TkA04G473380 | RubberDandelionOmics

Gene overview

TkA04G473380

Reference: TK1151 Chr: Chr04 Coordinates: 119538819-119540969 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1338 bp · TkA04G473380|TK1151|cDNA

TTTTGCAACAAGGTGGGAAAGTTAAAAAGGGTTCAAATGCTACTAGGGTTTTCGAGAATCAGATTGCTCCGCTAAGCTTAGCGTCGTCAATCGGGAGCCATAATCAATGGCGAATCGTACGGACCCGTCGGCGAAAAGCATACATGGAACAAACCCCCAAAACCTTATTGAGAAGATATTGAGGTCTAAGATTTACCAAAACGTCTTCTGGAAGGAGCAGTGTTTCGGTTTGACAGCTGAGACGCTTGTGGACAAGGCCA...

CDS

Download CDS FASTA

1071 bp · TkA04G473380|TK1151|CDS

ATGGCGAATCGTACGGACCCGTCGGCGAAAAGCATACATGGAACAAACCCCCAAAACCTTATTGAGAAGATATTGAGGTCTAAGATTTACCAAAACGTCTTCTGGAAGGAGCAGTGTTTCGGTTTGACAGCTGAGACGCTTGTGGACAAGGCCATGGAGCTCGATCACATCGGCGGTACCCACGGCGGAAACCGAAGACCCACGCCATTCATCTGCCTCGTCATGAAGATGCTCCAGATCCAGCCTGATAAAGAAATTGT...

Protein

Download Protein FASTA

356 aa · TkA04G473380|TK1151|PROTEIN

MANRTDPSAKSIHGTNPQNLIEKILRSKIYQNVFWKEQCFGLTAETLVDKAMELDHIGGTHGGNRRPTPFICLVMKMLQIQPDKEIVVEFIKNEDYKYVRVLGAFYLRLTGTDIDVYRYLEPLYNDYRKLRRKLGDGQYSLTHMDEVIDELLTKDYSCDIALPRIKKRLTIEAIGALEPRKSALEDDFEEEEEKEDEEQPMDTDVGGHDKDYYRAQSPTKERGRDRKRDSHRHRDRDYDREYERDYDRDRGRGRDRDRDR...

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	`TkA04G473380`
TK1151 ID	TkA04G473380
OH-1004 ID	LXL04_038879
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.500
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

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 TkA04G473380

Location Chr04:119538819-119540969 (-)

Description Similar to PRP38: Pre-mRNA-splicing factor 38

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g40650`	Probably required for the first pre-mRNA cleavage reaction catalyzed by the spliceosome.	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_038879 · 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:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010389 regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0032991 protein-containing complex Cellular Component

GO:0071005 U2-type precatalytic spliceosome Cellular Component

GO:0071011 precatalytic spliceosome Cellular Component

GO:0071013 catalytic step 2 spliceosome Cellular Component

GO:0003723 RNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G40650

dme:Dmel_CG30342

hsa:84950

mcf:102116944

pon:100171974

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.

Nucleus0.964

Rank 1 · TkA04G473380 · TK1151

Cytoplasm0.113

Rank 2 · TkA04G473380 · TK1151

Cell membrane0.017

Rank 3 · TkA04G473380 · TK1151

Mitochondrion0.013

Rank 4 · TkA04G473380 · TK1151

Endoplasmic reticulum0.010

Rank 5 · TkA04G473380 · 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.

PF03371PRP3810-172 aa

PF30264YodN_C123-151 aa

PF19252HIND129-135 aa

PF12871PRP38_assoc179-270 aa

PF12871PRP38_assoc268-306 aa

PF12871PRP38_assoc323-330 aa

PF19252HIND340-354 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G473380	`PF03371`	PRP38	10	172	8.7e-67	225.0
TkA04G473380	`PF30264`	YodN_C	123	151	0.078	13.7
TkA04G473380	`PF19252`	HIND	129	135	0.00033	20.7
TkA04G473380	`PF12871`	PRP38_assoc	179	270	5e-09	37.4
TkA04G473380	`PF12871`	PRP38_assoc	268	306	5e-09	37.4
TkA04G473380	`PF12871`	PRP38_assoc	323	330	5e-09	37.4
TkA04G473380	`PF19252`	HIND	340	354	0.00033	20.7

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
`Q8LB54`	Arabidopsis thaliana	sp\|Q8LB54\|PRP38_ARATH Pre-mRNA-splicing factor 38	82.100%	Swiss-Prot	Medium

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