TkA05G027340 | RubberDandelionOmics

Gene overview

TkA05G027340

Reference: TK1151 Chr: Chr05 Coordinates: 7400833-7401521 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

528 bp · TkA05G027340|TK1151|cDNA

TTCCGTTTAAACTGGGCTAGCTTCAGTTCAGGCGAAAAACGTCAAGAACCAGGCTCAGATCTTTCCATATTCATAGGAGATTTAGCTCCAGATGTTACTGATACAATCCTCTACGAAACATTCGCTGGTAGATGTTACTGTATATTAATGGTGTTTGTACTTTTAGCTGTGTTATTATCTGGTGGAAATGGTGGATTTGGCGGTACTCCTCAAAATTCTCAGTCTGATGGAGATTCTTCAAACACAACAATATTTGTGGG...

CDS

Download CDS FASTA

483 bp · TkA05G027340|TK1151|CDS

TTCCGTTTAAACTGGGCTAGCTTCAGTTCAGGCGAAAAACGTCAAGAACCAGGCTCAGATCTTTCCATATTCATAGGAGATTTAGCTCCAGATGTTACTGATACAATCCTCTACGAAACATTCGCTGGTAGATGTTACTGTATATTAATGGTGTTTGTACTTTTAGCTGTGTTATTATCTGGTGGAAATGGTGGATTTGGCGGTACTCCTCAAAATTCTCAGTCTGATGGAGATTCTTCAAACACAACAATATTTGTGGG...

Protein

Download Protein FASTA

160 aa · TkA05G027340|TK1151|PROTEIN

FRLNWASFSSGEKRQEPGSDLSIFIGDLAPDVTDTILYETFAGRCYCILMVFVLLAVLLSGGNGGFGGTPQNSQSDGDSSNTTIFVGGLDSEVTDEDLRQTFSQCGEILSVKIPLGKGCGFVQFASRGSAEDAIQNMHGTVIGNQTVRISWGKTPANRQV

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	`TkA05G027340`
TK1151 ID	TkA05G027340
OH-1004 ID	LXL04_019188
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 86.957 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 TkA05G027340

Location Chr05:7400833-7401521 (-)

Description Similar to RBP47C': Polyadenylate-binding protein RBP47C'

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19130`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g49600`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g47500`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g47490`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	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_019188 · 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:0034605 cellular response to heat Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0008143 poly(A) binding Molecular Function

KEGG gene cross-reference

ath:AT1G47490

ath:AT1G47500

ath:AT1G49600

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.

Nucleus0.681

Rank 1 · TkA05G027340 · TK1151

Cytoplasm0.563

Rank 2 · TkA05G027340 · TK1151

Cell membrane0.045

Rank 3 · TkA05G027340 · TK1151

Endoplasmic reticulum0.037

Rank 4 · TkA05G027340 · TK1151

Mitochondrion0.035

Rank 5 · TkA05G027340 · 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_123-42 aa

PF16367RRM_723-42 aa

PF29393DUF854250-79 aa

PF13893RRM_575-155 aa

PF05172RRM_Nup3578-146 aa

PF14605Nup35_RRM_282-133 aa

PF16367RRM_783-109 aa

PF16842RRM_occluded83-150 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G027340	`PF00076`	RRM_1	23	42	5.5e-23	81.3
TkA05G027340	`PF16367`	RRM_7	23	42	6.3e-06	26.8
TkA05G027340	`PF29393`	DUF8542	50	79	0.1	12.6
TkA05G027340	`PF13893`	RRM_5	75	155	0.0046	17.4
TkA05G027340	`PF05172`	RRM_Nup35	78	146	0.00059	20.5
TkA05G027340	`PF14605`	Nup35_RRM_2	82	133	0.0089	16.6
TkA05G027340	`PF16367`	RRM_7	83	109	6.3e-06	26.8
TkA05G027340	`PF16842`	RRM_occluded	83	150	0.023	15.3
TkA05G027340	`PF00076`	RRM_1	84	148	5.5e-23	81.3
TkA05G027340	`PF08777`	RRM_3	86	140	0.00048	20.9
TkA05G027340	`PF28976`	RRM_ACIN1	93	141	0.25	12.2
TkA05G027340	`PF29326`	RRM_MUD2_C	95	114	0.22	12.3
TkA05G027340	`PF29326`	RRM_MUD2_C	118	151	0.22	12.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q0WW84`	Arabidopsis thaliana	sp\|Q0WW84\|RB47B_ARATH Polyadenylate-binding protein RBP47B	46.300%	Swiss-Prot	Medium
`F4I3B3`	Arabidopsis thaliana	sp\|F4I3B3\|RB47A_ARATH Polyadenylate-binding protein RBP47A	47.200%	Swiss-Prot	Medium
`Q9SX80`	Arabidopsis thaliana	sp\|Q9SX80\|R47CP_ARATH Polyadenylate-binding protein RBP47C'	47.800%	Swiss-Prot	Medium
`Q9SX79`	Arabidopsis thaliana	sp\|Q9SX79\|RB47C_ARATH Polyadenylate-binding protein RBP47C	46.400%	Swiss-Prot	Medium

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