TkA03G281970 | RubberDandelionOmics

Gene overview

TkA03G281970

Reference: TK1151 Chr: Chr03 Coordinates: 69581985-69585274 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2016 bp · TkA03G281970|TK1151|cDNA

AATAAAAGGAATATGGTACTGTTCATTATTAATCGAATGGAAAAAAAACCCGTGGTGCTTACAAGTTACCATCTTGATTCGATTTCAGTGGCTTTCAAATCGAGGGAGGATCACAGGAAACAAATGGAACTGGAGGAAGCACGTAAAGCTGGGCTGGCACCTGCAGAAGTGGATGAAGATGGAAAGGAAATCAATCCCCATATTCCTCAATACATGTCGTCTGCCCCTTGGTATCTGAATGCAGAAAGACCGAGTCTAAA...

CDS

Download CDS FASTA

1662 bp · TkA03G281970|TK1151|CDS

ATGGTACTGTTCATTATTAATCGAATGGAAAAAAAACCCGTGGTGCTTACAAGTTACCATCTTGATTCGATTTCAGTGGCTTTCAAATCGAGGGAGGATCACAGGAAACAAATGGAACTGGAGGAAGCACGTAAAGCTGGGCTGGCACCTGCAGAAGTGGATGAAGATGGAAAGGAAATCAATCCCCATATTCCTCAATACATGTCGTCTGCCCCTTGGTATCTGAATGCAGAAAGACCGAGTCTAAAGCATCAAAGGAA...

Protein

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553 aa · TkA03G281970|TK1151|PROTEIN

MVLFIINRMEKKPVVLTSYHLDSISVAFKSREDHRKQMELEEARKAGLAPAEVDEDGKEINPHIPQYMSSAPWYLNAERPSLKHQRKWKSDPNYTKSWYDRGAKIYQADKYRKGACENCGAMTHTTKTCMERPRKLGAKWTSKNIAPDEKIETFELDYDGKRDRWNGYDAASYAHVIERYEARDEARKKFLKDQQLKKLEEKGNADEGVSDDEDNEDALKIDEAKVDESKQMDFAKVEKRVRTTGGGSTGTVRNLRIRED...

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	`TkA03G281970`
TK1151 ID	TkA03G281970
OH-1004 ID	LXL04_008159
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	93.400
Protein coverage (%)	TK1151 95.841 / OH-1004 94.170 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 TkA03G281970

Location Chr03:69581985-69585274 (-)

Description Similar to Os08g0127700: Pre-mRNA-splicing factor SLU7

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g65660`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron (By similarity).	The recessive epigenetic swellmap mutation affects the expression of two step II splicing factors required for the transcription of the cell proliferation gene STRUWWELPETER and for the timing of cell cycle arrest in the Arabidopsis leaf.2005 · DOI: 10.1105/tpc.105.032771
`At4g37120`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron (By similarity).	The recessive epigenetic swellmap mutation affects the expression of two step II splicing factors required for the transcription of the cell proliferation gene STRUWWELPETER and for the timing of cell cycle arrest in the Arabidopsis leaf.2005 · DOI: 10.1105/tpc.105.032771 SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively Regulates Seedling Photomorphogenesis in Arabidopsis .2022 · DOI: 10.3389/fpls.2022.836519

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2YQU8`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron.	No verified direct reference in this release
`Os08g0127700`	Participates in the second catalytic step of pre-mRNA splicing, when the free hydroxyl group of exon I attacks the 3'-splice site to generate spliced mRNA and the excised lariat intron.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008159 · 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:0008284 positive regulation of cell population proliferation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009637 response to blue light Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0010218 response to far red light Biological Process

GO:0010230 alternative respiration Biological Process

GO:0045292 mRNA cis splicing, via spliceosome Biological Process

GO:1900140 regulation of seedling development Biological Process

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G65660

ath:AT4G37120

dosa:Os08g0127700

gga:416157

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.

Nucleus0.758

Rank 1 · TkA03G281970 · TK1151

Cytoplasm0.279

Rank 2 · TkA03G281970 · TK1151

Cell membrane0.029

Rank 3 · TkA03G281970 · TK1151

Mitochondrion0.025

Rank 4 · TkA03G281970 · TK1151

Endoplasmic reticulum0.019

Rank 5 · TkA03G281970 · 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.

PF11708Slu728-46 aa

PF30379SLU7_N33-45 aa

PF30379SLU7_N110-135 aa

PF14392zf-CCHC_4114-129 aa

PF11708Slu7156-422 aa

PF28659GMI1_N294-321 aa

PF06884DUF1264467-528 aa

PF28659GMI1_N498-542 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G281970	`PF11708`	Slu7	28	46	1.3e-96	324.2
TkA03G281970	`PF30379`	SLU7_N	33	45	1.6e-09	37.7
TkA03G281970	`PF30379`	SLU7_N	110	135	1.6e-09	37.7
TkA03G281970	`PF14392`	zf-CCHC_4	114	129	0.17	12.2
TkA03G281970	`PF11708`	Slu7	156	422	1.3e-96	324.2
TkA03G281970	`PF28659`	GMI1_N	294	321	1.0	10.5
TkA03G281970	`PF06884`	DUF1264	467	528	0.03	14.6
TkA03G281970	`PF28659`	GMI1_N	498	542	1.0	10.5
TkA03G281970	`PF11708`	Slu7	507	520	1.3e-96	324.2

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
`Q9SHY8`	Arabidopsis thaliana	sp\|Q9SHY8\|SLU7A_ARATH Pre-mRNA-splicing factor SLU7-A	79.800%	Swiss-Prot	High
`O23174`	Arabidopsis thaliana	sp\|O23174\|SLU7B_ARATH Pre-mRNA-splicing factor SLU7-B	72.700%	Swiss-Prot	High
`A2YQU8`	Oryza sativa subsp. indica	sp\|A2YQU8\|SLU7_ORYSI Pre-mRNA-splicing factor SLU7	80.000%	Swiss-Prot	High
`Q6ZK48`	Oryza sativa subsp. japonica	sp\|Q6ZK48\|SLU7_ORYSJ Pre-mRNA-splicing factor SLU7	80.000%	Swiss-Prot	High

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