TkA04G133480 | RubberDandelionOmics

Gene overview

TkA04G133480

Reference: TK1151 Chr: Chr04 Coordinates: 34709385-34712261 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1208 bp · TkA04G133480|TK1151|cDNA

GTAATTTTGTGGCCATGTTATAGCTAATCGACTCGTAACCGACTTATCCATTGCCGGCCATCAAGTTTGGTTGGCTCAATAGTCCCATATAGATGTATTCATTGGCATTTCAATTTGCGATTTCTGGAAATGTGGAACGCATAGATATATAAATTGGGTTCTATTAGTATTTTGGCTGATTTACTGAAATGTTCATTTGCCATTGAAAATGAGTGGCCGCTTCTCACGCACTATTTATGTTGGGAACCTTCCCCTTGATA...

CDS

Download CDS FASTA

750 bp · TkA04G133480|TK1151|CDS

ATGAGTGGCCGCTTCTCACGCACTATTTATGTTGGGAACCTTCCCCTTGATATAAGAGAATGGGAAGTTGAAGACCTTTTCTATAAGTATGGGCGCATATTGGACATAGAATTAAAGATTCCACCTCGTCCTCCTTGTTATTGTTTTGTTGAGTTTGCTAATGCTCGAGATGCTGAAGATGCAATTAGGGGACGTGATGGCTACAATTTCGATGGTTGCCGCCTCAGGGTTGAGCTTGCTCATGGCGGTCGAGGACAATC...

Protein

Download Protein FASTA

249 aa · TkA04G133480|TK1151|PROTEIN

MSGRFSRTIYVGNLPLDIREWEVEDLFYKYGRILDIELKIPPRPPCYCFVEFANARDAEDAIRGRDGYNFDGCRLRVELAHGGRGQSSSSDRHGSSHGKGRSGLSRYSEFRVIVRKLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGTFGLVDYTNYDDMKYAIRKLDDTEFRNPWAKAYIRVRKYETRPSRSPSRSRSRSRSKSLERSVSRSPSKSRSASPVKPTKSRSRSRSRSKSKSQSPTQGQSQ

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	`TkA04G133480`
TK1151 ID	TkA04G133480
OH-1004 ID	LXL04_035398
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	100.000
Protein coverage (%)	TK1151 77.510 / OH-1004 78.776 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 TkA04G133480

Location Chr04:34709385-34712261 (-)

Description Similar to SR34A: Serine/arginine-rich splicing factor SR34A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g49430`	Probably involved in intron recognition and spliceosome assembly.	No verified direct reference in this release
`At1g09140`	Regulatory splicing factor that modulates alternative splicing and gene expression in specific cell types.	atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
`At1g02840`	General splicing factor.	atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
`At4g02430`	Probably involved in intron recognition and spliceosome assembly.	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_035398 · 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:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009636 response to toxic substance Biological Process

GO:0043279 response to alkaloid Biological Process

GO:0048025 negative regulation of mRNA splicing, via spliceosome Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT1G02840

ath:AT1G09140

ath:AT3G49430

ath:AT4G02430

rno:288701

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.

Nucleus0.960

Rank 1 · TkA04G133480 · TK1151

Cytoplasm0.201

Rank 2 · TkA04G133480 · TK1151

Cell membrane0.016

Rank 3 · TkA04G133480 · TK1151

Mitochondrion0.012

Rank 4 · TkA04G133480 · TK1151

Extracellular0.011

Rank 5 · TkA04G133480 · 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_76-34 aa

PF16842RRM_occluded7-77 aa

PF25701RRM_YTH18-75 aa

PF00076RRM_19-76 aa

PF25701RRM_YTH1109-174 aa

PF00076RRM_1112-174 aa

PF04415DUF515191-248 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G133480	`PF16367`	RRM_7	6	34	0.0041	17.8
TkA04G133480	`PF16842`	RRM_occluded	7	77	0.083	13.5
TkA04G133480	`PF25701`	RRM_YTH1	8	75	0.026	15.1
TkA04G133480	`PF00076`	RRM_1	9	76	2.9e-31	107.9
TkA04G133480	`PF25701`	RRM_YTH1	109	174	0.026	15.1
TkA04G133480	`PF00076`	RRM_1	112	174	2.9e-31	107.9
TkA04G133480	`PF04415`	DUF515	191	248	1.3	8.1

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`A2RVS6`	Arabidopsis thaliana	sp\|A2RVS6\|SR34A_ARATH Serine/arginine-rich splicing factor SR34A	77.000%	Swiss-Prot	High
`Q9XFR5`	Arabidopsis thaliana	sp\|Q9XFR5\|SR30_ARATH Serine/arginine-rich splicing factor SR30	71.400%	Swiss-Prot	High
`O22315`	Arabidopsis thaliana	sp\|O22315\|SR34_ARATH Serine/arginine-rich-splicing factor SR34	66.500%	Swiss-Prot	High
`F4JHI7`	Arabidopsis thaliana	sp\|F4JHI7\|SR34B_ARATH Serine/arginine-rich splicing factor SR34B	65.200%	Swiss-Prot	High

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