TkA07G018350 | RubberDandelionOmics

Gene overview

TkA07G018350

Reference: TK1151 Chr: Chr07 Coordinates: 4931697-4932962 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1236 bp · TkA07G018350|TK1151|cDNA

ATGGAGATGGAGAGATCAAACCTTGAATATTCAGAAATGGAGTTTCCTCAAGATTTCCGATGCCCCATATCCAGAGATCTCATGAAAGAACCAGTGATCATCTCAACAGGTGTTTCATACGAAAGAAAGAACATCGAAAAATGGTTCTTCACATACAAGAAGAAGACATGTCCGGCCACAATGCAAAACATCGAAAACTTCGGCGTCACCCCTAATCATACCCTCAAAAGACTCATACTTATATGGCAAAATAGTCATTC...

CDS

Download CDS FASTA

1236 bp · TkA07G018350|TK1151|CDS

ATGGAGATGGAGAGATCAAACCTTGAATATTCAGAAATGGAGTTTCCTCAAGATTTCCGATGCCCCATATCCAGAGATCTCATGAAAGAACCAGTGATCATCTCAACAGGTGTTTCATACGAAAGAAAGAACATCGAAAAATGGTTCTTCACATACAAGAAGAAGACATGTCCGGCCACAATGCAAAACATCGAAAACTTCGGCGTCACCCCTAATCATACCCTCAAAAGACTCATACTTATATGGCAAAATAGTCATTC...

Protein

Download Protein FASTA

411 aa · TkA07G018350|TK1151|PROTEIN

MEMERSNLEYSEMEFPQDFRCPISRDLMKEPVIISTGVSYERKNIEKWFFTYKKKTCPATMQNIENFGVTPNHTLKRLILIWQNSHSPSSSSPSLPSFKREEMVLLLKTLGSSPFKVNSLRKLKEIIEIGDEMKLDFIILGGLDSLFQLIVQILVDCSDFMAFRACEEALGVLQLLVISEEDDGNGKVIKLLSKPECMKSMVTILQRGSKDARVYTISILRKLGENSNFNWNVIVNDQGISMFKSMLELASDEISTKASS...

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	`TkA07G018350`
TK1151 ID	TkA07G018350
OH-1004 ID	LXL04_026923
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.300
Protein coverage (%)	TK1151 96.350 / OH-1004 94.200 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 TkA07G018350

Location Chr07:4931697-4932962 (+)

Description Similar to PUB23: E3 ubiquitin-protein ligase PUB23

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g35930`	E3 ubiquitin-protein ligase that negatively regulates water stress response.	Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress.2008 · DOI: 10.1105/tpc.108.060699 Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085
`At3g52450`	E3 ubiquitin-protein ligase that negatively regulates water stress response.	Arabidopsis PUB22 and PUB23 are homologous U-Box E3 ubiquitin ligases that play combinatory roles in response to drought stress.2008 · DOI: 10.1105/tpc.108.060699 Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085 The ubiquitin ligase PUB22 targets a subunit of the exocyst complex required for PAMP-triggered responses in Arabidopsis.2012 · DOI: 10.1105/tpc.112.104463
`At3g11840`	E3 ubiquitin-protein ligase that acts as a negative regulator of the immunity triggered by the pathogen-associated molecular patterns (PAMPs), in association with PUB22 and PUB23.	Negative regulation of PAMP-triggered immunity by an E3 ubiquitin ligase triplet in Arabidopsis.2008 · DOI: 10.1016/j.cub.2008.07.085
`At3g19380`	Functions as an E3 ubiquitin ligase.	No verified direct reference in this release
`At5g37490`	Functions as an E3 ubiquitin ligase.	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_026923 · 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:0002679 respiratory burst involved in defense response Biological Process

GO:0006952 defense response Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0051865 protein autoubiquitination Biological Process

GO:0098542 defense response to other organism Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0061630 ubiquitin protein ligase activity Molecular Function

KEGG gene cross-reference

ath:AT1G66160

ath:AT2G35930

ath:AT3G11840

ath:AT3G19380

ath:AT3G52450

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.

Nucleus0.629

Rank 1 · TkA07G018350 · TK1151

Cytoplasm0.424

Rank 2 · TkA07G018350 · TK1151

Cell membrane0.055

Rank 3 · TkA07G018350 · TK1151

Endoplasmic reticulum0.031

Rank 4 · TkA07G018350 · TK1151

Mitochondrion0.021

Rank 5 · TkA07G018350 · 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.

PF04564U-box16-87 aa

PF11789zf-Nse17-59 aa

PF25598ARM_PUB138-397 aa

PF00514Arm150-176 aa

PF04078Rcd1169-277 aa

PF01365RYDR_ITPR189-214 aa

PF22913NBAS_11th231-296 aa

PF00514Arm233-255 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G018350	`PF04564`	U-box	16	87	8.3e-16	58.6
TkA07G018350	`PF11789`	zf-Nse	17	59	0.00016	22.2
TkA07G018350	`PF25598`	ARM_PUB	138	397	6.4e-46	157.9
TkA07G018350	`PF00514`	Arm	150	176	0.0011	19.6
TkA07G018350	`PF04078`	Rcd1	169	277	0.0068	16.5
TkA07G018350	`PF01365`	RYDR_ITPR	189	214	0.023	14.9
TkA07G018350	`PF22913`	NBAS_11th	231	296	0.11	13.1
TkA07G018350	`PF00514`	Arm	233	255	0.0011	19.6
TkA07G018350	`PF01365`	RYDR_ITPR	242	316	0.023	14.9
TkA07G018350	`PF01365`	RYDR_ITPR	245	403	0.023	14.9
TkA07G018350	`PF28415`	SIL1_FES1_HPBP1_C	264	353	0.019	15.1
TkA07G018350	`PF00514`	Arm	279	294	0.0011	19.6
TkA07G018350	`PF22913`	NBAS_11th	358	400	0.11	13.1
TkA07G018350	`PF28415`	SIL1_FES1_HPBP1_C	362	397	0.019	15.1
TkA07G018350	`PF00514`	Arm	364	389	0.0011	19.6

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
`Q84TG3`	Arabidopsis thaliana	sp\|Q84TG3\|PUB23_ARATH E3 ubiquitin-protein ligase PUB23	32.600%	Swiss-Prot	Medium
`Q9SVC6`	Arabidopsis thaliana	sp\|Q9SVC6\|PUB22_ARATH E3 ubiquitin-protein ligase PUB22	30.900%	Swiss-Prot	Medium
`Q9SF15`	Arabidopsis thaliana	sp\|Q9SF15\|PUB24_ARATH E3 ubiquitin-protein ligase PUB24	29.300%	Swiss-Prot	Low
`Q9LT79`	Arabidopsis thaliana	sp\|Q9LT79\|PUB25_ARATH U-box domain-containing protein 25	27.800%	Swiss-Prot	Low
`Q5PNY6`	Arabidopsis thaliana	sp\|Q5PNY6\|PUB21_ARATH U-box domain-containing protein 21	25.700%	Swiss-Prot	Low

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