TkA04G016480 | RubberDandelionOmics

Gene overview

TkA04G016480

Reference: TK1151 Chr: Chr04 Coordinates: 4097879-4107440 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4032 bp · TkA04G016480|TK1151|cDNA

CTAAAATAAGCAATCATATTTGTCATTTGTGAATATCCTCAATATCTTTATTGAGGCAAAACCCTACTTACTAAATGCGAAAGGGACGAGGAAAATAGCAAATCCAGAGTCACTGAGAACACGCCGAAAGGTAGAGAGGAGGCGTGAACCATTTGGGCTAAAACCTAGCTTCTTTGCCACCTCGCGCCGATCTCCTTCCGTCGTTGCAGACATGGCAGTCCGCTTCAACCCCTGCGACACTCTCCTCATTCCATCCACCA...

CDS

Download CDS FASTA

3942 bp · TkA04G016480|TK1151|CDS

ATGGCAGTCCGCTTCAACCCCTGCGACACTCTCCTCATTCCATCCACCAACGCCGCCGCCGCCGCCACCACCACCTCCGCTTTCATCTCCTCCAAAACAAACTCTGCTAAGACCACCCAACCGACTCAAAATCAGAAACCAAATGTTGGTAAGCGAACTGATATCAAAAAGATTATGATTCTCGGTGCTGGTCCTATCGTTATCGGACAAGCTTGCGAATTTGATTATTCCGGTACGCAAGCTTGTAAAGCTTTAAGAGA...

Protein

Download Protein FASTA

1313 aa · TkA04G016480|TK1151|PROTEIN

MAVRFNPCDTLLIPSTNAAAAATTTSAFISSKTNSAKTTQPTQNQKPNVGKRTDIKKIMILGAGPIVIGQACEFDYSGTQACKALRENGYEVVLINSNPATIMTDPEMADRTYIEPMTPELVEQVIAKERPDAILPTMGGQTALNLAVALAESGVLDKYNVELIGAKLEAIKKAEDRELFKQAMKNIGLKTPPSGIGTTLQECLQIANTIGEFPLIIRPAFTLGGSGGGIAYNKQEFETICKSGLAASVTSQVLVEKSLL...

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	`TkA04G016480`
TK1151 ID	TkA04G016480
OH-1004 ID	LXL04_036936
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.700
Protein coverage (%)	TK1151 87.814 / OH-1004 99.916 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 TkA04G016480

Location Chr04:4097879-4107440 (+)

Description Similar to CARB: Carbamoyl-phosphate synthase large chain, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g29900`	Large subunit of the arginine-specific carbamoyl phosphate synthase (CPSase).	Analysis of ven3 and ven6 reticulate mutants reveals the importance of arginine biosynthesis in Arabidopsis leaf development.2011 · DOI: 10.1111/j.1365-313x.2010.04425.x
`At4g38570`	Catalyzes the biosynthesis of phosphatidylinositol (PtdIns) as well as PtdIns:inositol exchange reaction.	No verified direct reference in this release
`At1g68000`	Catalyzes the biosynthesis of phosphatidylinositol (PtdIns) as well as PtdIns:inositol exchange reaction.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0570700`	Large subunit of the arginine-specific carbamoyl phosphate synthase (CPSase).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036936 · 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:0006221 pyrimidine nucleotide biosynthetic process Biological Process

GO:0006526 L-arginine biosynthetic process Biological Process

GO:0006541 glutamine metabolic process Biological Process

GO:0016036 cellular response to phosphate starvation Biological Process

GO:0044205 'de novo' UMP biosynthetic process Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005951 carbamoyl-phosphate synthase complex Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0004087 carbamoyl-phosphate synthase (ammonia) activity Molecular Function

GO:0004088 carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

afu:AF_1274

ana:alr3809

ath:AT1G29900

dosa:Os01g0570700

syn:sll0370

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.

Cytoplasm0.345

Rank 1 · TkA04G016480 · TK1151

Plastid0.240

Rank 2 · TkA04G016480 · TK1151

Nucleus0.143

Rank 3 · TkA04G016480 · TK1151

Mitochondrion0.124

Rank 4 · TkA04G016480 · TK1151

Peroxisome0.086

Rank 5 · TkA04G016480 · 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.

PF02142MGS22-101 aa

PF13780DUF417654-84 aa

PF25596CPSase_L_D155-172 aa

PF13380CoA_binding_267-140 aa

PF08443RimK68-103 aa

PF17965MucBP_274-102 aa

PF01370Epimerase77-139 aa

PF03698UPF018082-97 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G016480	`PF02142`	MGS	22	101	2.9e-20	72.9
TkA04G016480	`PF13780`	DUF4176	54	84	0.0049	17.6
TkA04G016480	`PF25596`	CPSase_L_D1	55	172	1.3e-99	329.0
TkA04G016480	`PF13380`	CoA_binding_2	67	140	0.024	15.8
TkA04G016480	`PF08443`	RimK	68	103	0.03	14.7
TkA04G016480	`PF17965`	MucBP_2	74	102	0.27	12.4
TkA04G016480	`PF01370`	Epimerase	77	139	0.041	14.0
TkA04G016480	`PF03698`	UPF0180	82	97	0.22	12.5
TkA04G016480	`PF02655`	ATP-grasp_3	175	353	7.9e-06	26.8
TkA04G016480	`PF02786`	CPSase_L_D2	176	383	1e-111	372.2
TkA04G016480	`PF08442`	ATP-grasp_2	181	274	0.002	18.5
TkA04G016480	`PF13549`	ATP-grasp_5	181	211	0.008	16.3
TkA04G016480	`PF02222`	ATP-grasp	183	355	3.1e-12	47.2
TkA04G016480	`PF08443`	RimK	183	254	0.03	14.7
TkA04G016480	`PF07478`	Dala_Dala_lig_C	208	351	1.8e-15	57.7
TkA04G016480	`PF13535`	ATP-grasp_4	214	352	6.8e-09	36.3

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
`Q42601`	Arabidopsis thaliana	sp\|Q42601\|CARB_ARATH Carbamoyl phosphate synthase arginine-specific large chain, chloroplastic	84.200%	Swiss-Prot	High
`Q8GUK6`	Arabidopsis thaliana	sp\|Q8GUK6\|PIS2_ARATH Probable CDP-diacylglycerol--inositol 3-phosphatidyltransferase 2	74.700%	Swiss-Prot	Medium
`Q8LBA6`	Arabidopsis thaliana	sp\|Q8LBA6\|PIS1_ARATH CDP-diacylglycerol--inositol 3-phosphatidyltransferase 1	75.800%	Swiss-Prot	Medium
`B9EXM2`	Oryza sativa subsp. japonica	sp\|B9EXM2\|CARB_ORYSJ Carbamoyl phosphate synthase arginine-specific large chain, chloroplastic	81.900%	Swiss-Prot	High

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