LXL04_038239 | RubberDandelionOmics

Gene overview

LXL04_038239

Reference: OH-1004 Chr: Chr09 Coordinates: 34920322-34923985 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1650 bp · LXL04_038239|LXL04_038239|OH1004|cDNA

ATGAGTGCCAGAATGTCTGGACCTATTGTCGGTTTACAAAAAACCGACATTGAATACTCCGAGGAAAAGAAATATAAGCTTTCCTTCAAGCAAAGGGCAATAATTGCCTCCAACAAATTAAGAACTTCATTCGGGAGGAAAAGCAGGAAGAATGGGAAACCGGTGTCTGTTGTTGAACATGTTCATGATGCAGATGAACTAAAAATAGTCGATGCTTTTCGCCAAGCTTTGATCTTGGAAGAATTACTACCCACAAAACA...

CDS

Download CDS FASTA

1650 bp · LXL04_038239|LXL04_038239|OH1004|CDS

ATGAGTGCCAGAATGTCTGGACCTATTGTCGGTTTACAAAAAACCGACATTGAATACTCCGAGGAAAAGAAATATAAGCTTTCCTTCAAGCAAAGGGCAATAATTGCCTCCAACAAATTAAGAACTTCATTCGGGAGGAAAAGCAGGAAGAATGGGAAACCGGTGTCTGTTGTTGAACATGTTCATGATGCAGATGAACTAAAAATAGTCGATGCTTTTCGCCAAGCTTTGATCTTGGAAGAATTACTACCCACAAAACA...

Protein

Download Protein FASTA

549 aa · LXL04_038239|LXL04_038239|OH1004|PROTEIN

MSARMSGPIVGLQKTDIEYSEEKKYKLSFKQRAIIASNKLRTSFGRKSRKNGKPVSVVEHVHDADELKIVDAFRQALILEELLPTKHDDYHMMLRFLKARKFDIEKTKQMWADMIRWRKDYGTDTIIEDFDFAEKEEVVKYYPQGHHGVDKEGRPVYIEQLGKVDATKLLQVTTLERYVKYHVKEFERTFVDKFPACSIAAKRHIDQSTTILDVQGVGLKNMNKNARELIQCLQNIDGNNYPETLCRMYIVNAGSGFRLL...

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_038239`
TK1151 ID	TkA04G408490
OH-1004 ID	LXL04_038239
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	95.800
Protein coverage (%)	TK1151 100.000 / 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

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_038239

Location Chr09:34920322-34923985 (-)

Description Similar to SFH3: Phosphatidylinositol/phosphatidylcholine transfer protein SFH3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g21540`	Required for transport of secretory proteins from the Golgi complex (By similarity).	Identification of two phosphatidylinositol/phosphatidylcholine transfer protein genes that are predominately transcribed in the flowers of Arabidopsis thaliana.2007 · DOI: 10.1016/j.jplph.2006.03.014
`At4g36490`	Required for transport of secretory proteins from the Golgi complex (By similarity).	Identification of two phosphatidylinositol/phosphatidylcholine transfer protein genes that are predominately transcribed in the flowers of Arabidopsis thaliana.2007 · DOI: 10.1016/j.jplph.2006.03.014
`At2g18180`	Required for transport of secretory proteins from the Golgi complex.	No verified direct reference in this release
`At4g34580`	Required for transport of secretory proteins from the Golgi complex (By similarity).	The Arabidopsis COW1 gene encodes a phosphatidylinositol transfer protein essential for root hair tip growth.2004 · DOI: 10.1111/j.1365-313x.2004.02245.x OsSNDP1, a Sec14-nodulin domain-containing protein, plays a critical role in root hair elongation in rice.2013 · DOI: 10.1007/s11103-013-0033-4 The COW1 locus of arabidopsis acts after RHD2, and in parallel with RHD3 and TIP1, to determine the shape, rate of elongation, and number of root hairs produced from each site of hair formation.1997 · DOI: 10.1104/pp.115.3.981
`At4g39180`	Required for transport of secretory proteins from the Golgi complex (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038239 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006656 phosphatidylcholine biosynthetic process Biological Process

GO:0006892 post-Golgi vesicle-mediated transport Biological Process

GO:0009908 flower development Biological Process

GO:0009932 cell tip growth Biological Process

GO:0010053 root epidermal cell differentiation Biological Process

GO:0015031 protein transport Biological Process

GO:0048767 root hair elongation Biological Process

GO:0048768 root hair cell tip growth Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005794 Golgi apparatus Cellular Component

KEGG gene cross-reference

ath:AT2G18180

ath:AT2G21540

ath:AT4G34580

ath:AT4G36490

ath:AT4G39180

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.

Cell membrane0.312

Rank 1 · LXL04_038239 · OH-1004

Endoplasmic reticulum0.267

Rank 2 · LXL04_038239 · OH-1004

Cytoplasm0.206

Rank 3 · LXL04_038239 · OH-1004

Golgi apparatus0.177

Rank 4 · LXL04_038239 · OH-1004

Nucleus0.098

Rank 5 · LXL04_038239 · 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.

PF03765.22CRAL_TRIO_N87-113 aa

PF00650.26CRAL_TRIO141-302 aa

PF13716.12CRAL_TRIO_2214-304 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038239	`PF03765.22`	CRAL_TRIO_N	87	113	9e-06	26.5
LXL04_038239	`PF00650.26`	CRAL_TRIO	141	302	1.3e-30	107.0
LXL04_038239	`PF13716.12`	CRAL_TRIO_2	214	304	1.8e-06	29.0

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
`Q93ZE9`	Arabidopsis thaliana	Phosphatidylinositol/phosphatidylcholine transfer protein SFH3	57.885%	Swiss-Prot	strong database homology
`Q94A34`	Arabidopsis thaliana	Phosphatidylinositol/phosphatidylcholine transfer protein SFH12	57.559%	Swiss-Prot	strong database homology
`Q9SI13`	Arabidopsis thaliana	Phosphatidylinositol/phosphatidylcholine transfer protein SFH10	56.261%	Swiss-Prot	strong database homology
`F4JLE5`	Arabidopsis thaliana	Phosphatidylinositol/phosphatidylcholine transfer protein SFH1	55.415%	Swiss-Prot	strong database homology
`F4JVA9`	Arabidopsis thaliana	Phosphatidylinositol/phosphatidylcholine transfer protein SFH2	54.128%	Swiss-Prot	strong database homology

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