TkA01G078520 | RubberDandelionOmics

Gene overview

TkA01G078520

Reference: TK1151 Chr: Chr01 Coordinates: 20062711-20064676 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1219 bp · TkA01G078520|TK1151|cDNA

ATAAAAGTGGGGTCTAAATGAAATTATAGAGCATAACTAAACCTAAACGGAGTTCAGAGAAGAACACAAACCACAACTCGAGGTGTAGAGGAAACACCCACATGAGATAAAAACCCACAAACCCTCGTCGCTAGTCACAAACACAACGTGCTACGCTTTCACGGGCAATTTGCGATTGCTGAATTTGACGGAATGGCCAATGCCGCCGACGTAGATGCACTGGACTTTGAGCCCGATGACGACGATCTCATGGACGAAGA...

CDS

Download CDS FASTA

609 bp · TkA01G078520|TK1151|CDS

ATGGCCAATGCCGCCGACGTAGATGCACTGGACTTTGAGCCCGATGACGACGATCTCATGGACGAAGACGCCGCCGTCGACGTCGATGCTTCTTCACCTAGTGCTGCTGCTACTATCCCCAAACTTAAATCCGCTATCACTGGTGGATCTGTCGCTTCTTCAGCTCCAAAGAAAACTAAAGGCCGTGGTTTCCGTGAAGAAACAGACGCCGGGAGAACTAATCGTATGTCCGGTCGTTTCGACTCCCTCGATTCCGATGG...

Protein

Download Protein FASTA

202 aa · TkA01G078520|TK1151|PROTEIN

MANAADVDALDFEPDDDDLMDEDAAVDVDASSPSAAATIPKLKSAITGGSVASSAPKKTKGRGFREETDAGRTNRMSGRFDSLDSDGGPGPERSIEGWIILVTGVHEEAQEDDLQNAFGEFGEIKNLHLNLDRRTGFVKGYALIEYESYEEAEKAIASMDGGELLTQTVNVDWAFSRGPSRRKNNRRRSPHGHRSRSPRRRF

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	`TkA01G078520`
TK1151 ID	TkA01G078520
OH-1004 ID	LXL04_005170
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
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

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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 TkA01G078520

Location Chr01:20062711-20064676 (+)

Description Similar to Y14: RNA-binding protein Y14

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g51510`	Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os05g0140500`	Core component of the splicing-dependent multiprotein exon junction complex (EJC) deposited at splice junctions on mRNAs.	Uncovering Divergence of Rice Exon Junction Complex Core Heterodimer Gene Duplication Reveals Their Essential Role in Growth, Development, and Reproduction.2014 · DOI: 10.1104/pp.114.237958 Targeting MAGO proteins with a peptide aptamer reinforces their essential roles in multiple rice developmental pathways.2014 · DOI: 10.1111/tpj.12672

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_005170 · 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:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006417 regulation of translation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010628 positive regulation of gene expression Biological Process

GO:0051028 mRNA transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G51510

dosa:Os03g0809900

dosa:Os05g0140500

xla:379595

xla:399167

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.

Nucleus0.879

Rank 1 · TkA01G078520 · TK1151

Cytoplasm0.344

Rank 2 · TkA01G078520 · TK1151

Cell membrane0.026

Rank 3 · TkA01G078520 · TK1151

Mitochondrion0.018

Rank 4 · TkA01G078520 · TK1151

Endoplasmic reticulum0.016

Rank 5 · TkA01G078520 · 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.

PF13893RRM_589-171 aa

PF08777RRM_397-173 aa

PF00076RRM_1100-167 aa

PF25015RBD_AKAP-17A107-132 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G078520	`PF13893`	RRM_5	89	171	0.14	12.6
TkA01G078520	`PF08777`	RRM_3	97	173	0.009	16.8
TkA01G078520	`PF00076`	RRM_1	100	167	7.2e-16	58.5
TkA01G078520	`PF25015`	RBD_AKAP-17A	107	132	0.18	11.9

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4I9J7`	Arabidopsis thaliana	sp\|F4I9J7\|Y14_ARATH RNA-binding protein Y14	62.500%	Swiss-Prot	High
`B7FAL5`	Oryza sativa subsp. japonica	sp\|B7FAL5\|Y14A_ORYSJ RNA-binding protein Y14A	61.300%	Swiss-Prot	High

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