LXL04_038377 | RubberDandelionOmics

Gene overview

LXL04_038377

Reference: OH-1004 Chr: Chr09 Coordinates: 38876534-38878496 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1344 bp · LXL04_038377|LXL04_038377|OH1004|cDNA

ATGCAGCCATCTAACGGCAACGGCAACGGCAACGGAAACGCGGCGGATTTGACTCcgcaacagcaacaacaacaacagcagtGGTTGGCTATGCAACAATACCAACAGCAACAATGGTTAGCGATGCAGCAGTACCCTGCCGCCGCCGCGGCGTCTATGGCTATGCATCATCCGGCGATGATGTATCAACAACCGCCGCCAGCAGCATATATGCCCTATCCTTATCAGCAACAAGGACATCAACAGCAGTATCAACAGCA...

CDS

Download CDS FASTA

1344 bp · LXL04_038377|LXL04_038377|OH1004|CDS

ATGCAGCCATCTAACGGCAACGGCAACGGCAACGGAAACGCGGCGGATTTGACTCCGCAACAGCAACAACAACAACAGCAGTGGTTGGCTATGCAACAATACCAACAGCAACAATGGTTAGCGATGCAGCAGTACCCTGCCGCCGCCGCGGCGTCTATGGCTATGCATCATCCGGCGATGATGTATCAACAACCGCCGCCAGCAGCATATATGCCCTATCCTTATCAGCAACAAGGACATCAACAGCAGTATCAACAGCA...

Protein

Download Protein FASTA

447 aa · LXL04_038377|LXL04_038377|OH1004|PROTEIN

MQPSNGNGNGNGNAADLTPQQQQQQQQWLAMQQYQQQQWLAMQQYPAAAAASMAMHHPAMMYQQPPPAAYMPYPYQQQGHQQQYQQQSQQHQINNQIQSSSEDNKTIWVGDLQHWMDETYLQSCFSQTGEVQTIKLIRNKQTGQSERYGFIEFVSHSAAEKVLQSYNGTMMPNTDQAFRLNWASFSTGEKRGDNTGSDLSIFVGDLAPDVTDSMLNETFATRYPSVKGAKVVFDTNTGCSKGYGFVRFSDESERSRAMNE...

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_038377`
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_038377

Location Chr09:38876534-38878496 (-)

Description Similar to RBP47: Polyadenylate-binding protein RBP47

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19130`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g49600`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g47490`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	No verified direct reference in this release
`At1g47500`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.	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_038377 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0034063 stress granule assembly Biological Process

GO:0034605 cellular response to heat Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0010494 cytoplasmic stress granule Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0008143 poly(A) binding Molecular Function

KEGG gene cross-reference

ath:AT1G47490

ath:AT1G47500

ath:AT1G49600

ath:AT3G19130

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.

Nucleus0.820

Rank 1 · LXL04_038377 · OH-1004

Cytoplasm0.398

Rank 2 · LXL04_038377 · OH-1004

Cell membrane0.028

Rank 3 · LXL04_038377 · OH-1004

Endoplasmic reticulum0.018

Rank 4 · LXL04_038377 · OH-1004

Mitochondrion0.017

Rank 5 · LXL04_038377 · 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.

PF00076.29RRM_1107-174 aa

PF00076.29RRM_1201-271 aa

PF00076.29RRM_1326-389 aa

PF08777.18RRM_3328-382 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038377	`PF00076.29`	RRM_1	107	174	2.4e-54	181.8
LXL04_038377	`PF00076.29`	RRM_1	201	271	2.4e-54	181.8
LXL04_038377	`PF00076.29`	RRM_1	326	389	2.4e-54	181.8
LXL04_038377	`PF08777.18`	RRM_3	328	382	4.5e-07	30.6

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
`Q0WW84`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47B	62.943%	Swiss-Prot	strong database homology
`F4I3B3`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47A	65.569%	Swiss-Prot	strong database homology
`Q9SX79`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47C	54.135%	Swiss-Prot	strong database homology
`Q9SX80`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47C'	54.922%	Swiss-Prot	strong database homology

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