TkA03G345080 | RubberDandelionOmics

Gene overview

TkA03G345080

Reference: TK1151 Chr: Chr03 Coordinates: 84928546-84929154 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

564 bp · TkA03G345080|TK1151|cDNA

ATGGCACAGATTCAGGTGCAGCCTCCTCCAGTATCTGGACCGAATGCTATCGCCAGCGGTGCGGTGGCGGGTTCTAACCAGTCATTTGTGACGACCTCGCTTTACGTTGGGGATCTAGAGTTTAATGTGACTGATTCACAGTTGTACGATATGTTTTATCAGGTTGGACAAGTTGTTACGATTAGGATTTGTAGGGATTTGAGCACTCGGCGATCCCTTGGTTATGGTTATGTCAACTTTAACAATCCTAATGATGTGGC...

CDS

Download CDS FASTA

564 bp · TkA03G345080|TK1151|CDS

ATGGCACAGATTCAGGTGCAGCCTCCTCCAGTATCTGGACCGAATGCTATCGCCAGCGGTGCGGTGGCGGGTTCTAACCAGTCATTTGTGACGACCTCGCTTTACGTTGGGGATCTAGAGTTTAATGTGACTGATTCACAGTTGTACGATATGTTTTATCAGGTTGGACAAGTTGTTACGATTAGGATTTGTAGGGATTTGAGCACTCGGCGATCCCTTGGTTATGGTTATGTCAACTTTAACAATCCTAATGATGTGGC...

Protein

Download Protein FASTA

187 aa · TkA03G345080|TK1151|PROTEIN

MAQIQVQPPPVSGPNAIASGAVAGSNQSFVTTSLYVGDLEFNVTDSQLYDMFYQVGQVVTIRICRDLSTRRSLGYGYVNFNNPNDVARAIGVLNFNPVNGKSIRIMYSHRDPSIWKSGTANIFIKNLDKTIDNKALHDTFSSFGNILSCKIATNSIGQSKGYGFVQFDTEEAAQSHIWKRYTVWEEQ

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	`TkA03G345080`
TK1151 ID	TkA03G345080
OH-1004 ID	LXL04_008112
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	87.000
Protein coverage (%)	TK1151 94.652 / OH-1004 30.284 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA03G345080

Location Chr03:84928546-84929154 (-)

Description Similar to PAB2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34110`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g49760`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At2g23350`	Binds the poly(A) tail of mRNA.	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_008112 · 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:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006413 translational initiation Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006446 regulation of translational initiation Biological Process

GO:0048255 mRNA stabilization Biological Process

GO:0060211 regulation of nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:1900151 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G22760

ath:AT1G49760

ath:AT1G71770

ath:AT2G23350

ath:AT4G34110

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.

Cytoplasm0.652

Rank 1 · TkA03G345080 · TK1151

Nucleus0.390

Rank 2 · TkA03G345080 · TK1151

Cell membrane0.063

Rank 3 · TkA03G345080 · TK1151

Mitochondrion0.047

Rank 4 · TkA03G345080 · TK1151

Lysosome / Vacuole0.038

Rank 5 · TkA03G345080 · 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_516-110 aa

PF28978RRM_SRRT31-86 aa

PF00076RRM_134-104 aa

PF16367RRM_734-87 aa

PF22976RRM_1038-108 aa

PF26250RRM_RdRP1_258-91 aa

PF28978RRM_SRRT119-156 aa

PF16367RRM_7121-175 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G345080	`PF13893`	RRM_5	16	110	0.0014	19.1
TkA03G345080	`PF28978`	RRM_SRRT	31	86	0.01	16.7
TkA03G345080	`PF00076`	RRM_1	34	104	6e-36	122.9
TkA03G345080	`PF16367`	RRM_7	34	87	4.4e-05	24.1
TkA03G345080	`PF22976`	RRM_10	38	108	0.00085	20.1
TkA03G345080	`PF26250`	RRM_RdRP1_2	58	91	0.012	16.7
TkA03G345080	`PF28978`	RRM_SRRT	119	156	0.01	16.7
TkA03G345080	`PF16367`	RRM_7	121	175	4.4e-05	24.1
TkA03G345080	`PF00076`	RRM_1	122	175	6e-36	122.9
TkA03G345080	`PF13893`	RRM_5	122	155	0.0014	19.1
TkA03G345080	`PF22976`	RRM_10	126	174	0.00085	20.1
TkA03G345080	`PF26250`	RRM_RdRP1_2	142	173	0.012	16.7

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
`P42731`	Arabidopsis thaliana	sp\|P42731\|PABP2_ARATH Polyadenylate-binding protein 2	65.000%	Swiss-Prot	High
`Q9FXA2`	Arabidopsis thaliana	sp\|Q9FXA2\|PABP8_ARATH Polyadenylate-binding protein 8	68.000%	Swiss-Prot	High
`O22173`	Arabidopsis thaliana	sp\|O22173\|PABP4_ARATH Polyadenylate-binding protein 4	53.900%	Swiss-Prot	High

JBrowse

View in Genome Browser

Gene Card