LXL04_017178 | RubberDandelionOmics

Gene overview

LXL04_017178

Reference: OH-1004 Chr: Chr03 Coordinates: 142706155-142709364 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1494 bp · LXL04_017178|LXL04_017178|OH1004|cDNA

ATGCCTCCTAGGGTTTATACAATCAATCTCGCCTTCTCCAGATTATCGTTACCTGAAGAAATTGATATGGCAGCTTCTGATTCCGACCCCGAGATAGTTTCCGGATCAGAATCAGAATCAGAAGGCGATGAAGACATAAAACTATCGGAACCTTCAAAAACCGCAATCTACAACAAAGAAGGCATCCTCGATAAACTCAACGACATAGTCTGGCTCGAAGACATTGACTGGACCCACAAGCTCTCACTGGACATCCCACA...

CDS

Download CDS FASTA

1494 bp · LXL04_017178|LXL04_017178|OH1004|CDS

ATGCCTCCTAGGGTTTATACAATCAATCTCGCCTTCTCCAGATTATCGTTACCTGAAGAAATTGATATGGCAGCTTCTGATTCCGACCCCGAGATAGTTTCCGGATCAGAATCAGAATCAGAAGGCGATGAAGACATAAAACTATCGGAACCTTCAAAAACCGCAATCTACAACAAAGAAGGCATCCTCGATAAACTCAACGACATAGTCTGGCTCGAAGACATTGACTGGACCCACAAGCTCTCACTGGACATCCCACA...

Protein

Download Protein FASTA

497 aa · LXL04_017178|LXL04_017178|OH1004|PROTEIN

MPPRVYTINLAFSRLSLPEEIDMAASDSDPEIVSGSESESEGDEDIKLSEPSKTAIYNKEGILDKLNDIVWLEDIDWTHKLSLDIPQEDEIDVNDDLARELAFYNQALQGTREAFVKLETMKLPFLRPSDYYAEMVKTDSHMEKIKGRLIAEKRRMEEAEERRKMRDNKKKAKEVQAVKQRERVKQKKDEIESVKKWRKQRQQSGFAEKDSGDIGFEDGKGSERVKKGNKRQGVSPWDRTGGKGKREEKGGGGSGKRKSR...

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_017178`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_017178

Location Chr03:142706155-142709364 (+)

Description Similar to EBP2: Probable rRNA-processing protein EBP2 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g22660`	Required for the processing of the 27S pre-rRNA (By similarity).	The nucleolar GTPase nucleostemin-like 1 plays a role in plant growth and senescence by modulating ribosome biogenesis.2015 · DOI: 10.1093/jxb/erv337
`At5g40280`	Catalyzes the transfer of a farnesyl moiety from farnesyl diphosphate to a cysteine at the fourth position from the C-terminus of several proteins having the C-terminal sequence Cys-aliphatic- aliphatic-X (CaaX).	The CaaX specificities of Arabidopsis protein prenyltransferases explain era1 and ggb phenotypes.2010 · DOI: 10.1186/1471-2229-10-118 ASG2 is a farnesylated DWD protein that acts as ABA negative regulator in Arabidopsis.2016 · DOI: 10.1111/pce.12605

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017178 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009620 response to fungus Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009788 negative regulation of abscisic acid-activated signaling pathway Biological Process

GO:0009934 regulation of meristem structural organization Biological Process

GO:0018342 protein prenylation Biological Process

GO:0018343 protein farnesylation Biological Process

GO:0042273 ribosomal large subunit biogenesis Biological Process

GO:0047484 regulation of response to osmotic stress Biological Process

GO:0160062 cutin-based cuticle development Biological Process

GO:1901000 regulation of response to salt stress Biological Process

KEGG gene cross-reference

ath:AT3G22660

ath:AT5G40280

spo:2542121

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.

Nucleus0.828

Rank 1 · LXL04_017178 · OH-1004

Cytoplasm0.264

Rank 2 · LXL04_017178 · OH-1004

Mitochondrion0.024

Rank 3 · LXL04_017178 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_017178 · OH-1004

Cell membrane0.014

Rank 5 · LXL04_017178 · 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.

PF05890.18Ebp256-297 aa

PF00432.28Prenyltrans286-345 aa

PF00432.28Prenyltrans349-430 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017178	`PF05890.18`	Ebp2	56	297	1.9e-66	224.9
LXL04_017178	`PF00432.28`	Prenyltrans	286	345	6e-29	102.1
LXL04_017178	`PF00432.28`	Prenyltrans	349	430	6e-29	102.1

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
`Q9LUJ5`	Arabidopsis thaliana	Probable rRNA-processing protein EBP2 homolog	61.957%	Swiss-Prot	moderate database homology
`Q38920`	Arabidopsis thaliana	Protein farnesyltransferase subunit beta	49.419%	Swiss-Prot	weak database homology

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