LXL04_006468 | RubberDandelionOmics

Gene overview

LXL04_006468

Reference: OH-1004 Chr: Chr02 Coordinates: 11451020-11470766 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

15249 bp · LXL04_006468|LXL04_006468|OH1004|cDNA

ATGACTTCTAGCTCAGCTGGGATAAGGTACCGGGTTATAGTCCTGTGTGGAGCAAATGTCAGGGTTTCGATCCTGGCTGGAGCAACATGTGGGGATTTTCCCCTGAATAGTGGCCAGGTAAGAGGTCACATGCGGTCTGCTGAAGCCTCCTTTGCGGGAAACTGGGTCGGCGTATTGTGGCGTGGTTATTCCAGGGACTCGAACCTGGGTCCTTCGGGACAAAGTGCGCGGTGGCACATCAGTCACACACAAATACATTC...

CDS

Download CDS FASTA

15249 bp · LXL04_006468|LXL04_006468|OH1004|CDS

ATGACTTCTAGCTCAGCTGGGATAAGGTACCGGGTTATAGTCCTGTGTGGAGCAAATGTCAGGGTTTCGATCCTGGCTGGAGCAACATGTGGGGATTTTCCCCTGAATAGTGGCCAGGTAAGAGGTCACATGCGGTCTGCTGAAGCCTCCTTTGCGGGAAACTGGGTCGGCGTATTGTGGCGTGGTTATTCCAGGGACTCGAACCTGGGTCCTTCGGGACAAAGTGCGCGGTGGCACATCAGTCACACACAAATACATTC...

Protein

Download Protein FASTA

5082 aa · LXL04_006468|LXL04_006468|OH1004|PROTEIN

MTSSSAGIRYRVIVLCGANVRVSILAGATCGDFPLNSGQVRGHMRSAEASFAGNWVGVLWRGYSRDSNLGPSGQSARWHISHTQIHSSSVPRSIYPAMAEEIARLVGVLFDDKASSSSNDIRLRSEKLGLQTLYLILKQGVEINSNGKLGLQHWDQAQIQAVISVAYAIVSSTRSISVEQVEPIIVAVMEQSLEFALCCLEKSVATSDDISFIQLLEIALVDGTIKEADVSHPSTSLLTDSIKSIPLRTENVELQDHIEC...

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_006468`
TK1151 ID	TkA03G039760
OH-1004 ID	LXL04_006468
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
Protein coverage (%)	TK1151 100.000 / OH-1004 98.091 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006468

Location Chr02:11451020-11470766 (-)

Description Similar to BIG: Auxin transport protein BIG

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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

View annotation sources

Functional annotation source: OH1004 · LXL04_006468 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0006515 protein quality control for misfolded or incompletely synthesized proteins Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0007032 endosome organization Biological Process

GO:0009620 response to fungus Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0009733 response to auxin Biological Process

GO:0009734 auxin-activated signaling pathway Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009926 auxin polar transport Biological Process

GO:0010311 lateral root formation Biological Process

GO:0010508 positive regulation of autophagy Biological Process

KEGG gene cross-reference

ath:AT3G02260

dosa:Os09g0247700

hsa:23352

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.

Nucleus0.467

Rank 1 · LXL04_006468 · OH-1004

Cytoplasm0.380

Rank 2 · LXL04_006468 · OH-1004

Golgi apparatus0.101

Rank 3 · LXL04_006468 · OH-1004

Cell membrane0.087

Rank 4 · LXL04_006468 · OH-1004

Endoplasmic reticulum0.085

Rank 5 · LXL04_006468 · 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.

PF30802.1zf-UBR_11594-1650 aa

PF00569.24ZZ2637-2669 aa

PF24079.2UBR43539-3664 aa

PF30837.1UBR4_Ub4167-4293 aa

PF30838.1UBR4_TPR4310-4652 aa

PF13764.13E3_UbLigase_R44716-5056 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006468	`PF30802.1`	zf-UBR_1	1594	1650	1.2e-08	35.9
LXL04_006468	`PF00569.24`	ZZ	2637	2669	3.2e-09	37.2
LXL04_006468	`PF24079.2`	UBR4	3539	3664	2e-34	119.4
LXL04_006468	`PF30837.1`	UBR4_Ub	4167	4293	6.4e-48	161.8
LXL04_006468	`PF30838.1`	UBR4_TPR	4310	4652	6.5e-106	354.8
LXL04_006468	`PF13764.13`	E3_UbLigase_R4	4716	5056	1.5e-123	412.9

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
`Q9SRU2`	Arabidopsis thaliana	Auxin transport protein BIG	61.931%	Swiss-Prot	strong database homology
`B9G2A8`	Oryza sativa subsp. japonica	Auxin transport protein BIG	62.271%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card