LXL04_031213 | RubberDandelionOmics

Gene overview

LXL04_031213

Reference: OH-1004 Chr: Chr07 Coordinates: 2595936-2599242 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1866 bp · LXL04_031213|LXL04_031213|OH1004|cDNA

ATGATCCAATTTAGATTTGCTTTGTATAATATGGAAAAACCAACAAAGTCAGGACTAGCTCTTCAGCATAAGATAGTTGATGCGAGGAGTACAACCTCCCTTTCAACACCAGATCGTATGTCTTCGCTTTATGTTGGGGACTTGGAGGAGAACGTTAATGAAGGTCAATTGTTTGATCTCTTCAATGAGGTGGGACGAGTTCATTCCGTACGTGTTTGTCGAGATCAAGAAAATGGGGTTTCACTTGGTTACGGCTATGT...

CDS

Download CDS FASTA

1866 bp · LXL04_031213|LXL04_031213|OH1004|CDS

ATGATCCAATTTAGATTTGCTTTGTATAATATGGAAAAACCAACAAAGTCAGGACTAGCTCTTCAGCATAAGATAGTTGATGCGAGGAGTACAACCTCCCTTTCAACACCAGATCGTATGTCTTCGCTTTATGTTGGGGACTTGGAGGAGAACGTTAATGAAGGTCAATTGTTTGATCTCTTCAATGAGGTGGGACGAGTTCATTCCGTACGTGTTTGTCGAGATCAAGAAAATGGGGTTTCACTTGGTTACGGCTATGT...

Protein

Download Protein FASTA

621 aa · LXL04_031213|LXL04_031213|OH1004|PROTEIN

MIQFRFALYNMEKPTKSGLALQHKIVDARSTTSLSTPDRMSSLYVGDLEENVNEGQLFDLFNEVGRVHSVRVCRDQENGVSLGYGYVNFTTSEDATIALKFLNFKRLHGKQIRIMFSEPDPTMRRSGVGNVYIKNLDSSIDNKELYEAFCAFGNVSTCKVVVDSHGVSKGFGFIQFEKDEDAQIAIKNLNGVSIKGKQVYVGKFIRQEEWNDAKRSLKLTELAHANLYTKNLDETITDDEKLKALFSEFGTITSCKIMID...

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_031213`
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_031213

Location Chr07:2595936-2599242 (+)

Description Similar to PAB2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34110`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g49760`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g71770`	Binds the poly(A) tail of mRNA.	Differential organ-specific expression of three poly(A)-binding-protein genes from Arabidopsis thaliana.1993 · DOI: 10.1073/pnas.90.14.6686 A pollen-, ovule-, and early embryo-specific poly(A) binding protein from Arabidopsis complements essential functions in yeast.1996 · DOI: 10.1105/tpc.8.8.1261

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_031213 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Biological Process

GO:0006413 translational initiation Biological Process

GO:0006417 regulation of translation Biological Process

GO:0006446 regulation of translational initiation Biological Process

GO:0048255 mRNA stabilization Biological Process

GO:0060211 regulation of nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:1900151 regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT1G49760

ath:AT4G34110

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.

Plastid0.357

Rank 1 · LXL04_031213 · OH-1004

Mitochondrion0.281

Rank 2 · LXL04_031213 · OH-1004

Cytoplasm0.214

Rank 3 · LXL04_031213 · OH-1004

Nucleus0.203

Rank 4 · LXL04_031213 · OH-1004

Peroxisome0.048

Rank 5 · LXL04_031213 · 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_143-113 aa

PF00076.29RRM_1131-199 aa

PF00076.29RRM_1227-296 aa

PF00658.25MLLE363-427 aa

PF27980.1EML_helical539-620 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_031213	`PF00076.29`	RRM_1	43	113	2.1e-58	194.8
LXL04_031213	`PF00076.29`	RRM_1	131	199	2.1e-58	194.8
LXL04_031213	`PF00076.29`	RRM_1	227	296	2.1e-58	194.8
LXL04_031213	`PF00658.25`	MLLE	363	427	2e-23	82.9
LXL04_031213	`PF27980.1`	EML_helical	539	620	7.1e-26	91.0

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
`P42731`	Arabidopsis thaliana	Polyadenylate-binding protein 2	49.458%	Swiss-Prot	weak database homology
`Q9FXA2`	Arabidopsis thaliana	Polyadenylate-binding protein 8	48.921%	Swiss-Prot	weak database homology
`Q05196`	Arabidopsis thaliana	Polyadenylate-binding protein 5	49.822%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card