TkA01G539610 | RubberDandelionOmics

Gene overview

TkA01G539610

Reference: TK1151 Chr: Chr01 Coordinates: 135300986-135303574 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1373 bp · TkA01G539610|TK1151|cDNA

ACAAACCATCGTGTAGGCCCAAGCTGGAGGGGCCAAAATCAACAACCGACTGGAGAGTGACACCTGGCGATGCCATTCTTATTCTTGCTTTTATGTTCGTGAAGCTTCTTACAATGGCACGATCAAACGAACATCTTTGAAATAATTATCACAACTCCTACCTCCCTGAAATCCCAAAACTCTTTCAACCTTCGCTCAATCAGCTCAAATCTGTAGTTAGCAGCGAGAAAGAAAGAAACAATGTCTCACTTTGGCCGATC...

CDS

Download CDS FASTA

642 bp · TkA01G539610|TK1151|CDS

ATGTCTCACTTTGGCCGATCAGGACCGCCGGACATTTCCGACACCTACTCTCTCCTCATTCTCAACATTAATTTTCGGACGACGGCGGACGATCTGTTTCCGCTTTTTGATAAGTACGGGAAGGTCGTTGATATTTTCATCCCCAAAGATCGAAGGACTGGTGATTCCCGTGGCTTTGCGTTCGTTCGTTACAAGTATGCAGACGAAGCAGAGAAGGCAGTAGATAGGCTCGATGGAAGAGAAGTTGATGGTCGAGAAAT...

Protein

Download Protein FASTA

213 aa · TkA01G539610|TK1151|PROTEIN

MSHFGRSGPPDISDTYSLLILNINFRTTADDLFPLFDKYGKVVDIFIPKDRRTGDSRGFAFVRYKYADEAEKAVDRLDGREVDGREITVQFAKYGPNAERIHRGRIIEKSPRARGRSRSRSPRRSSRHHDDYYRDRDYRRSSRSRSRDRYYDRSHERERGYRYRSRSPEYDRGHGRSRYVDEHLSRSQSIESRSPRSRSLDSRSPSPRVHDDE

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	`TkA01G539610`
TK1151 ID	TkA01G539610
OH-1004 ID	LXL04_015041
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	39.500
Protein coverage (%)	TK1151 35.681 / OH-1004 39.791 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 TkA01G539610

Location Chr01:135300986-135303574 (+)

Description Similar to ORRM6: Organelle RRM domain-containing protein 6, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g64200`	Probably involved in intron recognition and spliceosome assembly, but not involved in alternative splicing regulation of the SCL33 intron.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_015041 · 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:0016554 cytidine to uridine editing Biological Process

GO:0080156 mitochondrial mRNA modification Biological Process

GO:1900871 chloroplast mRNA modification Biological Process

GO:1901002 positive regulation of response to salt stress Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G73530

ath:AT5G06210

ath:AT5G54580

dosa:Os02g0730800

osa:4330618

zma:100304402

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.

Nucleus0.972

Rank 1 · TkA01G539610 · TK1151

Cytoplasm0.174

Rank 2 · TkA01G539610 · TK1151

Cell membrane0.014

Rank 3 · TkA01G539610 · TK1151

Mitochondrion0.009

Rank 4 · TkA01G539610 · TK1151

Endoplasmic reticulum0.007

Rank 5 · TkA01G539610 · 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.

PF13893RRM_512-95 aa

PF00076RRM_119-88 aa

PF14605Nup35_RRM_236-74 aa

PF29326RRM_MUD2_C57-92 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G539610	`PF13893`	RRM_5	12	95	0.00011	22.5
TkA01G539610	`PF00076`	RRM_1	19	88	3.2e-20	72.5
TkA01G539610	`PF14605`	Nup35_RRM_2	36	74	0.069	13.8
TkA01G539610	`PF29326`	RRM_MUD2_C	57	92	0.045	14.5

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
`Q9FMG4`	Arabidopsis thaliana	sp\|Q9FMG4\|SC35_ARATH Serine/arginine-rich splicing factor SC35	83.300%	Swiss-Prot	Medium

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