LXL04_014113 | RubberDandelionOmics

Gene overview

LXL04_014113

Reference: OH-1004 Chr: Chr03 Coordinates: 42234114-42239393 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2730 bp · LXL04_014113|LXL04_014113|OH1004|cDNA

ATGGGTGTTCCGGCGTTTTACAGGTGGTTAGCTGACCGGTACCCTCGATCAATAGCGGACGTCGTGGAGGAAGAAGTAGGCGAGGGGCACGGGGTTGACGTATTAAGGCCGAACCCTAACAACATCGAGTTTGATAATTTGTACTTGGACATGAATGGAATTATTCATCCCTGTTTTCACCCTGAAGGAAAGCCTGCTCCAGCTACATATGATGATGTATTCAAGTCAATATTCGACTACATTGATCATCTCTTCTCATT...

CDS

Download CDS FASTA

2730 bp · LXL04_014113|LXL04_014113|OH1004|CDS

ATGGGTGTTCCGGCGTTTTACAGGTGGTTAGCTGACCGGTACCCTCGATCAATAGCGGACGTCGTGGAGGAAGAAGTAGGCGAGGGGCACGGGGTTGACGTATTAAGGCCGAACCCTAACAACATCGAGTTTGATAATTTGTACTTGGACATGAATGGAATTATTCATCCCTGTTTTCACCCTGAAGGAAAGCCTGCTCCAGCTACATATGATGATGTATTCAAGTCAATATTCGACTACATTGATCATCTCTTCTCATT...

Protein

Download Protein FASTA

909 aa · LXL04_014113|LXL04_014113|OH1004|PROTEIN

MGVPAFYRWLADRYPRSIADVVEEEVGEGHGVDVLRPNPNNIEFDNLYLDMNGIIHPCFHPEGKPAPATYDDVFKSIFDYIDHLFSLVRPRKILYMAIDGVAPRAKMNQQRSRRFRAAKDAAEAEAEEERLRLEFEAQGAALAPKEKLETSDSNVITPGTQFMSVLSVALQYYIQCRLNHNPGWQYTKVILSDSNVPGEGEHKVMSFIRLQRNLPGFNPNTRHCLYGLDADLIMLALATHEVHFSILREVITLPGQQEKC...

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_014113`
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_014113

Location Chr03:42234114-42239393 (+)

Description Similar to XRN4: 5'-3' exoribonuclease 4

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g54490`	Possesses 5'->3' exoribonuclease activity.	AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.2004 · DOI: 10.1016/j.molcel.2004.06.006 A link between mRNA turnover and RNA interference in Arabidopsis.2004 · DOI: 10.1126/science.1101092 ETHYLENE-INSENSITIVE5 encodes a 5'-->3' exoribonuclease required for regulation of the EIN3-targeting F-box proteins EBF1/2.2006 · DOI: 10.1073/pnas.0605528103 The exoribonuclease XRN4 is a component of the ethylene response pathway in Arabidopsis.2006 · DOI: 10.1105/tpc.106.046508
`At1g75660`	Possesses 5'->3' exoribonuclease activity.	Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors.2007 · DOI: 10.1105/tpc.107.055319 Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA.2010 · DOI: 10.1093/nar/gkq172
`UniProt: Q9FQ02`	Possesses 5'->3' exoribonuclease activity.	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_014113 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000956 nuclear-transcribed mRNA catabolic process Biological Process

GO:0000967 rRNA 5'-end processing Biological Process

GO:0006369 termination of RNA polymerase II transcription Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006402 mRNA catabolic process Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0010286 heat acclimation Biological Process

GO:0010587 miRNA catabolic process Biological Process

GO:0031087 deadenylation-independent decapping of nuclear-transcribed mRNA Biological Process

GO:0040029 epigenetic regulation of gene expression Biological Process

GO:0051301 cell division Biological Process

KEGG gene cross-reference

ath:AT1G54490

ath:AT1G75660

ath:AT5G42540

dme:Dmel_CG10354

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.

Cytoplasm0.675

Rank 1 · LXL04_014113 · OH-1004

Nucleus0.363

Rank 2 · LXL04_014113 · OH-1004

Endoplasmic reticulum0.069

Rank 3 · LXL04_014113 · OH-1004

Cell membrane0.068

Rank 4 · LXL04_014113 · OH-1004

Golgi apparatus0.061

Rank 5 · LXL04_014113 · 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.

PF03159.25XRN_N1-249 aa

PF17846.7XRN_M316-417 aa

PF17846.7XRN_M428-711 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014113	`PF03159.25`	XRN_N	1	249	3.2e-99	332.0
LXL04_014113	`PF17846.7`	XRN_M	316	417	2.7e-156	521.7
LXL04_014113	`PF17846.7`	XRN_M	428	711	2.7e-156	521.7

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
`Q9FQ04`	Arabidopsis thaliana	5'-3' exoribonuclease 4	65.254%	Swiss-Prot	strong database homology
`Q9FQ03`	Arabidopsis thaliana	5'-3' exoribonuclease 3	66.824%	Swiss-Prot	weak database homology
`Q9FQ02`	Arabidopsis thaliana	5'-3' exoribonuclease 2	63.194%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card