TkA01G566010 | RubberDandelionOmics

Gene overview

TkA01G566010

Reference: TK1151 Chr: Chr01 Coordinates: 142431013-142441432 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2280 bp · TkA01G566010|TK1151|cDNA

ATGAGACAGCTGCTTCATCTTAGACGGCCTTTTGTTGATACAATAATAACCGATGGCTATAGTAACGAGCTGTTTAGGGTGAGAAGGCCCTTTTGGTGGATAACAAGCTCCATCTATGCAGGAGTAGTTGGAAAGGAAATTGGTGTGGTTCATAGAAGATGGCATGGAGACGAGCAGTTTGCAGTAGTTGAAAATCCGGGTTTTTGGAACTGGACATCTACTTCAAAAGGAGCTGATGGTGAAGTATTAGGTGAAAAGGC...

CDS

Download CDS FASTA

2280 bp · TkA01G566010|TK1151|CDS

ATGAGACAGCTGCTTCATCTTAGACGGCCTTTTGTTGATACAATAATAACCGATGGCTATAGTAACGAGCTGTTTAGGGTGAGAAGGCCCTTTTGGTGGATAACAAGCTCCATCTATGCAGGAGTAGTTGGAAAGGAAATTGGTGTGGTTCATAGAAGATGGCATGGAGACGAGCAGTTTGCAGTAGTTGAAAATCCGGGTTTTTGGAACTGGACATCTACTTCAAAAGGAGCTGATGGTGAAGTATTAGGTGAAAAGGC...

Protein

Download Protein FASTA

759 aa · TkA01G566010|TK1151|PROTEIN

MRQLLHLRRPFVDTIITDGYSNELFRVRRPFWWITSSIYAGVVGKEIGVVHRRWHGDEQFAVVENPGFWNWTSTSKGADGEVLGEKACVMERTRSQNELNRVVYGQDHLTRDDSAFILSLKASLLDCFPITDLYHYLYSSLTKGILSEEEGGVLFCSDKDATRKTIMATRASFAFGDHPDVDISQIPDRVKFKLAAIEEAVSLSIWTTITLCRALSLENVLILVAALLLEKQVIITSPNLASCACNDSRTLLCDKDLKQK...

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	`TkA01G566010`
TK1151 ID	TkA01G566010
OH-1004 ID	LXL04_026453
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	91.900
Protein coverage (%)	TK1151 4.875 / OH-1004 1.670 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 TkA01G566010

Location Chr01:142431013-142441432 (+)

Description Similar to BRR2A: DExH-box ATP-dependent RNA helicase DExH12

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20960`	RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes.	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_026453 · 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:0000244 spliceosomal tri-snRNP complex assembly Biological Process

GO:0000354 cis assembly of pre-catalytic spliceosome Biological Process

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:0010228 vegetative to reproductive phase transition of meristem 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:0005682 U5 snRNP Cellular Component

KEGG gene cross-reference

ath:AT1G20960

ath:AT2G42270

hsa:23020

mmu:320632

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.

Cytoplasm0.357

Rank 1 · TkA01G566010 · TK1151

Nucleus0.263

Rank 2 · TkA01G566010 · TK1151

Cell membrane0.186

Rank 3 · TkA01G566010 · TK1151

Mitochondrion0.149

Rank 4 · TkA01G566010 · TK1151

Endoplasmic reticulum0.131

Rank 5 · TkA01G566010 · 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.

PF03803Scramblase1-63 aa

PF02141DENN210-241 aa

PF10536PMD282-321 aa

PF10536PMD326-403 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G566010	`PF03803`	Scramblase	1	63	9.8e-07	29.0
TkA01G566010	`PF02141`	DENN	210	241	0.0096	16.5
TkA01G566010	`PF10536`	PMD	282	321	0.014	15.4
TkA01G566010	`PF10536`	PMD	326	403	0.014	15.4

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
`Q9SYP1`	Arabidopsis thaliana	sp\|Q9SYP1\|DEXHC_ARATH DExH-box ATP-dependent RNA helicase DExH12	89.200%	Swiss-Prot	Low

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