TkA03G394250 | RubberDandelionOmics

Gene overview

TkA03G394250

Reference: TK1151 Chr: Chr03 Coordinates: 97891198-97895674 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1405 bp · TkA03G394250|TK1151|cDNA

CTAAGTTTGTACTTCTGTCCTGTTCAGGTCTGCTTATTTCTTCGAGAGCTTTCCATTGCTCATTCTCTTTCTCCCACGCGGAGTATCGAAACCCTAACACACCAAATTGCTCGCAGATTTGTATTCGTCAAGAATGCAACATCAACATCAGCGACTGATACAGCAACAACAGCAAGCGTTGATGCAGCAAGCTCTCCTTCAACAACAATCTCTTTATCATCCAGGCCTCTTAGCTCCACCACAGGTTCGCACAGACCATT...

CDS

Download CDS FASTA

675 bp · TkA03G394250|TK1151|CDS

ATGTTGTCTCTAAATGGAAGGCATTTGTTTGGACAATCTATTAAAGTTAATTGGGCATATGTCACCGGACAAAGGGAAGACACATCAGGTCATTTTAACATATTTGTTGGTGATCTCTGCTCTGAGGTTACTGATGCTATGTTGTATCCATGCTTCTCTGTCTATTCTAGCTGTTCGGATGCAAGGGTTATGTGGGATCAAAAAACCGGACGTTCACGAGGTTTTGGGTTTGTCTCTTTCCGGAACCAACAGGATGCTGA...

Protein

Download Protein FASTA

224 aa · TkA03G394250|TK1151|PROTEIN

MLSLNGRHLFGQSIKVNWAYVTGQREDTSGHFNIFVGDLCSEVTDAMLYPCFSVYSSCSDARVMWDQKTGRSRGFGFVSFRNQQDAESAINELSGKWLGSGQIRCNWATKGAVNGKEATNEDGKEATNGDAPENNPQYTTVYVGNLGPERKCVCNMRKVSVLFDTVTTRKEAALAIQLGNTTQSFLYGKQIKCSWGSKPTPPGTSSNPVPPPVLSGGDLLSYDL

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	`TkA03G394250`
TK1151 ID	TkA03G394250
OH-1004 ID	LXL04_002210
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	65.500
Protein coverage (%)	TK1151 99.554 / OH-1004 60.900 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

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Basic Information and Functional Annotation

Gene ID TkA03G394250

Location Chr03:97891198-97895674 (+)

Description Similar to UBP1B: Oligouridylate-binding protein 1B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g17370`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of the pre-mRNA processing machinery.	No verified direct reference in this release
`At3g14100`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of the pre-mRNA processing machinery.	No verified direct reference in this release
`At1g54080`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of the pre-mRNA processing machinery.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0520300`	RNA-binding protein.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002210 · 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:0034063 stress granule assembly Biological Process

GO:0071456 cellular response to hypoxia Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G17370

ath:AT1G54080

ath:AT3G14100

dosa:Os08g0520300

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.

Cytoplasm0.552

Rank 1 · TkA03G394250 · TK1151

Nucleus0.441

Rank 2 · TkA03G394250 · TK1151

Cell membrane0.081

Rank 3 · TkA03G394250 · TK1151

Mitochondrion0.069

Rank 4 · TkA03G394250 · TK1151

Endoplasmic reticulum0.057

Rank 5 · TkA03G394250 · 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.

PF00076RRM_134-103 aa

PF00076RRM_1141-149 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G394250	`PF00076`	RRM_1	34	103	2.3e-17	63.4
TkA03G394250	`PF00076`	RRM_1	141	149	2.3e-17	63.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9LQI9`	Arabidopsis thaliana	sp\|Q9LQI9\|UBP1B_ARATH Oligouridylate-binding protein 1B	60.400%	Swiss-Prot	High
`Q9LJH8`	Arabidopsis thaliana	sp\|Q9LJH8\|UBP1C_ARATH Oligouridylate-binding protein 1C	60.000%	Swiss-Prot	High
`Q9SYG4`	Arabidopsis thaliana	sp\|Q9SYG4\|UBP1A_ARATH Oligouridylate-binding protein 1A	58.100%	Swiss-Prot	High
`Q6YZW2`	Oryza sativa subsp. japonica	sp\|Q6YZW2\|RB208_ORYSJ RNA-binding protein 208	55.000%	Swiss-Prot	High

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