LXL04_008888 | RubberDandelionOmics

Gene overview

LXL04_008888

Reference: OH-1004 Chr: Chr02 Coordinates: 111252315-111255143 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

819 bp · LXL04_008888|LXL04_008888|OH1004|cDNA

ATGAAATATCTTGACTCTCAGAAAAGGAAGTGTCATATTCCCTTCTCGGGTCGCGATTTTAAAATCAGCCACGCGTATTCTTTCTCGAGTCCGACCATTCCGTCTTCTATCTTTCTCCCACTCTTACGATTTCAAGGGTTTCCAGTTTACAATCGCACCTGTTTAGTGTATAGCGGCTCCTCACATTCACAGCGACGTGGAAATGTTACAAGAATCACTCCCAGTTGTTCAAATCATTCATGGAGCTTACTTGCAATTGA...

CDS

Download CDS FASTA

819 bp · LXL04_008888|LXL04_008888|OH1004|CDS

ATGAAATATCTTGACTCTCAGAAAAGGAAGTGTCATATTCCCTTCTCGGGTCGCGATTTTAAAATCAGCCACGCGTATTCTTTCTCGAGTCCGACCATTCCGTCTTCTATCTTTCTCCCACTCTTACGATTTCAAGGGTTTCCAGTTTACAATCGCACCTGTTTAGTGTATAGCGGCTCCTCACATTCACAGCGACGTGGAAATGTTACAAGAATCACTCCCAGTTGTTCAAATCATTCATGGAGCTTACTTGCAATTGA...

Protein

Download Protein FASTA

272 aa · LXL04_008888|LXL04_008888|OH1004|PROTEIN

MKYLDSQKRKCHIPFSGRDFKISHAYSFSSPTIPSSIFLPLLRFQGFPVYNRTCLVYSGSSHSQRRGNVTRITPSCSNHSWSLLAIDGNNILSVCSSLVDVPQIVYGSLTKDASWQWRNVSTPISESKEKAIDCFRSNDHGILIATDVAARGLDIPGVRTVVHYQLTHSAEVYVHRSERTARASADGCSIAVIPPKESSKKVSNLGLNIEKPALTLHPQNDKVLMLAQETKMALCETCGSFLIANDALERTQSHVTGKQH...

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_008888`
TK1151 ID	TkA04G141770
OH-1004 ID	LXL04_008888
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	95.200
Protein coverage (%)	TK1151 18.806 / OH-1004 23.162 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_008888

Location Chr02:111252315-111255143 (+)

Description Similar to RH13: DEAD-box ATP-dependent RNA helicase 13

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g16840`	DEAD-box ATP-dependent RNA helicase 13.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0510400`	DEAD-box ATP-dependent RNA helicase 13.	No verified direct reference in this release
`UniProt: A2XVF7`	DEAD-box ATP-dependent RNA helicase 13.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_008888 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0009409 response to cold Biological Process

GO:0031425 chloroplast RNA processing Biological Process

GO:0042254 ribosome biogenesis 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:0005524 ATP binding Molecular Function

GO:0016887 ATP hydrolysis activity Molecular Function

KEGG gene cross-reference

ath:AT3G16840

ddi:DDB_G0281841

dosa:Os04g0510400

spo:2540874

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.

Nucleus0.375

Rank 1 · LXL04_008888 · OH-1004

Cytoplasm0.357

Rank 2 · LXL04_008888 · OH-1004

Mitochondrion0.157

Rank 3 · LXL04_008888 · OH-1004

Cell membrane0.083

Rank 4 · LXL04_008888 · OH-1004

Plastid0.073

Rank 5 · LXL04_008888 · 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.

PF19283.5APEH_N66-130 aa

PF00271.38Helicase_C126-183 aa

PF03194.21LUC7207-269 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008888	`PF19283.5`	APEH_N	66	130	3e-17	63.0
LXL04_008888	`PF00271.38`	Helicase_C	126	183	1.7e-16	61.1
LXL04_008888	`PF03194.21`	LUC7	207	269	1.2e-15	58.6

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
`Q93Y39`	Arabidopsis thaliana	DEAD-box ATP-dependent RNA helicase 13	49.600%	Swiss-Prot	weak database homology
`A3AVH5`	Oryza sativa subsp. japonica	DEAD-box ATP-dependent RNA helicase 13	39.726%	Swiss-Prot	moderate database homology
`A2XVF7`	Oryza sativa subsp. indica	DEAD-box ATP-dependent RNA helicase 13	39.726%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card