LXL04_019188 | RubberDandelionOmics

Gene overview

LXL04_019188

Reference: OH-1004 Chr: Chr04 Coordinates: 25884060-25884775 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

555 bp · LXL04_019188|LXL04_019188|OH1004|cDNA

ATGTCCCACGAATCTGCTGACAAAGTCCTTCAAAGCTACAACGGAACCACGATGCCAAATACAGATCAAGCTTTCCGTTTAAACTGGGCTAGCTTCAGTTCAGGCGAAAAACGTCAAGAACCAGGCTCAGATCTTTCCATATTCATAGGAGATTTAGCTCCAGATGTTACTGATACAATCCTCTACGAAACATTCGCTGGTAGATGTTACTGTATATTAATGGTGTTTGTACTTTTAGCTGTGTTATTATCTGGTGGAAA...

CDS

Download CDS FASTA

555 bp · LXL04_019188|LXL04_019188|OH1004|CDS

ATGTCCCACGAATCTGCTGACAAAGTCCTTCAAAGCTACAACGGAACCACGATGCCAAATACAGATCAAGCTTTCCGTTTAAACTGGGCTAGCTTCAGTTCAGGCGAAAAACGTCAAGAACCAGGCTCAGATCTTTCCATATTCATAGGAGATTTAGCTCCAGATGTTACTGATACAATCCTCTACGAAACATTCGCTGGTAGATGTTACTGTATATTAATGGTGTTTGTACTTTTAGCTGTGTTATTATCTGGTGGAAA...

Protein

Download Protein FASTA

184 aa · LXL04_019188|LXL04_019188|OH1004|PROTEIN

MSHESADKVLQSYNGTTMPNTDQAFRLNWASFSSGEKRQEPGSDLSIFIGDLAPDVTDTILYETFAGRCYCILMVFVLLAVLLSGGNGGFGGTPQNSQSDGDSSNTTIFVGGLDSEVTDEDLRQTFSQCGEILSVKIPLGKGCGFVQFASRGSAEDAIQNMHGTVIGNQTVRISWGKTPANRQV

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_019188`
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_019188

Location Chr04:25884060-25884775 (-)

Description Similar to RBP47C': Polyadenylate-binding protein RBP47C'

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`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
`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
`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
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019188 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing 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

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.

Nucleus0.700

Rank 1 · LXL04_019188 · OH-1004

Cytoplasm0.537

Rank 2 · LXL04_019188 · OH-1004

Cell membrane0.039

Rank 3 · LXL04_019188 · OH-1004

Mitochondrion0.032

Rank 4 · LXL04_019188 · OH-1004

Endoplasmic reticulum0.030

Rank 5 · LXL04_019188 · 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_1108-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019188	`PF00076.29`	RRM_1	108	172	2.6e-25	88.8

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
`Q9SX80`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47C'	50.000%	Swiss-Prot	strong database homology
`Q9SX79`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47C	49.130%	Swiss-Prot	moderate database homology
`F4I3B3`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47A	46.414%	Swiss-Prot	moderate database homology
`Q0WW84`	Arabidopsis thaliana	Polyadenylate-binding protein RBP47B	42.562%	Swiss-Prot	moderate database homology

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