TkA04G023980 | RubberDandelionOmics

Gene overview

TkA04G023980

Reference: TK1151 Chr: Chr04 Coordinates: 6218588-6222141 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1468 bp · TkA04G023980|TK1151|cDNA

CCGTTCTCTGCTTTCTTGCACAGAAAGACGTTGAAGAGCCTTCAAAATCCCAACTTTCGATCCGAATTTCCCCATCGGAGACGAGCAAATCATCATGGGTCAAGGAACTCCGGGCGGTTTAAACCGACAACCTGGTGATCGCAAGAACGAGGGCGACAAAAAGGAGAAGAAATTCGAACCGGCAGCGCCGCCTGCTCGAGTTGGCCGGAAACAACGTAAGCAGAAGGGACCAGAGGCAGCCGCTCGATTACCGACGGTAA...

CDS

Download CDS FASTA

1332 bp · TkA04G023980|TK1151|CDS

ATGGGTCAAGGAACTCCGGGCGGTTTAAACCGACAACCTGGTGATCGCAAGAACGAGGGCGACAAAAAGGAGAAGAAATTCGAACCGGCAGCGCCGCCTGCTCGAGTTGGCCGGAAACAACGTAAGCAGAAGGGACCAGAGGCAGCCGCTCGATTACCGACGGTAACGCCACATTCAAAATGTAGGCTTCGGCTCCTAAAGCTCGAGCGAATCAAAGATTATCTGTTAATGGAAGAGGAGTTCGTGGCCAATCAGGAGCG...

Protein

Download Protein FASTA

443 aa · TkA04G023980|TK1151|PROTEIN

MGQGTPGGLNRQPGDRKNEGDKKEKKFEPAAPPARVGRKQRKQKGPEAAARLPTVTPHSKCRLRLLKLERIKDYLLMEEEFVANQERLKPQEEKTEEDRSKVDDLRGTPMSVGNLEELIDENHAIVSSSVGPEYYVGILSFVDKDQLEPGCAILMHNKVLSVVGLLQDDVDPMVSVMKVEKAPLESYADIGGLDAQIQEIKEAVELPLTHPELYEDIGIKPPKGVILYGEPGTGKTLLAKAVANSTSATFLRVVGSELIQ...

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	`TkA04G023980`
TK1151 ID	TkA04G023980
OH-1004 ID	LXL04_000872
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.800
Protein coverage (%)	TK1151 100.000 / OH-1004 93.096 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 TkA04G023980

Location Chr04:6218588-6222141 (-)

Description Similar to RPT2A: 26S proteasome regulatory subunit 4 homolog A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g29040`	The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins.	The HALTED ROOT gene encoding the 26S proteasome subunit RPT2a is essential for the maintenance of Arabidopsis meristems.2004 · DOI: 10.1242/dev.01096 26S proteasome regulatory particle mutants have increased oxidative stress tolerance.2008 · DOI: 10.1111/j.1365-313x.2007.03322.x Loss of 26S proteasome function leads to increased cell size and decreased cell number in Arabidopsis shoot organs.2009 · DOI: 10.1104/pp.109.135970 Regulation of leaf organ size by the Arabidopsis RPT2a 19S proteasome subunit.2009 · DOI: 10.1111/j.1365-313x.2009.03932.x Control of endoreduplication of trichome by RPT2a, a subunit of the 19S proteasome in Arabidopsis.2010 · DOI: 10.1007/s10265-010-0321-x Arabidopsis thaliana 26S proteasome subunits RPT2a and RPT5a are crucial for zinc deficiency-tolerance.2011 · DOI: 10.1271/bbb.100794 Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b.2011 · DOI: 10.1093/pcp/pcr093 RPT2a, a 26S proteasome AAA-ATPase, is directly involved in Arabidopsis CC-NBS-LRR protein uni-1D-induced signaling pathways.2011 · DOI: 10.1093/pcp/pcr099 The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis.2011 · DOI: 10.1105/tpc.111.089482 RPN1a, a 26S proteasome subunit, is required for innate immunity in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05048.x Arabidopsis RPT2a, 19S proteasome subunit, regulates gene silencing via DNA methylation.2012 · DOI: 10.1371/journal.pone.0037086 Proteomic analysis of the 26S proteasome reveals its direct interaction with transit peptides of plastid protein precursors for their degradation.2014 · DOI: 10.1021/pr401245g
`At2g20140`	The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins.	Arabidopsis RPT2a encoding the 26S proteasome subunit is required for various aspects of root meristem maintenance, and regulates gametogenesis redundantly with its homolog, RPT2b.2011 · DOI: 10.1093/pcp/pcr093 The RPT2 subunit of the 26S proteasome directs complex assembly, histone dynamics, and gametophyte and sporophyte development in Arabidopsis.2011 · DOI: 10.1105/tpc.111.089482

Rice

Reference gene ID	Possible function	Papers / DOI
`Os07g0691800`	The 26S proteasome is involved in the ATP-dependent degradation of ubiquitinated proteins.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000872 · 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:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0007292 female gamete generation Biological Process

GO:0009408 response to heat Biological Process

GO:0009933 meristem structural organization Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010311 lateral root formation Biological Process

GO:0010498 proteasomal protein catabolic process Biological Process

GO:0035266 meristem growth Biological Process

GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process Biological Process

KEGG gene cross-reference

ath:AT2G20140

ath:AT4G29040

dme:Dmel_CG5289

dosa:Os07g0691800

rno:117263

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.

Nucleus0.562

Rank 1 · TkA04G023980 · TK1151

Cytoplasm0.477

Rank 2 · TkA04G023980 · TK1151

Cell membrane0.055

Rank 3 · TkA04G023980 · TK1151

Endoplasmic reticulum0.048

Rank 4 · TkA04G023980 · TK1151

Mitochondrion0.039

Rank 5 · TkA04G023980 · 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.

PF13521AAA_2865-104 aa

PF07724AAA_276-117 aa

PF16450Prot_ATP_ID_OB_C112-166 aa

PF06569DUF1128174-193 aa

PF13191AAA_16215-252 aa

PF06745ATPase217-240 aa

PF00005ABC_tran219-248 aa

PF05673DUF815220-289 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G023980	`PF13521`	AAA_28	65	104	0.09	13.7
TkA04G023980	`PF07724`	AAA_2	76	117	0.00036	21.3
TkA04G023980	`PF16450`	Prot_ATP_ID_OB_C	112	166	2e-10	41.1
TkA04G023980	`PF06569`	DUF1128	174	193	0.098	13.5
TkA04G023980	`PF13191`	AAA_16	215	252	0.0005	21.3
TkA04G023980	`PF06745`	ATPase	217	240	0.0078	16.3
TkA04G023980	`PF00005`	ABC_tran	219	248	0.26	12.6
TkA04G023980	`PF05673`	DUF815	220	289	5.3e-05	23.2
TkA04G023980	`PF02367`	TsaE	220	248	0.085	13.5
TkA04G023980	`PF12775`	AAA_7	222	247	0.14	12.4
TkA04G023980	`PF06068`	TIP49	223	261	0.014	15.3
TkA04G023980	`PF01695`	IstB_IS21	223	246	0.12	12.6
TkA04G023980	`PF00158`	Sigma54_activat	223	247	0.12	12.8
TkA04G023980	`PF07728`	AAA_5	224	294	0.00027	21.7
TkA04G023980	`PF05496`	RuvB_N	224	292	0.0029	18.1
TkA04G023980	`PF13173`	AAA_14	224	293	0.087	13.5

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9SZD4`	Arabidopsis thaliana	sp\|Q9SZD4\|PRS4A_ARATH 26S proteasome regulatory subunit 4 homolog A	95.000%	Swiss-Prot	High
`Q9SL67`	Arabidopsis thaliana	sp\|Q9SL67\|PRS4B_ARATH 26S proteasome regulatory subunit 4 homolog B	94.600%	Swiss-Prot	High
`P46466`	Oryza sativa subsp. japonica	sp\|P46466\|PRS4_ORYSJ 26S proteasome regulatory subunit 4 homolog	91.300%	Swiss-Prot	High

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