LXL04_007906 | RubberDandelionOmics

Gene overview

LXL04_007906

Reference: OH-1004 Chr: Chr02 Coordinates: 73886593-73903446 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3096 bp · LXL04_007906|LXL04_007906|OH1004|cDNA

ATGTCGTCGTCGCAGAGAGTCCAACAAGCAAAACCAAAGACTACACATTGGGATGCTCTGTTCAGTTTGAGTCAAACAGAAAGTGATCAAAGGCTGTTGGAATGCCTTGTGCTTAACCTTTGTGATCATCCTTGCTGGTCCTATTGCCAAGGGTTTTCTGACATGGTTTTATTAATGGACAACATGGTTGATATGCTTTCTGATGTTAAGCTTCAGCCAACTAAGATCCTGACCGCTATATGTGGCATGTTGCATACATT...

CDS

Download CDS FASTA

3096 bp · LXL04_007906|LXL04_007906|OH1004|CDS

ATGTCGTCGTCGCAGAGAGTCCAACAAGCAAAACCAAAGACTACACATTGGGATGCTCTGTTCAGTTTGAGTCAAACAGAAAGTGATCAAAGGCTGTTGGAATGCCTTGTGCTTAACCTTTGTGATCATCCTTGCTGGTCCTATTGCCAAGGGTTTTCTGACATGGTTTTATTAATGGACAACATGGTTGATATGCTTTCTGATGTTAAGCTTCAGCCAACTAAGATCCTGACCGCTATATGTGGCATGTTGCATACATT...

Protein

Download Protein FASTA

1031 aa · LXL04_007906|LXL04_007906|OH1004|PROTEIN

MSSSQRVQQAKPKTTHWDALFSLSQTESDQRLLECLVLNLCDHPCWSYCQGFSDMVLLMDNMVDMLSDVKLQPTKILTAICGMLHTLKSNKGIKEKNLSHSISEQGFEMGIALPSFLLNIEVASGGIVLRWIVGVCLSFKIFKVYWKLKNIKQEHAKFWKQHPALVKAHLTPELQHDFKRVVELASRLLQELMKATVLDPADYTGLEAALDNHKVSLYFTESPTNPFLRCVDIELVSKMCHEKGAIVCIDGTFATPLNQK...

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_007906`
TK1151 ID	TkA03G238660
OH-1004 ID	LXL04_007906
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	81.200
Protein coverage (%)	TK1151 100.000 / OH-1004 98.545 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_007906

Location Chr02:73886593-73903446 (-)

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
`At3g01120`	Catalyzes the first committed step of methionine (Met) biosynthesis.	No verified direct reference in this release
`At1g35530`	Involved in ordered homologous recombination (HR) events in somatic and meiotic cells.	The Fanconi anemia ortholog FANCM ensures ordered homologous recombination in both somatic and meiotic cells in Arabidopsis.2012 · DOI: 10.1105/tpc.112.096644 FANCM limits meiotic crossovers.2012 · DOI: 10.1126/science.1220381 The requirement for recombination factors differs considerably between different pathways of homologous double-strand break repair in somatic plant cells.2012 · DOI: 10.1111/j.1365-313x.2012.05119.x MHF1 plays Fanconi anaemia complementation group M protein (FANCM)-dependent and FANCM-independent roles in DNA repair and homologous recombination in plants.2014 · DOI: 10.1111/tpj.12507 FANCM-associated proteins MHF1 and MHF2, but not the other Fanconi anemia factors, limit meiotic crossovers.2014 · DOI: 10.1093/nar/gku614 AAA-ATPase FIDGETIN-LIKE 1 and Helicase FANCM Antagonize Meiotic Crossovers by Distinct Mechanisms.2015 · DOI: 10.1371/journal.pgen.1005369

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_007906 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0001887 selenium compound metabolic process Biological Process

GO:0009086 methionine biosynthetic process 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:0019346 transsulfuration Biological Process

GO:0048281 inflorescence morphogenesis Biological Process

GO:0048364 root development Biological Process

KEGG gene cross-reference

ath:AT3G01120

ath:AT3G02260

nta:107822634

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.

Nucleus0.326

Rank 1 · LXL04_007906 · OH-1004

Cytoplasm0.310

Rank 2 · LXL04_007906 · OH-1004

Mitochondrion0.144

Rank 3 · LXL04_007906 · OH-1004

Cell membrane0.117

Rank 4 · LXL04_007906 · OH-1004

Endoplasmic reticulum0.105

Rank 5 · LXL04_007906 · 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.

PF01053.27Cys_Met_Meta_PP191-268 aa

PF30838.1UBR4_TPR651-713 aa

PF30838.1UBR4_TPR724-754 aa

PF30838.1UBR4_TPR812-846 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_007906	`PF01053.27`	Cys_Met_Meta_PP	191	268	8.2e-19	68.1
LXL04_007906	`PF30838.1`	UBR4_TPR	651	713	2.1e-29	103.4
LXL04_007906	`PF30838.1`	UBR4_TPR	724	754	2.1e-29	103.4
LXL04_007906	`PF30838.1`	UBR4_TPR	812	846	2.1e-29	103.4

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	46.748%	Swiss-Prot	weak database homology
`P55217`	Arabidopsis thaliana	Cystathionine gamma-synthase 1, chloroplastic	77.632%	Swiss-Prot	weak database homology
`I3XHK1`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase FANCM	43.017%	Swiss-Prot	weak database homology
`B9G2A8`	Oryza sativa subsp. japonica	Auxin transport protein BIG	47.423%	Swiss-Prot	weak database homology

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