TkA02G486760 | RubberDandelionOmics

Gene overview

TkA02G486760

Reference: TK1151 Chr: Chr02 Coordinates: 124472228-124473940 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

678 bp · TkA02G486760|TK1151|cDNA

ATGTTCGCTGCTTCTCTGCTTCTTCAGTCGTTCGTCCTCCTGGGTTCGCTGCACCACAGATTCCGGGTTTTGGAAGGTAAGGTTACCACTCTTGATTACGATCATATAGGTCAGCTTATGTTTTGGGAATTGCACAGTGAATGTCTAGACCCTTTTCATGTTCCTGAATGTGAGGCATTTGACATCTTTGTTAACGAGAGTCTGTTTGCTGGCAAAGTTAAGATGGTTCTTCAACAGGGACTGCATATGCAACGTCTCAA...

CDS

Download CDS FASTA

678 bp · TkA02G486760|TK1151|CDS

ATGTTCGCTGCTTCTCTGCTTCTTCAGTCGTTCGTCCTCCTGGGTTCGCTGCACCACAGATTCCGGGTTTTGGAAGGTAAGGTTACCACTCTTGATTACGATCATATAGGTCAGCTTATGTTTTGGGAATTGCACAGTGAATGTCTAGACCCTTTTCATGTTCCTGAATGTGAGGCATTTGACATCTTTGTTAACGAGAGTCTGTTTGCTGGCAAAGTTAAGATGGTTCTTCAACAGGGACTGCATATGCAACGTCTCAA...

Protein

Download Protein FASTA

225 aa · TkA02G486760|TK1151|PROTEIN

MFAASLLLQSFVLLGSLHHRFRVLEGKVTTLDYDHIGQLMFWELHSECLDPFHVPECEAFDIFVNESLFAGKVKMVLQQGLHMQRLKVKESEAFRAVASNTGGATAKDLFEDVAEELETKYHYDKTRVNDAMKTKKVSVAPTWTFSDFKDAMQDDVITPPLSDTNFQLVFEDLLKRAKEKEKKEQKRRRRFAKDFTELLDNIKEINDSSTWEDCKQLFEESNVYR

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	`TkA02G486760`
TK1151 ID	TkA02G486760
OH-1004 ID	LXL04_011787
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	80.300
Protein coverage (%)	TK1151 90.222 / OH-1004 97.727 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 TkA02G486760

Location Chr02:124472228-124473940 (-)

Description Similar to PRP40A: Pre-mRNA-processing protein 40A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19670`	Binds the phosphorylated C-terminal domain (CTD) of the largest subunit of RNA polymerase II and functions as a scaffold for RNA processing machineries.	Arabidopsis thaliana PRP40s are RNA polymerase II C-terminal domain-associating proteins.2009 · DOI: 10.1016/j.abb.2009.01.004

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011787 · 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:0008380 RNA splicing Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:0005634 nucleus Cellular Component

GO:0005685 U1 snRNP Cellular Component

GO:0016592 mediator complex Cellular Component

GO:0071004 U2-type prespliceosome Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0070063 RNA polymerase binding Molecular Function

KEGG gene cross-reference

ath:AT1G44910

ath:AT3G19670

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.

Cytoplasm0.456

Rank 1 · TkA02G486760 · TK1151

Nucleus0.448

Rank 2 · TkA02G486760 · TK1151

Mitochondrion0.116

Rank 3 · TkA02G486760 · TK1151

Endoplasmic reticulum0.052

Rank 4 · TkA02G486760 · TK1151

Cell membrane0.046

Rank 5 · TkA02G486760 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF13025DUF388685-91 aa

PF01846FF89-112 aa

PF19269Anticodon_291-133 aa

PF24017Beta-prop_SCAP95-210 aa

PF25432FF_PRPF40A120-179 aa

PF01846FF136-155 aa

PF13025DUF3886149-200 aa

PF19269Anticodon_2177-223 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G486760	`PF13025`	DUF3886	85	91	0.0033	18.3
TkA02G486760	`PF01846`	FF	89	112	3.1e-06	27.9
TkA02G486760	`PF19269`	Anticodon_2	91	133	0.4	11.8
TkA02G486760	`PF24017`	Beta-prop_SCAP	95	210	0.13	11.8
TkA02G486760	`PF25432`	FF_PRPF40A	120	179	9.2e-21	74.2
TkA02G486760	`PF01846`	FF	136	155	3.1e-06	27.9
TkA02G486760	`PF13025`	DUF3886	149	200	0.0033	18.3
TkA02G486760	`PF19269`	Anticodon_2	177	223	0.4	11.8
TkA02G486760	`PF01846`	FF	193	220	3.1e-06	27.9
TkA02G486760	`PF25432`	FF_PRPF40A	203	212	9.2e-21	74.2

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
`F4JCC1`	Arabidopsis thaliana	sp\|F4JCC1\|PR40B_ARATH Pre-mRNA-processing protein 40B	40.400%	Swiss-Prot	Medium

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