LXL04_025654 | RubberDandelionOmics

Gene overview

LXL04_025654

Reference: OH-1004 Chr: Chr05 Coordinates: 114801614-114803798 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1227 bp · LXL04_025654|LXL04_025654|OH1004|cDNA

ATGGCGGGAACGTCAGTGGTGCCGGCGAACAGAGGTCGGCGGAACACGATGGTGGACGACGAGAAGCTGGTCTTTGAGACCTCGCGTGGAGTGGAGCCCATCATGAGCTTTGACCAGATGGGTATCAAAGACGATCTACTCCGTGGGATTTACCAACACGGGTTCGAGAAACCCTCGGCAATTCAACAGAGAGCTGTTAGGCCTATCATTGAAGGTCGTGATGTCATTGCTCAGGCTCAATCTGGTACCGGAAAAACCTC...

CDS

Download CDS FASTA

1227 bp · LXL04_025654|LXL04_025654|OH1004|CDS

ATGGCGGGAACGTCAGTGGTGCCGGCGAACAGAGGTCGGCGGAACACGATGGTGGACGACGAGAAGCTGGTCTTTGAGACCTCGCGTGGAGTGGAGCCCATCATGAGCTTTGACCAGATGGGTATCAAAGACGATCTACTCCGTGGGATTTACCAACACGGGTTCGAGAAACCCTCGGCAATTCAACAGAGAGCTGTTAGGCCTATCATTGAAGGTCGTGATGTCATTGCTCAGGCTCAATCTGGTACCGGAAAAACCTC...

Protein

Download Protein FASTA

408 aa · LXL04_025654|LXL04_025654|OH1004|PROTEIN

MAGTSVVPANRGRRNTMVDDEKLVFETSRGVEPIMSFDQMGIKDDLLRGIYQHGFEKPSAIQQRAVRPIIEGRDVIAQAQSGTGKTSMIALTVCQIVDTASREVQALILSPTRELAAQTEKQILAIGDFISIQAHACIGGKSVGEDIRKLENGVHVVSGTPGRVCDMIKRRTLRTRAIKLLILDESDEMLSRGFKDQIYDVYRYLPPELQVCLVSATLPNEILEMTSKFMTDPVRILVKRDELTLEGIKQFFVAVERENW...

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_025654`
TK1151 ID	TkA06G047300
OH-1004 ID	LXL04_025654
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025654

Location Chr05:114801614-114803798 (+)

Description Similar to Eukaryotic initiation factor 4A-3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g19760`	ATP-dependent RNA helicase.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0639100`	ATP-dependent RNA helicase.	No verified direct reference in this release
`Os03g0566800`	ATP-dependent RNA helicase.	Two highly similar DEAD box proteins, OsRH2 and OsRH34, homologous to eukaryotic initiation factor 4AIII, play roles of the exon junction complex in regulating growth and development in rice.2016 · DOI: 10.1186/s12870-016-0769-5

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025654 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0001666 response to hypoxia Biological Process

GO:0006417 regulation of translation Biological Process

GO:0009950 dorsal/ventral axis specification Biological Process

GO:0051028 mRNA transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT3G19760

dosa:Os01g0639100

dosa:Os03g0566800

dre:394053

osa:4326580

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.

Cytoplasm0.533

Rank 1 · LXL04_025654 · OH-1004

Nucleus0.506

Rank 2 · LXL04_025654 · OH-1004

Mitochondrion0.052

Rank 3 · LXL04_025654 · OH-1004

Cell membrane0.051

Rank 4 · LXL04_025654 · OH-1004

Endoplasmic reticulum0.043

Rank 5 · LXL04_025654 · 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.

PF04851.22ResIII59-191 aa

PF00270.36DEAD60-222 aa

PF00271.38Helicase_C261-369 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025654	`PF04851.22`	ResIII	59	191	9.1e-06	26.4
LXL04_025654	`PF00270.36`	DEAD	60	222	1.2e-43	149.5
LXL04_025654	`PF00271.38`	Helicase_C	261	369	1.5e-36	125.7

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
`Q94A52`	Arabidopsis thaliana	Eukaryotic initiation factor 4A-III homolog	88.491%	Swiss-Prot	strong database homology
`Q5VNM3`	Oryza sativa subsp. japonica	Eukaryotic initiation factor 4A-III homolog A	91.304%	Swiss-Prot	strong database homology
`Q10I26`	Oryza sativa subsp. japonica	Eukaryotic initiation factor 4A-III homolog B	90.793%	Swiss-Prot	strong database homology

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