LXL04_023636 | RubberDandelionOmics

Gene overview

LXL04_023636

Reference: OH-1004 Chr: Chr05 Coordinates: 57892456-57899312 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2094 bp · LXL04_023636|LXL04_023636|OH1004|cDNA

ATGGGACACCTGGCGACTCAAAAGTGTACCGATGAAGGTGGGGTTTTACCTTTGCTTCATGCTTTGGAAGGGGGCGCGGGAGAGAATGAAATCGGGGCGAGAGCTGAGAACTTGTTGGATACGATTTCGGATAAAGAAGGTAAAGGCGACCTCAGGGAAACCATTGGCgatttaaacaaaaaaatacaCTCCAAAAACAGCGAACTCTTAAATCTCCAAACTGCCCTTGGTCAATATTATGCTGAAATCGACGCCAAGGA...

CDS

Download CDS FASTA

2094 bp · LXL04_023636|LXL04_023636|OH1004|CDS

ATGGGACACCTGGCGACTCAAAAGTGTACCGATGAAGGTGGGGTTTTACCTTTGCTTCATGCTTTGGAAGGGGGCGCGGGAGAGAATGAAATCGGGGCGAGAGCTGAGAACTTGTTGGATACGATTTCGGATAAAGAAGGTAAAGGCGACCTCAGGGAAACCATTGGCGATTTAAACAAAAAAATACACTCCAAAAACAGCGAACTCTTAAATCTCCAAACTGCCCTTGGTCAATATTATGCTGAAATCGACGCCAAGGA...

Protein

Download Protein FASTA

697 aa · LXL04_023636|LXL04_023636|OH1004|PROTEIN

MGHLATQKCTDEGGVLPLLHALEGGAGENEIGARAENLLDTISDKEGKGDLRETIGDLNKKIHSKNSELLNLQTALGQYYAEIDAKDHLERELASVRQESAKLSELLKEAYGQAETTKQEKMEIMEKLRGAERVVTEIKGRVNKLEENNSKLRRALEQSMTRLNRMSMDSDFSVDRPIVIKLLVTYFQRNHSKEDSLRTRSRGSGSRSKGWRVKVWSVVFLVCQVALDVHDDDGDNDGDDYESEISNSRNSSFSDRRTSL...

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_023636`
TK1151 ID	TkA06G473210
OH-1004 ID	LXL04_023636
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	41.100
Protein coverage (%)	TK1151 80.258 / OH-1004 44.763 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

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Basic Information and Functional Annotation

Gene ID LXL04_023636

Location Chr05:57892456-57899312 (+)

Description Similar to GC4: Golgin candidate 4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g46180`	Golgi matrix protein playing a role in tethering of vesicles to Golgi membranes and in maintaining the overall structure of the Golgi apparatus.	No verified direct reference in this release
`At3g61570`	Golgi matrix protein playing a role in tethering of vesicles to Golgi membranes and in maintaining the overall structure of the Golgi apparatus.	No verified direct reference in this release
`At3g02260`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development).	BIG: a calossin-like protein required for polar auxin transport in Arabidopsis.2001 · DOI: 10.1101/gad.905201 Mutations in the huge Arabidopsis gene BIG affect a range of hormone and light responses.2003 · DOI: 10.1046/j.1365-313x.2003.01779.x The auxin transport inhibitor response 3 (tir3) allele of BIG and auxin transport inhibitors affect the gibberellin status of Arabidopsis.2005 · DOI: 10.1111/j.1365-313x.2004.02287.x CRM1/BIG-mediated auxin action regulates Arabidopsis inflorescence development.2007 · DOI: 10.1093/pcp/pcm094 Arabidopsis mutants define downstream branches in the phototransduction pathway.1994 · DOI: 10.1101/gad.8.3.339 Reduced naphthylphthalamic acid binding in the tir3 mutant of Arabidopsis is associated with a reduction in polar auxin transport and diverse morphological defects.1997 · DOI: 10.1105/tpc.9.5.745

Rice

Reference gene ID	Possible function	Papers / DOI
`Os09g0247700`	Required for auxin efflux and polar auxin transport (PAT) influencing auxin-mediated developmental responses (e.g. cell elongation, apical dominance, lateral root production, inflorescence architecture, general growth and development) (By similarity).	No verified direct reference in this release

Functional annotation source

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Functional annotation source: OH1004 · LXL04_023636 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0007030 Golgi organization Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005768 endosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0031267 small GTPase binding Molecular Function

KEGG gene cross-reference

ath:AT2G46180

ath:AT3G61570

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.

Cytoplasm0.669

Rank 1 · LXL04_023636 · OH-1004

Nucleus0.299

Rank 2 · LXL04_023636 · OH-1004

Golgi apparatus0.082

Rank 3 · LXL04_023636 · OH-1004

Cell membrane0.076

Rank 4 · LXL04_023636 · OH-1004

Lysosome / Vacuole0.073

Rank 5 · LXL04_023636 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF30838.1UBR4_TPR1-56 aa

PF30838.1UBR4_TPR340-397 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_023636	`PF30838.1`	UBR4_TPR	1	56	1.8e-24	87.2
LXL04_023636	`PF30838.1`	UBR4_TPR	340	397	1.8e-24	87.2

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
`Q8VYU6`	Arabidopsis thaliana	Golgin candidate 4	62.759%	Swiss-Prot	weak database homology
`Q84WU4`	Arabidopsis thaliana	Golgin candidate 3	60.927%	Swiss-Prot	weak database homology
`Q9SRU2`	Arabidopsis thaliana	Auxin transport protein BIG	80.769%	Swiss-Prot	weak database homology
`B9G2A8`	Oryza sativa subsp. japonica	Auxin transport protein BIG	59.494%	Swiss-Prot	weak database homology

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