-564 aa

PF00806PUF309-342 aa

PF00806PUF344-378 aa

PF00806PUF385-413 aa

PF00806PUF422-451 aa

PF00806PUF457-489 aa

PF00806PUF495-511 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G539710	`PF00806`	PUF	9	24	4.3e-66	218.5
TkA01G539710	`PF22493`	PUF_NOP9	301	564	2.7e-22	80.1
TkA01G539710	`PF00806`	PUF	309	342	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	344	378	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	385	413	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	422	451	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	457	489	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	495	511	4.3e-66	218.5
TkA01G539710	`PF00806`	PUF	528	562	4.3e-66	218.5
TkA01G539710	`PF22493`	PUF_NOP9	568	593	2.7e-22	80.1
TkA01G539710	`PF00806`	PUF	569	599	4.3e-66	218.5

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
`Q9C9R6`	Arabidopsis thaliana	sp\|Q9C9R6\|PUM7_ARATH Putative pumilio homolog 7, chloroplastic	45.000%	Swiss-Prot	Medium
`Q9LM20`	Arabidopsis thaliana	sp\|Q9LM20\|PUM8_ARATH Putative pumilio homolog 8, chloroplastic	48.100%	Swiss-Prot	Medium
`Q9LVC3`	Arabidopsis thaliana	sp\|Q9LVC3\|PUM12_ARATH Pumilio homolog 12	40.800%	Swiss-Prot	Medium
`Q9LDW3`	Arabidopsis thaliana	sp\|Q9LDW3\|PUM11_ARATH Pumilio homolog 11	45.000%	Swiss-Prot	Low
`Q1PFN9`	Arabidopsis thaliana	sp\|Q1PFN9\|PUM9_ARATH Pumilio homolog 9	41.500%	Swiss-Prot	Medium

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