LXL04_005439 | RubberDandelionOmics

Gene overview

LXL04_005439

Reference: OH-1004 Chr: Chr01 Coordinates: 163888717-163891279 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1557 bp · LXL04_005439|LXL04_005439|OH1004|cDNA

ATGGCATATGTCATCGATCAGAACGGTAGAGTTGCTATTGTTCCAAATTATTCACCAGTAAACttcataaaccctaatttcgTACGTAATCATCATCCTCAACAATTGTATCCCCTGCAATTTGCTTTGCATCCCGCTGTAATTGCTCAGATTGGACTGGATAGGTCAATCTCTCTCAAGGAGCTTATAAAGGATGAGGGTCTTGTGCCTTCTCAAGAGGAAGAACAGAGGCGGAACAATGTCATTCGAAAACTTCGAGA...

CDS

Download CDS FASTA

1557 bp · LXL04_005439|LXL04_005439|OH1004|CDS

ATGGCATATGTCATCGATCAGAACGGTAGAGTTGCTATTGTTCCAAATTATTCACCAGTAAACTTCATAAACCCTAATTTCGTACGTAATCATCATCCTCAACAATTGTATCCCCTGCAATTTGCTTTGCATCCCGCTGTAATTGCTCAGATTGGACTGGATAGGTCAATCTCTCTCAAGGAGCTTATAAAGGATGAGGGTCTTGTGCCTTCTCAAGAGGAAGAACAGAGGCGGAACAATGTCATTCGAAAACTTCGAGA...

Protein

Download Protein FASTA

518 aa · LXL04_005439|LXL04_005439|OH1004|PROTEIN

MAYVIDQNGRVAIVPNYSPVNFINPNFVRNHHPQQLYPLQFALHPAVIAQIGLDRSISLKELIKDEGLVPSQEEEQRRNNVIRKLRETVTTWIKKVARLHGLPPNHIRAASATILTYGSCGLGVSFFFFFFFFFFFFFFFFQFIKILLCPNLFPDRVQVYNAESDIDALCVGPWFASLTEDFFVILHDMLAKRVEVSDIHCIKDAKVPLMRFKFEGIAVDLPYAQLQVTTVPENVDTLNFLYLNGRIDETSWKSLSGVRA...

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_005439`
TK1151 ID	TkA01G050460
OH-1004 ID	LXL04_005439
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	92.900
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_005439

Location Chr01:163888717-163891279 (-)

Description Similar to PAPS3: Nuclear poly(A) polymerase 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g06560`	Essential protein.	No verified direct reference in this release
`At4g32850`	Essential protein.	No verified direct reference in this release
`At2g25850`	Essential protein.	No verified direct reference in this release
`At1g17980`	Essential protein.	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_005439 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006397 mRNA processing Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009908 flower development Biological Process

GO:0031123 RNA 3'-end processing Biological Process

GO:0045824 negative regulation of innate immune response Biological Process

GO:0048366 leaf development Biological Process

GO:0048451 petal formation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005847 mRNA cleavage and polyadenylation specificity factor complex Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT1G17980

ath:AT2G25850

ath:AT3G06560

ath:AT4G32850

ddi:DDB_G0288259

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.

Cytoplasm0.504

Rank 1 · LXL04_005439 · OH-1004

Nucleus0.485

Rank 2 · LXL04_005439 · OH-1004

Mitochondrion0.061

Rank 3 · LXL04_005439 · OH-1004

Cell membrane0.060

Rank 4 · LXL04_005439 · OH-1004

Endoplasmic reticulum0.056

Rank 5 · LXL04_005439 · 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.

PF20750.4PAP_NTPase55-125 aa

PF20750.4PAP_NTPase156-268 aa

PF04928.23PAP_central274-407 aa

PF04926.21PAP_RNA-bind415-452 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_005439	`PF20750.4`	PAP_NTPase	55	125	2.8e-37	129.2
LXL04_005439	`PF20750.4`	PAP_NTPase	156	268	2.8e-37	129.2
LXL04_005439	`PF04928.23`	PAP_central	274	407	2.5e-31	109.1
LXL04_005439	`PF04926.21`	PAP_RNA-bind	415	452	2.1e-06	28.3

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
`Q56XM9`	Arabidopsis thaliana	Nuclear poly(A) polymerase 3	52.350%	Swiss-Prot	strong database homology
`Q8VYW1`	Arabidopsis thaliana	Nuclear poly(A) polymerase 4	34.868%	Swiss-Prot	moderate database homology
`O82312`	Arabidopsis thaliana	Nuclear poly(A) polymerase 2	35.088%	Swiss-Prot	moderate database homology
`Q9LMT2`	Arabidopsis thaliana	Nuclear poly(A) polymerase 1	36.052%	Swiss-Prot	moderate database homology

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