LXL04_024249 | RubberDandelionOmics

Gene overview

LXL04_024249

Reference: OH-1004 Chr: Chr05 Coordinates: 85711011-85712391 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

823 bp · LXL04_024249|LXL04_024249|OH1004|cDNA

AACTAATCACCCTTTCCGTCTTCCGATTCTCTTGACTATGTCTTCAATCAAATCCCAATTTCGTGTTATTCTGTAGACTCTCTCTCTCCCTCAACGATCACAAACCCTGATTTCGATCCATTCTCCATCTGCAGAGGGGTACGTCCATCAATGTACACACCCAATTTCCAAAATGGAAACTAATATCAGCGAATCAACAACAAGAGAAACCACAACCAATGACGCAGGTGATTTCGAATGCAACATTTGCTTGGAATTAG...

CDS

Download CDS FASTA

717 bp · LXL04_024249|LXL04_024249|OH1004|CDS

CTGATTTCGATCCATTCTCCATCTGCAGAGGGGTACGTCCATCAATGTACACACCCAATTTCCAAAATGGAAACTAATATCAGCGAATCAACAACAAGAGAAACCACAACCAATGACGCAGGTGATTTCGAATGCAACATTTGCTTGGAATTAGCAGAAGACCCAATCGTAACTCTCTGTGGCCATCTCTTTTGTTGGCCATGTCTTTACAAATGGCTTCACATCCACTCACGTTCCCAAGAATGTCCAGTCTGCAAAGC...

Protein

Download Protein FASTA

238 aa · LXL04_024249|LXL04_024249|OH1004|PROTEIN

MISIHSPSAEGYVHQCTHPISKMETNISESTTRETTTNDAGDFECNICLELAEDPIVTLCGHLFCWPCLYKWLHIHSRSQECPVCKALIQEDKLVPLYGRGKTQTDPRSKPIPEFEIPNRPTGQRPATAPAQDTNTNFPNFGFSGFVPMASARFGNFAMSAGIGGLFPSLLDMQVHGFQNPLHYGPNRHGYGPRFSGGFHGGHHVHDIFHSRRGNQEYNLLKTLLLMIGIFVVLVMIL

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	`LXL04_024249`
TK1151 ID	TkA06G159860
OH-1004 ID	LXL04_024249
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.200
Protein coverage (%)	TK1151 87.050 / 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID	`LXL04_024249`
Location	Chr05:85711011-85712391 (+)
Description	Similar to rnf-5: E3 ubiquitin ligase rnf-5
Arabidopsis / Rice Reference Genes and Papers	Download references for this gene Arabidopsis No hit for this species in the current source table. Rice No hit for this species in the current source table.
Functional annotation source	View annotation sources Functional annotation source: OH1004 · `LXL04_024249` · GCA_047496595.1_OSU_TarKok_2.0.
GO annotations (OH1004 source)	GO:0006511 ubiquitin-dependent protein catabolic process Biological Process GO:0006914 autophagy Biological Process GO:0009617 response to bacterium Biological Process GO:0010507 negative regulation of autophagy Biological Process GO:0016567 protein ubiquitination Biological Process GO:0018996 molting cycle, collagen and cuticulin-based cuticle Biological Process GO:0030163 protein catabolic process Biological Process GO:0031648 protein destabilization Biological Process GO:0036503 ERAD pathway Biological Process GO:0040039 inductive cell migration Biological Process GO:0044314 protein K27-linked ubiquitination Biological Process GO:0045087 innate immune response Biological Process
KEGG gene cross-reference	cel:CELE_C16C10.7 gga:416965 mmu:193670 rno:360967 rno:407784 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.

Endoplasmic reticulum0.501

Rank 1 · LXL04_024249 · OH-1004

Cytoplasm0.230

Rank 2 · LXL04_024249 · OH-1004

Nucleus0.207

Rank 3 · LXL04_024249 · OH-1004

Golgi apparatus0.181

Rank 4 · LXL04_024249 · OH-1004

Lysosome / Vacuole0.108

Rank 5 · LXL04_024249 · OH-1004

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.

PF13920.13zf-C3HC4_343-90 aa

PF13639.13zf-RING_244-86 aa

PF13923.13zf-C3HC4_244-85 aa

PF14634.13zf-RING_544-86 aa

PF00097.32zf-C3HC445-85 aa

PF13445.13zf-RING_UBOX45-83 aa

PF15227.13zf-C3HC4_445-85 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024249	`PF13920.13`	zf-C3HC4_3	43	90	2.8e-08	34.2
LXL04_024249	`PF13639.13`	zf-RING_2	44	86	1.4e-09	38.7
LXL04_024249	`PF13923.13`	zf-C3HC4_2	44	85	2e-08	34.6
LXL04_024249	`PF14634.13`	zf-RING_5	44	86	7.6e-08	32.9
LXL04_024249	`PF00097.32`	zf-C3HC4	45	85	1.1e-09	38.7
LXL04_024249	`PF13445.13`	zf-RING_UBOX	45	83	4.7e-09	36.8
LXL04_024249	`PF15227.13`	zf-C3HC4_4	45	85	1.6e-06	28.8

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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