LXL04_027187 | RubberDandelionOmics

Gene overview

LXL04_027187

Reference: OH-1004 Chr: Chr06 Coordinates: 10681293-10685328 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1947 bp · LXL04_027187|LXL04_027187|OH1004|cDNA

atGGCTCAGATTCAGGTGCAACCTCCTACGGTATCTGGACCGAACGGTGTGGCGTCGGCGGCAACGGCGACGGCCAATGCTAGCGGCGTTGTTGCTGCTGCGGCTGTTGCTGGCGCTGCCGTAGCGGTGGCCGGTGCTAATCAGGCGTTTGTGACAACGTCGCTTTACGTTGGGGACCTTGAGTTTAACGTCACTGATTCGCAGCTGTACGATCTGTTTAACCAAGTTGGTCAGGTTGTCTCTGTTAGGGTTTGTAGGGA...

CDS

Download CDS FASTA

1947 bp · LXL04_027187|LXL04_027187|OH1004|CDS

ATGGCTCAGATTCAGGTGCAACCTCCTACGGTATCTGGACCGAACGGTGTGGCGTCGGCGGCAACGGCGACGGCCAATGCTAGCGGCGTTGTTGCTGCTGCGGCTGTTGCTGGCGCTGCCGTAGCGGTGGCCGGTGCTAATCAGGCGTTTGTGACAACGTCGCTTTACGTTGGGGACCTTGAGTTTAACGTCACTGATTCGCAGCTGTACGATCTGTTTAACCAAGTTGGTCAGGTTGTCTCTGTTAGGGTTTGTAGGGA...

Protein

Download Protein FASTA

648 aa · LXL04_027187|LXL04_027187|OH1004|PROTEIN

MAQIQVQPPTVSGPNGVASAATATANASGVVAAAAVAGAAVAVAGANQAFVTTSLYVGDLEFNVTDSQLYDLFNQVGQVVSVRVCRDLTTRRSLGYGYVNYSNPPDAARAIDVLNFTAINGKAIRIMYSHRDPSIRKSGTANIFIKNLDKSIDNKVLHDTFSTFGNILSCKIAVDITGQSKGYGFVQFDTEEAAQTAIDKLNGMLINDKQVYVGHFLRKQERDSSLSRTKFNNVYVKNLSETTTDEDLKQTFGEYGIITS...

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_027187`
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_027187

Location Chr06:10681293-10685328 (+)

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
`At2g23350`	Binds the poly(A) tail of mRNA.	No verified direct reference in this release
`At1g22760`	Binds the poly(A) tail of mRNA.	Unexpected complexity of poly(A)-binding protein gene families in flowering plants: three conserved lineages that are at least 200 million years old and possible auto- and cross-regulation.2003 · DOI: 10.1093/genetics/163.1.311 Evidence that poly(A) binding protein has an evolutionarily conserved function in facilitating mRNA biogenesis and export.2003 · DOI: 10.1261/rna.5128903
`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_027187 · 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.

Cytoplasm0.349

Rank 1 · LXL04_027187 · OH-1004

Cell membrane0.248

Rank 2 · LXL04_027187 · OH-1004

Endoplasmic reticulum0.195

Rank 3 · LXL04_027187 · OH-1004

Golgi apparatus0.168

Rank 4 · LXL04_027187 · OH-1004

Nucleus0.141

Rank 5 · LXL04_027187 · 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_155-125 aa

PF00076.29RRM_1143-211 aa

PF00076.29RRM_1234-302 aa

PF00076.29RRM_1337-368 aa

PF00122.26E1-E2_ATPase446-542 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027187	`PF00076.29`	RRM_1	55	125	1.4e-76	253.0
LXL04_027187	`PF00076.29`	RRM_1	143	211	1.4e-76	253.0
LXL04_027187	`PF00076.29`	RRM_1	234	302	1.4e-76	253.0
LXL04_027187	`PF00076.29`	RRM_1	337	368	1.4e-76	253.0
LXL04_027187	`PF00122.26`	E1-E2_ATPase	446	542	1.4e-20	73.7

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	68.852%	Swiss-Prot	moderate database homology
`Q9FXA2`	Arabidopsis thaliana	Polyadenylate-binding protein 8	72.381%	Swiss-Prot	weak database homology
`O22173`	Arabidopsis thaliana	Polyadenylate-binding protein 4	65.015%	Swiss-Prot	moderate database homology
`O64380`	Arabidopsis thaliana	Polyadenylate-binding protein 3	57.618%	Swiss-Prot	moderate database homology
`Q05196`	Arabidopsis thaliana	Polyadenylate-binding protein 5	60.991%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card