TkA08G340620 | RubberDandelionOmics

Gene overview

TkA08G340620

Reference: TK1151 Chr: Chr08 Coordinates: 87336775-87340653 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2648 bp · TkA08G340620|TK1151|cDNA

CCGCATAATGCGGTTTAGAACTTTCGTGGTGCGGTTTGCGGTTTGAAAAAAGTTAAAACCGCATATGCGATGCGGTTTGCGGTTTGACTCTAAACCGCAAAAAACCGCACCGCACACACCCCTAAATTGTAATCATGTAAATTATTGCTATATTCGAATCTCAATATCTAACCGACATCCACAAACCTGGGATTCGTACATTTTAGAAGTCACGTTCAAACACCCCTAAATTGATTATGTGATTTATTAAGCATATAAAT...

CDS

Download CDS FASTA

1812 bp · TkA08G340620|TK1151|CDS

ATGGCGCATGATAGTGACCTCCCTTGCGACGGAGATGGCCGCTGCATGATCTGCAAAATCAGTCCACCGGTGGAAGAGACGCTTACTTGCAAGACCTGTGCAACTCCTTGGCACGTTAACTGTCTATCTGCTCGTCCCCAAACCCTAGCCGATGCTGTCCAATGGGAGTGTCCAGACTGTTTCAGTCTCATCTCTTCTCATCCGCCTCCGTCAACAGTCACATCGGGATCTGAACAATCCGCTACGTTAATTGCCGCTAT...

Protein

Download Protein FASTA

603 aa · TkA08G340620|TK1151|PROTEIN

MAHDSDLPCDGDGRCMICKISPPVEETLTCKTCATPWHVNCLSARPQTLADAVQWECPDCFSLISSHPPPSTVTSGSEQSATLIAAIRAIESDASLSDQEKAKRRQQLLSGGGSDDGDKTTGANNETGDGSDSDVLKLISGSFNCSFCMQLPERPVTTPCGHNFCLKCFEKWIGQGKRTCAICRSPIPPKMASQPRINSSLVTAIRMAKLTKSNTPSLPPKPYYSILNQNKPDKAYTTERAKKTGKANACSGKIFVTVPP...

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	`TkA08G340620`
TK1151 ID	TkA08G340620
OH-1004 ID	LXL04_025714
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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 TkA08G340620

Location Chr08:87336775-87340653 (+)

Description Similar to ORTH2: E3 ubiquitin-protein ligase ORTHRUS 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g57820`	E3 ubiquitin-protein ligase.	VIM1, a methylcytosine-binding protein required for centromeric heterochromatinization.2007 · DOI: 10.1101/gad.1512007 ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.2008 · DOI: 10.1111/j.1365-313x.2008.03631.x Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.2008 · DOI: 10.1371/journal.pgen.1000156
`At1g66040`	E3 ubiquitin-protein ligase.	No verified direct reference in this release
`At5g39550`	E3 ubiquitin-protein ligase.	ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.2008 · DOI: 10.1111/j.1365-313x.2008.03631.x Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.2008 · DOI: 10.1371/journal.pgen.1000156
`At1g66050`	E3 ubiquitin-protein ligase.	ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.2008 · DOI: 10.1111/j.1365-313x.2008.03631.x Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.2008 · DOI: 10.1371/journal.pgen.1000156
`At1g57800`	E3 ubiquitin-protein 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_025714 · 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:0006325 chromatin organization Biological Process

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0016567 protein ubiquitination Biological Process

GO:0031508 pericentric heterochromatin formation Biological Process

GO:0044027 negative regulation of gene expression via chromosomal CpG island methylation Biological Process

GO:0051301 cell division Biological Process

GO:0005634 nucleus Cellular Component

GO:0010369 chromocenter Cellular Component

GO:0003682 chromatin binding Molecular Function

GO:0004842 ubiquitin-protein transferase activity Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0008327 methyl-CpG binding Molecular Function

KEGG gene cross-reference

ath:AT1G57800

ath:AT1G57820

ath:AT1G66040

ath:AT1G66050

ath:AT5G39550

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.

Nucleus0.865

Rank 1 · TkA08G340620 · TK1151

Cytoplasm0.178

Rank 2 · TkA08G340620 · TK1151

Cell membrane0.055

Rank 3 · TkA08G340620 · TK1151

Endoplasmic reticulum0.026

Rank 4 · TkA08G340620 · TK1151

Plastid0.017

Rank 5 · TkA08G340620 · 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.

PF13923zf-C3HC4_214-60 aa

PF13639zf-RING_214-60 aa

PF12678zf-rbx114-60 aa

PF00628PHD15-60 aa

PF23004PHDvar_NSD15-48 aa

PF15227zf-C3HC4_439-60 aa

PF14570zf-RING_456-60 aa

PF14447Prok-RING_457-62 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA08G340620	`PF13923`	zf-C3HC4_2	14	60	7.9e-09	35.9
TkA08G340620	`PF13639`	zf-RING_2	14	60	2e-08	35.1
TkA08G340620	`PF12678`	zf-rbx1	14	60	0.011	16.7
TkA08G340620	`PF00628`	PHD	15	60	0.00044	20.9
TkA08G340620	`PF23004`	PHDvar_NSD	15	48	0.044	14.5
TkA08G340620	`PF15227`	zf-C3HC4_4	39	60	1.2e-06	29.2
TkA08G340620	`PF14570`	zf-RING_4	56	60	0.034	14.6
TkA08G340620	`PF14447`	Prok-RING_4	57	62	0.0044	17.6
TkA08G340620	`PF04564`	U-box	142	193	0.0046	17.8
TkA08G340620	`PF13920`	zf-C3HC4_3	144	187	6.8e-09	36.1
TkA08G340620	`PF13639`	zf-RING_2	144	184	2e-08	35.1
TkA08G340620	`PF14634`	zf-RING_5	144	184	6.5e-05	23.5
TkA08G340620	`PF25447`	RING_ZNF598	144	185	3.6	8.7
TkA08G340620	`PF13445`	zf-RING_UBOX	145	180	5.3e-11	43.0
TkA08G340620	`PF00097`	zf-C3HC4	145	183	7.1e-11	42.5
TkA08G340620	`PF13923`	zf-C3HC4_2	145	183	7.9e-09	35.9

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
`Q8VYZ0`	Arabidopsis thaliana	sp\|Q8VYZ0\|ORTH2_ARATH E3 ubiquitin-protein ligase ORTHRUS 2	63.600%	Swiss-Prot	High
`Q9C8E1`	Arabidopsis thaliana	sp\|Q9C8E1\|ORTH4_ARATH Putative E3 ubiquitin-protein ligase ORTHRUS 4	60.500%	Swiss-Prot	High
`Q9FKA7`	Arabidopsis thaliana	sp\|Q9FKA7\|ORTH1_ARATH E3 ubiquitin-protein ligase ORTHRUS 1	59.600%	Swiss-Prot	High
`Q680I0`	Arabidopsis thaliana	sp\|Q680I0\|ORTH5_ARATH E3 ubiquitin-protein ligase ORTHRUS 5	60.500%	Swiss-Prot	High
`Q9FVS2`	Arabidopsis thaliana	sp\|Q9FVS2\|ORTH3_ARATH E3 ubiquitin-protein ligase ORTHRUS 3	56.000%	Swiss-Prot	High

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