TkA07G137890 | RubberDandelionOmics

Gene overview

TkA07G137890

Reference: TK1151 Chr: Chr07 Coordinates: 35689540-35693258 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1700 bp · TkA07G137890|TK1151|cDNA

TTGGGCCTGATCGAAGGCACCCGGTGTCTTGCTCAGAAAGCTATAGATGCTTTTCTACGATTACATGTCTTCTTCTTCCCCAATCGCCCTTCTCTCTTGCTAGGGTTCACATAAGAAGTTCGTAATTGCTTTTGATTCAACGATTTCATCTCCCCAGTCCGTATCTTTGAATCCAACATGGAAGGAGGAGGCAGTTTGGACTCGAAAATCGAGTCTCTGTTGAATGCGGAGAAGCAGATGAGGCTTAATGGCGATATAGG...

CDS

Download CDS FASTA

1329 bp · TkA07G137890|TK1151|CDS

ATGGAAGGAGGAGGCAGTTTGGACTCGAAAATCGAGTCTCTGTTGAATGCGGAGAAGCAGATGAGGCTTAATGGCGATATAGGTGGTACAAAGAAGGCCGCGATTGATATTCTCCAACTTTGTTTCGAGGCTCGTGCTTGGAAGACACTCAATGATCAAATTGTTGTGTTGTCGAAGCGGCGTGGTCAGTTGAAGCAGGCTGTGACTGCCATGGTCCAACAAGCAATGCAGTACATCGATGAAACCCCAGACATTGAAAC...

Protein

Download Protein FASTA

442 aa · TkA07G137890|TK1151|PROTEIN

MEGGGSLDSKIESLLNAEKQMRLNGDIGGTKKAAIDILQLCFEARAWKTLNDQIVVLSKRRGQLKQAVTAMVQQAMQYIDETPDIETKIELIKTLNSVSAGKIYVEIERARLIKRLAKIKEEQGQIAEAADLMQEIAVETFGAMAKTEKIAFILEQVRLCLDRQDYVRAQILSRKISPRVFETDPAKEKKKPKDGEGLVEEAPANIPTLLELKRIYYEHMIRYYSHSNDYLEICRCYKSIYEIPSVKENSSQWIPILRKI...

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	`TkA07G137890`
TK1151 ID	TkA07G137890
OH-1004 ID	LXL04_031586
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	23.400
Protein coverage (%)	TK1151 71.946 / OH-1004 73.300 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 TkA07G137890

Location Chr07:35689540-35693258 (-)

Description Similar to CSN4: COP9 signalosome complex subunit 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g09900`	Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins.	The RPN5 subunit of the 26s proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis.2009 · DOI: 10.1105/tpc.108.064444
`At5g64760`	Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins (By similarity).	The RPN5 subunit of the 26s proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis.2009 · DOI: 10.1105/tpc.108.064444

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031586 · 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:0000338 protein deneddylation Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010971 positive regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0008180 COP9 signalosome Cellular Component

GO:0016607 nuclear speck Cellular Component

GO:0032991 protein-containing complex Cellular Component

KEGG gene cross-reference

ath:AT5G42970

bta:540223

ddi:DDB_G0293844

rno:360915

ssc:100125960

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.

Cytoplasm0.688

Rank 1 · TkA07G137890 · TK1151

Nucleus0.313

Rank 2 · TkA07G137890 · TK1151

Golgi apparatus0.103

Rank 3 · TkA07G137890 · TK1151

Cell membrane0.083

Rank 4 · TkA07G137890 · TK1151

Lysosome / Vacuole0.071

Rank 5 · TkA07G137890 · 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.

PF22241PSMD12-CSN4_N11-188 aa

PF19599DUF610456-94 aa

PF25058ARM_TT2158-178 aa

PF03228Adeno_VII61-132 aa

PF07988LMSTEN66-90 aa

PF24999LAMB470-93 aa

PF24999LAMB4115-133 aa

PF07988LMSTEN182-190 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G137890	`PF22241`	PSMD12-CSN4_N	11	188	3.5e-77	259.7
TkA07G137890	`PF19599`	DUF6104	56	94	0.033	15.2
TkA07G137890	`PF25058`	ARM_TT21	58	178	0.00067	20.4
TkA07G137890	`PF03228`	Adeno_VII	61	132	0.19	12.9
TkA07G137890	`PF07988`	LMSTEN	66	90	0.12	12.5
TkA07G137890	`PF24999`	LAMB4	70	93	5.9	7.5
TkA07G137890	`PF24999`	LAMB4	115	133	5.9	7.5
TkA07G137890	`PF07988`	LMSTEN	182	190	0.12	12.5
TkA07G137890	`PF22241`	PSMD12-CSN4_N	211	248	3.5e-77	259.7
TkA07G137890	`PF24999`	LAMB4	273	282	5.9	7.5
TkA07G137890	`PF01399`	PCI	281	306	6.3e-18	65.5
TkA07G137890	`PF01399`	PCI	333	399	6.3e-18	65.5
TkA07G137890	`PF18098`	RPN5_C	405	437	9.7e-11	42.3
TkA07G137890	`PF24999`	LAMB4	419	433	5.9	7.5

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
`Q9FIB6`	Arabidopsis thaliana	sp\|Q9FIB6\|PS12A_ARATH 26S proteasome non-ATPase regulatory subunit 12 homolog A	80.500%	Swiss-Prot	High
`Q8VWK0`	Arabidopsis thaliana	sp\|Q8VWK0\|PS12B_ARATH 26S proteasome non-ATPase regulatory subunit 12 homolog B	78.900%	Swiss-Prot	High

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