TkA05G113870 | RubberDandelionOmics

Gene overview

TkA05G113870

Reference: TK1151 Chr: Chr05 Coordinates: 30408376-30411352 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1324 bp · TkA05G113870|TK1151|cDNA

ATGGGCTTGTATACATACGCCATACGGTATACTAGTCTAAGGGAAGAAGAACACGAGGTGTACGGAGGAGATATTCCAGATGTGGGTGAAATGGAAGGGGATGTTGATCCTCATCACGCCGATGTCGAGATGGCTACCGCAGACGAAGACGCCGTCAAGGAACTCGATGAGATGAAGAAACGATTGAAGGAGATGGAAGAAGAAGCAGCCGCTCTTCGCGAAATGCAAGCCAAAGTAGAAAAAGAAATGGGTGCTGTTCA...

CDS

Download CDS FASTA

705 bp · TkA05G113870|TK1151|CDS

ATGGGCTTGTATACATACGCCATACGGTATACTAGTCTAAGGGAAGAAGAACACGAGGTGTACGGAGGAGATATTCCAGATGTGGGTGAAATGGAAGGGGATGTTGATCCTCATCACGCCGATGTCGAGATGGCTACCGCAGACGAAGACGCCGTCAAGGAACTCGATGAGATGAAGAAACGATTGAAGGAGATGGAAGAAGAAGCAGCCGCTCTTCGCGAAATGCAAGCCAAAGTAGAAAAAGAAATGGGTGCTGTTCA...

Protein

Download Protein FASTA

234 aa · TkA05G113870|TK1151|PROTEIN

MGLYTYAIRYTSLREEEHEVYGGDIPDVGEMEGDVDPHHADVEMATADEDAVKELDEMKKRLKEMEEEAAALREMQAKVEKEMGAVQDPAGAAVSQASKEEVDTRSIFVGNVDYACTPEEVQQHFQSCGTVNRVTILTDKFGQPKGFAYVEFLEVEGVQEALALNESELHGRQLKVMAKRTNVPGMKQYRGRRFNPYMGYRGFRRPYVPPYFYPPYAYGKVPRFRRPSRYMPYY

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	`TkA05G113870`
TK1151 ID	TkA05G113870
OH-1004 ID	LXL04_015635
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
Protein identity (%)	98.700
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

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Basic Information and Functional Annotation

Gene ID TkA05G113870

Location Chr05:30408376-30411352 (+)

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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015635 · 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: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: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

GO:0016604 nuclear body Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0033620 Mei2 nuclear dot complex Cellular Component

KEGG gene cross-reference

ath:AT5G10350

ath:AT5G51120

ath:AT5G65260

spo:2539733

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.

Nucleus0.738

Rank 1 · TkA05G113870 · TK1151

Cytoplasm0.395

Rank 2 · TkA05G113870 · TK1151

Mitochondrion0.040

Rank 3 · TkA05G113870 · TK1151

Cell membrane0.039

Rank 4 · TkA05G113870 · TK1151

Endoplasmic reticulum0.037

Rank 5 · TkA05G113870 · 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.

PF18150DUF560010-58 aa

PF28544Helical_needle25-127 aa

PF13600DUF414032-84 aa

PF23991DUF731035-97 aa

PF29075NOCA1_mid43-82 aa

PF03938OmpH44-101 aa

PF05266DUF72445-99 aa

PF00076RRM_149-63 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G113870	`PF18150`	DUF5600	10	58	0.13	13.7
TkA05G113870	`PF28544`	Helical_needle	25	127	0.04	14.5
TkA05G113870	`PF13600`	DUF4140	32	84	0.059	14.5
TkA05G113870	`PF23991`	DUF7310	35	97	0.095	13.9
TkA05G113870	`PF29075`	NOCA1_mid	43	82	0.0083	16.7
TkA05G113870	`PF03938`	OmpH	44	101	0.05	14.5
TkA05G113870	`PF05266`	DUF724	45	99	0.21	12.2
TkA05G113870	`PF00076`	RRM_1	49	63	2.4e-17	63.2
TkA05G113870	`PF18150`	DUF5600	51	85	0.13	13.7
TkA05G113870	`PF00076`	RRM_1	107	175	2.4e-17	63.2
TkA05G113870	`PF24475`	RBD_DEAH11	129	180	0.12	13.2
TkA05G113870	`PF28544`	Helical_needle	171	186	0.04	14.5

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
`Q9FJN9`	Arabidopsis thaliana	sp\|Q9FJN9\|PABN2_ARATH Polyadenylate-binding protein 2	63.800%	Swiss-Prot	High
`Q9LX90`	Arabidopsis thaliana	sp\|Q9LX90\|PABN3_ARATH Polyadenylate-binding protein 3	60.600%	Swiss-Prot	High
`Q93VI4`	Arabidopsis thaliana	sp\|Q93VI4\|PABN1_ARATH Polyadenylate-binding protein 1	56.800%	Swiss-Prot	High

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