TkA05G458430 | RubberDandelionOmics

Gene overview

TkA05G458430

Reference: TK1151 Chr: Chr05 Coordinates: 114867462-114869437 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

405 bp · TkA05G458430|TK1151|cDNA

ATGATTTCGGTCACCTCCACCCTTAGCGTCACCAATTATGGCGGCCTCCATCCCTTACCATCACCGATTCTGGCGGACTTCACCCCTACTGTATATATCCTCATTGGGTTTGCTTTTGTCTATATGGAGGATGAAAGTGATGCTGAAGATGCTATTCGTGCACGTGACCGCTATGAATTTGGTAGGAAGGGACGCCAACTTCGTGTTGAGTGGACAAAGCTTGAGTTTCTATCGCCGATTCCGGGCACCCCCCCTCAAAA...

CDS

Download CDS FASTA

405 bp · TkA05G458430|TK1151|CDS

ATGATTTCGGTCACCTCCACCCTTAGCGTCACCAATTATGGCGGCCTCCATCCCTTACCATCACCGATTCTGGCGGACTTCACCCCTACTGTATATATCCTCATTGGGTTTGCTTTTGTCTATATGGAGGATGAAAGTGATGCTGAAGATGCTATTCGTGCACGTGACCGCTATGAATTTGGTAGGAAGGGACGCCAACTTCGTGTTGAGTGGACAAAGCTTGAGTTTCTATCGCCGATTCCGGGCACCCCCCCTCAAAA...

Protein

Download Protein FASTA

134 aa · TkA05G458430|TK1151|PROTEIN

MISVTSTLSVTNYGGLHPLPSPILADFTPTVYILIGFAFVYMEDESDAEDAIRARDRYEFGRKGRQLRVEWTKLEFLSPIPGTPPQNVERLKGSFYFLAAHLILGLLHRLNKQEERMHKVRDLSSLVFFLQRLF

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	`TkA05G458430`
TK1151 ID	TkA05G458430
OH-1004 ID	LXL04_027187
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	78.100
Protein coverage (%)	TK1151 23.881 / OH-1004 4.938 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 TkA05G458430

Location Chr05:114867462-114869437 (-)

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
`At4g25500`	Required for constitutive and alternative pre-mRNA splicing (Probable).	A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.2013 · DOI: 10.1371/journal.pgen.1003875 The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.2015 · DOI: 10.1093/nar/gkv751
`At5g52040`	Required for constitutive and alternative pre-mRNA splicing (Probable).	A KH-domain RNA-binding protein interacts with FIERY2/CTD phosphatase-like 1 and splicing factors and is important for pre-mRNA splicing in Arabidopsis.2013 · DOI: 10.1371/journal.pgen.1003875 The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis.2015 · DOI: 10.1093/nar/gkv751
`At3g61860`	Required for constitutive and alternative pre-mRNA splicing.	No verified direct reference in this release
`At2g46610`	Probably involved in intron recognition and spliceosome assembly.	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_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.

Cytoplasm0.453

Rank 1 · TkA05G458430 · TK1151

Nucleus0.433

Rank 2 · TkA05G458430 · TK1151

Mitochondrion0.133

Rank 3 · TkA05G458430 · TK1151

Cell membrane0.071

Rank 4 · TkA05G458430 · TK1151

Endoplasmic reticulum0.066

Rank 5 · TkA05G458430 · 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_136-62 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G458430	`PF00076`	RRM_1	36	62	0.00039	20.9

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
`P92965`	Arabidopsis thaliana	sp\|P92965\|RS40_ARATH Serine/arginine-rich splicing factor RS40	87.500%	Swiss-Prot	Low
`P92966`	Arabidopsis thaliana	sp\|P92966\|SRS41_ARATH Serine/arginine-rich splicing factor RS41	84.200%	Swiss-Prot	Low
`P92964`	Arabidopsis thaliana	sp\|P92964\|SRS31_ARATH Serine/arginine-rich splicing factor RS31	49.200%	Swiss-Prot	Low
`Q9ZPX8`	Arabidopsis thaliana	sp\|Q9ZPX8\|RS31A_ARATH Serine/arginine-rich splicing factor RS31A	63.200%	Swiss-Prot	Low

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