LXL04_008112 | RubberDandelionOmics

Gene overview

LXL04_008112

Reference: OH-1004 Chr: Chr02 Coordinates: 86630785-86633862 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1905 bp · LXL04_008112|LXL04_008112|OH1004|cDNA

ATGGCGCAGATTCAGGTGCAGCCTCCTCCAGTATCTGGACCGAATGTTGCGGCAGCGGCGACGATCAATGCTGGTGTTGTTGCAGCTACTGCTATCGCCAGCGGTGCGGTGGCGGGTTCTAACCAGTCATTTGTGACGACCTCGCTTTACGTTGGGGATCTAGAGTTTAATGTGACTGATTCGCAGTTGTACGATATGTTTAATCAGGTTGGACAAGTTGTTTCGGTTAGGATTTGTAGGGATTTGAGCACTCGGCGATC...

CDS

Download CDS FASTA

1905 bp · LXL04_008112|LXL04_008112|OH1004|CDS

ATGGCGCAGATTCAGGTGCAGCCTCCTCCAGTATCTGGACCGAATGTTGCGGCAGCGGCGACGATCAATGCTGGTGTTGTTGCAGCTACTGCTATCGCCAGCGGTGCGGTGGCGGGTTCTAACCAGTCATTTGTGACGACCTCGCTTTACGTTGGGGATCTAGAGTTTAATGTGACTGATTCGCAGTTGTACGATATGTTTAATCAGGTTGGACAAGTTGTTTCGGTTAGGATTTGTAGGGATTTGAGCACTCGGCGATC...

Protein

Download Protein FASTA

634 aa · LXL04_008112|LXL04_008112|OH1004|PROTEIN

MAQIQVQPPPVSGPNVAAAATINAGVVAATAIASGAVAGSNQSFVTTSLYVGDLEFNVTDSQLYDMFNQVGQVVSVRICRDLSTRRSLGYGYVNFNNPNDAARAIGVLNFTPVNGKSIRIMYSHRDPSIRKSGTANIFIKNLDKTIDNKALHDTFSTFGNILSCKIATDSIGQSKGYGFVQFDTEEAAQNAIDKLNGMLMNDKQVYVGPFLRKQERDPSSTRTKFNNVYVKNLPESTTDDDLKKTFGEYGLITSAVVMRD...

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_008112`
TK1151 ID	TkA03G345080
OH-1004 ID	LXL04_008112
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	87.000
Protein coverage (%)	TK1151 94.652 / OH-1004 30.284 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_008112

Location Chr02:86630785-86633862 (+)

Description Similar to PAB2: Polyadenylate-binding protein 2

Arabidopsis / Rice Reference Genes and Papers

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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_008112 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening Biological Process

GO:0006397 mRNA processing 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:0005739 mitochondrion Cellular Component

KEGG gene cross-reference

ath:AT1G22760

ath:AT1G49760

ath:AT1G71770

ath:AT2G23350

ath:AT4G34110

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.

Cytoplasm0.663

Rank 1 · LXL04_008112 · OH-1004

Nucleus0.417

Rank 2 · LXL04_008112 · OH-1004

Cell membrane0.057

Rank 3 · LXL04_008112 · OH-1004

Mitochondrion0.050

Rank 4 · LXL04_008112 · OH-1004

Endoplasmic reticulum0.037

Rank 5 · LXL04_008112 · 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_149-119 aa

PF00076.29RRM_1137-205 aa

PF00076.29RRM_1228-296 aa

PF00076.29RRM_1331-399 aa

PF00658.25MLLE541-607 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008112	`PF00076.29`	RRM_1	49	119	3.6e-88	290.2
LXL04_008112	`PF00076.29`	RRM_1	137	205	3.6e-88	290.2
LXL04_008112	`PF00076.29`	RRM_1	228	296	3.6e-88	290.2
LXL04_008112	`PF00076.29`	RRM_1	331	399	3.6e-88	290.2
LXL04_008112	`PF00658.25`	MLLE	541	607	1e-26	93.4

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	65.741%	Swiss-Prot	strong database homology
`Q9FXA2`	Arabidopsis thaliana	Polyadenylate-binding protein 8	63.537%	Swiss-Prot	strong database homology
`O22173`	Arabidopsis thaliana	Polyadenylate-binding protein 4	62.939%	Swiss-Prot	strong database homology
`O64380`	Arabidopsis thaliana	Polyadenylate-binding protein 3	54.146%	Swiss-Prot	strong database homology
`Q05196`	Arabidopsis thaliana	Polyadenylate-binding protein 5	52.607%	Swiss-Prot	strong database homology

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