TkA04G411350 | RubberDandelionOmics

Gene overview

TkA04G411350

Reference: TK1151 Chr: Chr04 Coordinates: 103577807-103587990 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

724 bp · TkA04G411350|TK1151|cDNA

CCGAATACATGATCCAATGACGTCAACTAACCATAGTCAGGAGTGAAGTAGGAGCCTCTTCAGCTATATAATCGAGGCGACTTCAGCTAGGGTTTCATCATTTCACATTGTATTGAAATTTGAAAAAAAAAATTCATTTGTCAATGGCGTCTGCGGATGTGGAGTTCAGATGTTTCGTCGGTGGTCTTGCCTGGGCGACTACCGACCAGTCCTTAGAAGAAGCTTTCTCTCAATATGGAGACATTTTGGAATCGAAGATT...

CDS

Download CDS FASTA

495 bp · TkA04G411350|TK1151|CDS

ATGGCGTCTGCGGATGTGGAGTTCAGATGTTTCGTCGGTGGTCTTGCCTGGGCGACTACCGACCAGTCCTTAGAAGAAGCTTTCTCTCAATATGGAGACATTTTGGAATCGAAGATTATCAACGACCGTGAAACCGGCAGATCTAGAGGTTTCGGATTTGTAACCTTCAAGGACGAGAAAGCGATGAGAGATGCAATCGAGGGAATGAACGGCCAGAGCCTCGACGGCCGTAACATTACCGTCAACGAGGCACAGTCTCG...

Protein

Download Protein FASTA

164 aa · TkA04G411350|TK1151|PROTEIN

MASADVEFRCFVGGLAWATTDQSLEEAFSQYGDILESKIINDRETGRSRGFGFVTFKDEKAMRDAIEGMNGQSLDGRNITVNEAQSRGSGGGGGGGRREGGGGYGGGGGGYGRREGGGGGYGGGGGGYGGGGGGYGGGGRDRGYGGGGGGYSRGGGDSEGNWRN

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	`TkA04G411350`
TK1151 ID	TkA04G411350
OH-1004 ID	LXL04_013260
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	50.000
Protein coverage (%)	TK1151 48.780 / OH-1004 29.304 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 TkA04G411350

Location Chr04:103577807-103587990 (-)

Description Similar to 28 kDa ribonucleoprotein, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21660`	Plays a role in RNA transcription or processing during stress.	AtGRP7 is involved in the regulation of abscisic acid and stress responses in Arabidopsis.2006 · DOI: 10.2478/s11658-006-0042-2 Cold shock domain proteins and glycine-rich RNA-binding proteins from Arabidopsis thaliana can promote the cold adaptation process in Escherichia coli.2007 · DOI: 10.1093/nar/gkl1076 Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation.2007 · DOI: 10.1111/j.1365-313x.2007.03302.x Glycine-rich RNA-binding protein 7 affects abiotic stress responses by regulating stomata opening and closing in Arabidopsis thaliana.2008 · DOI: 10.1111/j.1365-313x.2008.03518.x The small glycine-rich RNA binding protein AtGRP7 promotes floral transition in Arabidopsis thaliana.2008 · DOI: 10.1111/j.1365-313x.2008.03591.x Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.2008 · DOI: 10.1093/nar/gkn847 RNA-protein interaction mediating post-transcriptional regulation in the circadian system.2009 · DOI: 10.1007/978-1-59745-289-2_21 Structural determinants crucial to the RNA chaperone activity of glycine-rich RNA-binding proteins 4 and 7 in Arabidopsis thaliana during the cold adaptation process.2011 · DOI: 10.1093/jxb/err101 Structure function analysis of an ADP-ribosyltransferase type III effector and its RNA-binding target in plant immunity.2011 · DOI: 10.1074/jbc.m111.290122 An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.2012 · DOI: 10.1093/nar/gks873 A Plant SMALL RNA-BINDING PROTEIN 1 Family Mediates Cell-to-Cell Trafficking of RNAi Signals.2020 · DOI: 10.1016/j.molp.2019.12.001 AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana.1997 · DOI: 10.1073/pnas.94.16.8515
`At4g39260`	Plays a role in RNA transcription or processing during stress.	Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis.2008 · DOI: 10.1093/nar/gkn847 Quantitative analysis of single-molecule RNA-protein interaction.2009 · DOI: 10.1016/j.bpj.2009.03.022 An hnRNP-like RNA-binding protein affects alternative splicing by in vivo interaction with transcripts in Arabidopsis thaliana.2012 · DOI: 10.1093/nar/gks873

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013260 · 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:0006396 RNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0009409 response to cold Biological Process

GO:0009451 RNA modification Biological Process

GO:0009631 cold acclimation Biological Process

GO:0016553 base conversion or substitution editing Biological Process

GO:0043489 RNA stabilization Biological Process

GO:0045087 innate immune response Biological Process

GO:1901259 chloroplast rRNA processing Biological Process

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

KEGG gene cross-reference

ath:AT4G24770

ath:AT5G50250

nsy:104227036

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.

Nucleus0.780

Rank 1 · TkA04G411350 · TK1151

Cytoplasm0.551

Rank 2 · TkA04G411350 · TK1151

Extracellular0.182

Rank 3 · TkA04G411350 · TK1151

Cell membrane0.062

Rank 4 · TkA04G411350 · TK1151

Endoplasmic reticulum0.056

Rank 5 · TkA04G411350 · 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.

PF16367RRM_79-68 aa

PF00076RRM_111-80 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G411350	`PF16367`	RRM_7	9	68	4e-05	24.2
TkA04G411350	`PF00076`	RRM_1	11	80	3.3e-24	85.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q03250`	Arabidopsis thaliana	sp\|Q03250\|RBG7_ARATH Glycine-rich RNA-binding protein 7	85.600%	Swiss-Prot	Medium
`Q03251`	Arabidopsis thaliana	sp\|Q03251\|RBG8_ARATH Glycine-rich RNA-binding protein 8	79.300%	Swiss-Prot	Medium

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