LXL04_007917 | RubberDandelionOmics

Gene overview

LXL04_007917

Reference: OH-1004 Chr: Chr02 Coordinates: 74599831-74608504 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1788 bp · LXL04_007917|LXL04_007917|OH1004|cDNA

atgtTGCAGGCTTTCCCTGATGCTCTGTTTCACCACTTGATCTTAGCAATGTCACATCCAGATCATGAAACACGAGTTGTTGCACACCGTGAATGTGCTTATGCCAGCTATGTGGAGTCTGTGGAGGTCGAGAAGAAGCATTTAATGGACGCCATGTTCATTCGAGACCCTTGTCCCCGGCTGTATGGACAGGCATTTGAAGAATTCCATTCACGAATCTTTGGGTCTGCACCAGTTAAGTCCATGGCTGAAACACGTAG...

CDS

Download CDS FASTA

1788 bp · LXL04_007917|LXL04_007917|OH1004|CDS

ATGTTGCAGGCTTTCCCTGATGCTCTGTTTCACCACTTGATCTTAGCAATGTCACATCCAGATCATGAAACACGAGTTGTTGCACACCGTGAATGTGCTTATGCCAGCTATGTGGAGTCTGTGGAGGTCGAGAAGAAGCATTTAATGGACGCCATGTTCATTCGAGACCCTTGTCCCCGGCTGTATGGACAGGCATTTGAAGAATTCCATTCACGAATCTTTGGGTCTGCACCAGTTAAGTCCATGGCTGAAACACGTAG...

Protein

Download Protein FASTA

595 aa · LXL04_007917|LXL04_007917|OH1004|PROTEIN

MLQAFPDALFHHLILAMSHPDHETRVVAHRECAYASYVESVEVEKKHLMDAMFIRDPCPRLYGQAFEEFHSRIFGSAPVKSMAETRRKARLIGQDSPGGITEPIKSGIRDSKAGEVRTCLLLGCGMYFPKVEMSTGILVISGCFDLLKGVDGEITEPMIKELDEDREESQDPEAIEPAEGILLIVESRDNINITQNALTVSNQQRNTEMVARILPYLTYGELAAMEALVQHFDEGRIQSFAFETFLRSFDSFDAERALRW...

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_007917`
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_007917

Location Chr02:74599831-74608504 (-)

Description Similar to BIG: Auxin transport protein BIG

Arabidopsis / Rice Reference Genes and Papers

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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

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Functional annotation source: OH1004 · LXL04_007917 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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:0048281 inflorescence morphogenesis Biological Process

GO:0048364 root development Biological Process

GO:0071596 ubiquitin-dependent protein catabolic process via the N-end rule pathway Biological Process

GO:0140455 cytoplasm protein quality control Biological Process

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT3G02260

dosa:Os09g0247700

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.

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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.

Cytoplasm0.442

Rank 1 · LXL04_007917 · OH-1004

Nucleus0.367

Rank 2 · LXL04_007917 · OH-1004

Mitochondrion0.176

Rank 3 · LXL04_007917 · OH-1004

Cell membrane0.100

Rank 4 · LXL04_007917 · OH-1004

Endoplasmic reticulum0.074

Rank 5 · LXL04_007917 · 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_TPR197-234 aa

PF30838.1UBR4_TPR268-303 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007917	`PF30838.1`	UBR4_TPR	197	234	8.9e-20	71.8
LXL04_007917	`PF30838.1`	UBR4_TPR	268	303	8.9e-20	71.8

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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Protein	Organism	Description	Identity	Database	Confidence
`Q9SRU2`	Arabidopsis thaliana	Auxin transport protein BIG	53.608%	Swiss-Prot	weak database homology
`B9G2A8`	Oryza sativa subsp. japonica	Auxin transport protein BIG	57.534%	Swiss-Prot	weak database homology

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