TkA04G011250 | RubberDandelionOmics

Gene overview

TkA04G011250

Reference: TK1151 Chr: Chr04 Coordinates: 2724433-2729174 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1743 bp · TkA04G011250|TK1151|cDNA

ATTAATCCCATGGGGGACTATGATTTTAGTCCACACGTGGATATTATAGACAGCACAAATCCACTGCGACATTTTCCCCAAGAAAACAAGAGTCATATAGATGGATTTGCTTCCTTCCCTCCCTCCCTCACGTCCAAGCATCGAATCCCTCTTTAACCCTTAATTAGCCACAAAGCTCTTACCTTTTTCAGTCAATCGTTGTAACAAACTAGAAAAAACCCTAACCAAATCACCAATTAGCTGTATTTCGGTCCCAAACT...

CDS

Download CDS FASTA

720 bp · TkA04G011250|TK1151|CDS

ATGCTATCAATGTGTAAAGAGGTTCCTTGGTTCTTGGACGACGAAAGTGCTCGTGTGTATGTTGTTGGAGCTCGTGGTGCTGCTGGTTTGGTGTTAACTATTGGAAGTGAAGTCTTTGAGGAATCAGGAAGATCACTTGTTCGTGGAACTTTAGATTATCTGCAAGGTCTCAAGATGCTTGGAGTCAAGAGAATTGAACGCGTTCTTCCAACGGGCACTCCCTTAACGGTTGTTGGTGAGGCTATTAAAGATGACATTGG...

Protein

Download Protein FASTA

239 aa · TkA04G011250|TK1151|PROTEIN

MLSMCKEVPWFLDDESARVYVVGARGAAGLVLTIGSEVFEESGRSLVRGTLDYLQGLKMLGVKRIERVLPTGTPLTVVGEAIKDDIGTVRIQRPLKGPFYVSHKTIDQLIANLGKWARWYKYASMSFAAFGFYLIAKHAFQYIMERKRHWELKKRVRDAAAKRAVSDNEGSNDKAENGFGGTRKDGQMPDICVICLEQEYNSVFVPCGHMCCCVTCSSHLTSCPLCRSRIGQVVKTFRH

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	`TkA04G011250`
TK1151 ID	TkA04G011250
OH-1004 ID	LXL04_037003
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 69.679 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 TkA04G011250

Location Chr04:2724433-2729174 (-)

Description Similar to SP1: E3 ubiquitin-protein ligase SP1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`UniProt: Q8L7N4`	E3 ubiquitin-protein ligase involved in the regulation of protein import in the chloroplast.	No verified direct reference in this release
`At1g59560`	Possesses E3 ubiquitin-protein ligase activity.	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_037003 · 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:0000209 protein polyubiquitination Biological Process

GO:0000266 mitochondrial fission Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0009893 positive regulation of metabolic process Biological Process

GO:0010637 negative regulation of mitochondrial fusion Biological Process

GO:0010821 regulation of mitochondrion organization Biological Process

GO:0016558 protein import into peroxisome matrix Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0016925 protein sumoylation Biological Process

GO:0022603 regulation of anatomical structure morphogenesis Biological Process

GO:0030162 regulation of proteolysis Biological Process

GO:0031647 regulation of protein stability Biological Process

KEGG gene cross-reference

ath:AT1G59560

ath:AT1G63900

hsa:79594

xla:414680

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.

Endoplasmic reticulum0.252

Rank 1 · TkA04G011250 · TK1151

Mitochondrion0.203

Rank 2 · TkA04G011250 · TK1151

Cytoplasm0.183

Rank 3 · TkA04G011250 · TK1151

Nucleus0.181

Rank 4 · TkA04G011250 · TK1151

Peroxisome0.114

Rank 5 · TkA04G011250 · 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.

PF12483GIDE3-131 aa

PF13920zf-C3HC4_3190-232 aa

PF13639zf-RING_2191-227 aa

PF24921RING_XB3-XBAT31191-230 aa

PF14447Prok-RING_4192-231 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G011250	`PF12483`	GIDE	3	131	5.7e-35	120.9
TkA04G011250	`PF13920`	zf-C3HC4_3	190	232	1.2e-13	51.3
TkA04G011250	`PF13639`	zf-RING_2	191	227	0.055	14.5
TkA04G011250	`PF24921`	RING_XB3-XBAT31	191	230	0.46	11.3
TkA04G011250	`PF14447`	Prok-RING_4	192	231	2.6e-06	27.9

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
`Q8L7N4`	Arabidopsis thaliana	sp\|Q8L7N4\|SP1_ARATH E3 ubiquitin-protein ligase SP1	71.100%	Swiss-Prot	High
`Q94HV7`	Arabidopsis thaliana	sp\|Q94HV7\|SPL1P_ARATH E3 ubiquitin-protein ligase SPL1	53.000%	Swiss-Prot	High

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