LXL04_006125 | RubberDandelionOmics

Gene overview

LXL04_006125

Reference: OH-1004 Chr: Chr02 Coordinates: 2036636-2041849 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1941 bp · LXL04_006125|LXL04_006125|OH1004|cDNA

ATGGGTGCTGCAACTGAAGCTACTCCAGCTCCCCGTTATGCCCCAGATGACCCCAACCTTCCAAAACCATGGAAAGGGTTAGTTGATGGAACAACCGGCTACCTCTACTATTGGAATCCAGTCACCAATGTTACCCAATATGAAAAGCCCTCAGGTTCTAAAAGTTCAGATCAACAAAAGTCATCTTCAGTAGCCATAAGCTCTTCTGTTCAGTCTTCACAAAAAGAAAACCGTGTcattgatgatgatgatgatagaTA...

CDS

Download CDS FASTA

1941 bp · LXL04_006125|LXL04_006125|OH1004|CDS

ATGGGTGCTGCAACTGAAGCTACTCCAGCTCCCCGTTATGCCCCAGATGACCCCAACCTTCCAAAACCATGGAAAGGGTTAGTTGATGGAACAACCGGCTACCTCTACTATTGGAATCCAGTCACCAATGTTACCCAATATGAAAAGCCCTCAGGTTCTAAAAGTTCAGATCAACAAAAGTCATCTTCAGTAGCCATAAGCTCTTCTGTTCAGTCTTCACAAAAAGAAAACCGTGTCATTGATGATGATGATGATAGATA...

Protein

Download Protein FASTA

646 aa · LXL04_006125|LXL04_006125|OH1004|PROTEIN

MGAATEATPAPRYAPDDPNLPKPWKGLVDGTTGYLYYWNPVTNVTQYEKPSGSKSSDQQKSSSVAISSSVQSSQKENRVIDDDDDRYGKTSNGGSKFSSRGHESTRSGSYNSHNAPNGAVAAGPGGSGLSPDAYRKRHEITVTGDNVPPPFTSFEDTGFPSELLREVLEAGFAAPTPIQAQSWPVALQSRDIVAIAKTGSGKTLGYLVPGFIHLKRVLKNRQMGPTVLVLSPTRELATQIQAEALKFGKSSKILCTCLYG...

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_006125`
TK1151 ID	TkA03G010560
OH-1004 ID	LXL04_006125
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.800
Protein coverage (%)	TK1151 90.339 / OH-1004 82.508 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_006125

Location Chr02:2036636-2041849 (-)

Description Similar to RH46: DEAD-box ATP-dependent RNA helicase 46

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g14610`	DEAD-box ATP-dependent RNA helicase 46.	No verified direct reference in this release
`At3g01540`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	Characterization of a DEAD box ATPase/RNA helicase protein of Arabidopsis thaliana.1998 · DOI: 10.1093/nar/26.11.2638

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0172200`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release
`Os01g0549400`	ATP-dependent RNA helicase involved nonsense-mediated mRNA decay and ribosome biogenesis through rRNA processing.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_006125 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

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

GO:0006364 rRNA processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003724 RNA helicase activity Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0016887 ATP hydrolysis activity Molecular Function

KEGG gene cross-reference

ath:AT3G01540

ath:AT5G14610

dosa:Os01g0172200

dosa:Os01g0549400

nsy:104219642

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.

Nucleus0.746

Rank 1 · LXL04_006125 · OH-1004

Cytoplasm0.365

Rank 2 · LXL04_006125 · OH-1004

Endoplasmic reticulum0.044

Rank 3 · LXL04_006125 · OH-1004

Cell membrane0.035

Rank 4 · LXL04_006125 · OH-1004

Mitochondrion0.022

Rank 5 · LXL04_006125 · 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.

PF00397.33WW20-50 aa

PF00270.36DEAD176-345 aa

PF04851.22ResIII188-339 aa

PF00271.38Helicase_C383-491 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006125	`PF00397.33`	WW	20	50	1.6e-07	32.0
LXL04_006125	`PF00270.36`	DEAD	176	345	6.8e-52	176.3
LXL04_006125	`PF04851.22`	ResIII	188	339	3.7e-09	37.4
LXL04_006125	`PF00271.38`	Helicase_C	383	491	8e-38	129.8

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
`Q9LYJ9`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 46	73.321%	Swiss-Prot	strong database homology
`Q8H136`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 14	66.823%	Swiss-Prot	strong database homology
`Q5VQL1`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 14	58.529%	Swiss-Prot	strong database homology
`Q5JKF2`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 40	66.725%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card