TkA02G550450 | RubberDandelionOmics

Gene overview

TkA02G550450

Reference: TK1151 Chr: Chr02 Coordinates: 142022419-142022796 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

378 bp · TkA02G550450|TK1151|cDNA

ATGGCGACAATCAGTTTGAGAAAGGGGAACACAAGGCTTCCACCGGAGGTTAACAGGGTCCTCTACGTACGCAACTTGCCGTTCAACATCACTTCAGAAGAGATGTACGATATATTCGGAAAATACGGTGCAATTCGTCAGATACGTATCGGAACGAACAAGGATACGCGAGGCACTGCCTTCGTAGTCTACGAAGATATCTACGATGCGAAGACAGCAGTCGATCATCTTTCCGGTTTTAACGTTGCCAATCGGTACCT...

CDS

Download CDS FASTA

378 bp · TkA02G550450|TK1151|CDS

ATGGCGACAATCAGTTTGAGAAAGGGGAACACAAGGCTTCCACCGGAGGTTAACAGGGTCCTCTACGTACGCAACTTGCCGTTCAACATCACTTCAGAAGAGATGTACGATATATTCGGAAAATACGGTGCAATTCGTCAGATACGTATCGGAACGAACAAGGATACGCGAGGCACTGCCTTCGTAGTCTACGAAGATATCTACGATGCGAAGACAGCAGTCGATCATCTTTCCGGTTTTAACGTTGCCAATCGGTACCT...

Protein

Download Protein FASTA

125 aa · TkA02G550450|TK1151|PROTEIN

MATISLRKGNTRLPPEVNRVLYVRNLPFNITSEEMYDIFGKYGAIRQIRIGTNKDTRGTAFVVYEDIYDAKTAVDHLSGFNVANRYLIVLYYQQAKMSKKFDQKKKEEELTKLQEKYGVTAKDLQ

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	`TkA02G550450`
TK1151 ID	TkA02G550450
OH-1004 ID	LXL04_012606
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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 TkA02G550450

Location Chr02:142022419-142022796 (-)

Description Similar to At5g12190: Splicing factor 3B subunit 6-like protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g12190`	May be necessary for the splicing of pre-mRNA.	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_012606 · 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:0000387 spliceosomal snRNP assembly Biological Process

GO:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:1903241 U2-type prespliceosome assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005684 U2-type spliceosomal complex Cellular Component

GO:0005689 U12-type spliceosomal complex Cellular Component

GO:0034693 U11/U12 snRNP Cellular Component

KEGG gene cross-reference

ath:AT5G12190

cel:CELE_C50D2.5

dme:Dmel_CG13298

hsa:51639

mmu:66055

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.

Nucleus0.894

Rank 1 · TkA02G550450 · TK1151

Cytoplasm0.226

Rank 2 · TkA02G550450 · TK1151

Mitochondrion0.021

Rank 3 · TkA02G550450 · TK1151

Cell membrane0.018

Rank 4 · TkA02G550450 · TK1151

Endoplasmic reticulum0.009

Rank 5 · TkA02G550450 · 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_517-108 aa

PF22976RRM_1018-78 aa

PF28976RRM_ACIN119-80 aa

PF28442DUF840020-47 aa

PF00076RRM_121-87 aa

PF16367RRM_721-75 aa

PF25015RBD_AKAP-17A35-52 aa

PF29326RRM_MUD2_C55-94 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G550450	`PF13893`	RRM_5	17	108	3.5e-08	33.9
TkA02G550450	`PF22976`	RRM_10	18	78	0.021	15.7
TkA02G550450	`PF28976`	RRM_ACIN1	19	80	0.23	12.3
TkA02G550450	`PF28442`	DUF8400	20	47	0.088	13.7
TkA02G550450	`PF00076`	RRM_1	21	87	1.6e-18	67.1
TkA02G550450	`PF16367`	RRM_7	21	75	0.024	15.3
TkA02G550450	`PF25015`	RBD_AKAP-17A	35	52	0.69	10.0
TkA02G550450	`PF29326`	RRM_MUD2_C	55	94	0.03	15.1
TkA02G550450	`PF06675`	DUF1177	58	120	0.12	12.0
TkA02G550450	`PF25015`	RBD_AKAP-17A	60	105	0.69	10.0
TkA02G550450	`PF28442`	DUF8400	96	114	0.088	13.7
TkA02G550450	`PF00076`	RRM_1	104	119	1.6e-18	67.1

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
`Q9FMP4`	Arabidopsis thaliana	sp\|Q9FMP4\|SF3B6_ARATH Splicing factor 3B subunit 6-like protein	89.400%	Swiss-Prot	High

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