TkA04G163040 | RubberDandelionOmics

Gene overview

TkA04G163040

Reference: TK1151 Chr: Chr04 Coordinates: 42094963-42097825 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1190 bp · TkA04G163040|TK1151|cDNA

ATAACCCTTGCTGAGCCTGTCCCATTAGTCTGTATTCCCCAAAATACCCTCAAGAAAATACCAAAATAACAAGGTTTACGTTTCTTTCACCCCCAAATCCCACTTGAATCATCGGGCGCAGATAAAACCCTATTTTCACTCGCTCAGTTCCGAACACACAACGCAAAATCGTGTGTATTCAGTCGCGCACAATCACAGTTCCGTGTGATCTGTAAAGAGAGTTAACAAGTTATGGATCACACGGCGGAGCAAGATCAAGA...

CDS

Download CDS FASTA

675 bp · TkA04G163040|TK1151|CDS

ATGGATCACACGGCGGAGCAAGATCAAGAACACGAAGTCTACGGTGGAGAGATACCAGATGAAGGAGAGATGGACACAGATTTCGAGATGTCGAGGGACGAGGCGGAAGACGTTGAAAATAATAGTTCCAAGGATTTGGAGGATATGAAGAAGAGGCTGAAGGAGATTGAAGAAGAGGCAGGGGCGCTTCGTGAAATGCAGGCAAAAGTTGAGAAAGAGATGGGCTCAGTTCAAGATCCATCGAGTGCATCTGCTACACT...

Protein

Download Protein FASTA

224 aa · TkA04G163040|TK1151|PROTEIN

MDHTAEQDQEHEVYGGEIPDEGEMDTDFEMSRDEAEDVENNSSKDLEDMKKRLKEIEEEAGALREMQAKVEKEMGSVQDPSSASATLAEKEEADARSIYVGNVDYACTPEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFVELESVQNSLLLNESELHGRQLKVAAKRTNVPGMKQFRGRRPSPYAGFRSRRPYMPGPPVFPPYGYGRIPRARRPMWYRPY

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	`TkA04G163040`
TK1151 ID	TkA04G163040
OH-1004 ID	LXL04_035153
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
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 TkA04G163040

Location Chr04:42094963-42097825 (+)

Description Similar to PABN2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g51120`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	No verified direct reference in this release
`At5g65260`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	No verified direct reference in this release
`At5g10350`	Involved in the 3'-end formation of mRNA precursors (pre-mRNA) by the addition of a poly(A) tail of 200-250 nt to the upstream cleavage product.	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_035153 · 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:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0031124 mRNA 3'-end processing Biological Process

GO:0033621 nuclear mRNA surveillance of meiosis-specific transcripts Biological Process

GO:0180010 co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0000785 chromatin Cellular Component

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:AT5G10350

ath:AT5G51120

ath:AT5G65260

dme:Dmel_CG2163

spo:2539733

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.

Nucleus0.830

Rank 1 · TkA04G163040 · TK1151

Cytoplasm0.313

Rank 2 · TkA04G163040 · TK1151

Mitochondrion0.029

Rank 3 · TkA04G163040 · TK1151

Cell membrane0.026

Rank 4 · TkA04G163040 · TK1151

Endoplasmic reticulum0.019

Rank 5 · TkA04G163040 · 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.

PF30191LAG2_N4-93 aa

PF09789CC1496-91 aa

PF07295DUF145124-98 aa

PF09787Golgin_A526-82 aa

PF30116HTL141-59 aa

PF01517HDV_ag43-131 aa

PF00076RRM_198-166 aa

PF30116HTL1154-179 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G163040	`PF30191`	LAG2_N	4	93	2.9	7.6
TkA04G163040	`PF09789`	CC149	6	91	0.027	14.5
TkA04G163040	`PF07295`	DUF1451	24	98	0.037	14.9
TkA04G163040	`PF09787`	Golgin_A5	26	82	0.36	11.0
TkA04G163040	`PF30116`	HTL1	41	59	0.13	12.6
TkA04G163040	`PF01517`	HDV_ag	43	131	0.0041	17.9
TkA04G163040	`PF00076`	RRM_1	98	166	1.3e-15	57.7
TkA04G163040	`PF30116`	HTL1	154	179	0.13	12.6

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
`Q93VI4`	Arabidopsis thaliana	sp\|Q93VI4\|PABN1_ARATH Polyadenylate-binding protein 1	74.000%	Swiss-Prot	High
`Q9FJN9`	Arabidopsis thaliana	sp\|Q9FJN9\|PABN2_ARATH Polyadenylate-binding protein 2	69.100%	Swiss-Prot	High
`Q9LX90`	Arabidopsis thaliana	sp\|Q9LX90\|PABN3_ARATH Polyadenylate-binding protein 3	66.100%	Swiss-Prot	High

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