TkA03G552670 | RubberDandelionOmics

Gene overview

TkA03G552670

Reference: TK1151 Chr: Chr03 Coordinates: 139936408-139940269 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

698 bp · TkA03G552670|TK1151|cDNA

TTAACGTCACTGATTCGCAGCTGTACGATCTGTTTAACCAAGTTGGTCAGGTTGTCTCTGTTAGGGTTTGTAGGGATTTGACCACTCGGCGATCCCTTGGTTATGGTTACGTTAACTACAGCAACCCTCCCGATGCGCAAGGGCTATTGATGTACTGAATTTCACTGCCATAAATGGAAAGGCAATCCGCATCATGTACTCTCATAGGGACCCAAGCATCCGTAAAAGCGGAACAGCAAACATCTTCATTAAGAACTTGG...

CDS

Download CDS FASTA

303 bp · TkA03G552670|TK1151|CDS

ATGTACTCTCATAGGGACCCAAGCATCCGTAAAAGCGGAACAGCAAACATCTTCATTAAGAACTTGGATAAGTCAATTGACAACAAAGCCCTTCACGACACCTTCTCAACCTTCGGCAACATCCTCTCCTGCAAAATCGCAGTCGACATCACCGGCCAATCAAAAGGCTACGGATTCGTCCAATTCGACACCGAAGAAGCCGCCCAAACCGCAATCGACAAAACTAAACGGAATGCTGATAAACGACAAAACACGTCTAT...

Protein

Download Protein FASTA

100 aa · TkA03G552670|TK1151|PROTEIN

MYSHRDPSIRKSGTANIFIKNLDKSIDNKALHDTFSTFGNILSCKIAVDITGQSKGYGFVQFDTEEAAQTAIDKTKRNADKRQNTSMSAIFLESKNAIPH

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	`TkA03G552670`
TK1151 ID	TkA03G552670
OH-1004 ID	LXL04_027187
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	98.600
Protein coverage (%)	TK1151 74.000 / OH-1004 11.420 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 TkA03G552670

Location Chr03:139936408-139940269 (+)

Description Similar to PAB2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34110`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g49760`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g22760`	Binds the poly(A) tail of mRNA.	Unexpected complexity of poly(A)-binding protein gene families in flowering plants: three conserved lineages that are at least 200 million years old and possible auto- and cross-regulation.2003 · DOI: 10.1093/genetics/163.1.311 Evidence that poly(A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and export.2003 · DOI: 10.1261/rna.5128903

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_027187 · 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:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0006413 translational initiation Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006446 regulation of translational initiation Biological Process

GO:0048255 mRNA stabilization Biological Process

GO:0060211 regulation of nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:1900151 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT1G49760

ath:AT4G34110

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.

Cytoplasm0.552

Rank 1 · TkA03G552670 · TK1151

Nucleus0.400

Rank 2 · TkA03G552670 · TK1151

Mitochondrion0.102

Rank 3 · TkA03G552670 · TK1151

Cell membrane0.068

Rank 4 · TkA03G552670 · TK1151

Endoplasmic reticulum0.036

Rank 5 · TkA03G552670 · 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.

PF28441RRM_1110-25 aa

PF30865C16C6_0411-58 aa

PF24572RBD_RDR614-51 aa

PF16367RRM_716-95 aa

PF00076RRM_117-75 aa

PF11608RRM_MARF117-78 aa

PF08777RRM_320-89 aa

PF26250RRM_RdRP1_238-72 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G552670	`PF28441`	RRM_11	10	25	0.032	15.3
TkA03G552670	`PF30865`	C16C6_04	11	58	0.032	13.9
TkA03G552670	`PF24572`	RBD_RDR6	14	51	0.091	13.6
TkA03G552670	`PF16367`	RRM_7	16	95	0.00011	22.8
TkA03G552670	`PF00076`	RRM_1	17	75	2.2e-19	69.8
TkA03G552670	`PF11608`	RRM_MARF1	17	78	0.26	12.2
TkA03G552670	`PF08777`	RRM_3	20	89	0.0053	17.5
TkA03G552670	`PF26250`	RRM_RdRP1_2	38	72	0.042	15.0
TkA03G552670	`PF28441`	RRM_11	50	82	0.032	15.3
TkA03G552670	`PF08206`	OB_RNB	50	66	0.09	13.2
TkA03G552670	`PF14703`	PHM7_cyt	51	82	0.12	13.3
TkA03G552670	`PF24572`	RBD_RDR6	55	78	0.091	13.6

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
`P42731`	Arabidopsis thaliana	sp\|P42731\|PABP2_ARATH Polyadenylate-binding protein 2	77.000%	Swiss-Prot	High
`Q9FXA2`	Arabidopsis thaliana	sp\|Q9FXA2\|PABP8_ARATH Polyadenylate-binding protein 8	81.100%	Swiss-Prot	High
`O64380`	Arabidopsis thaliana	sp\|O64380\|PABP3_ARATH Polyadenylate-binding protein 3	74.300%	Swiss-Prot	High

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