LXL04_036984 | RubberDandelionOmics

Gene overview

LXL04_036984

Reference: OH-1004 Chr: Chr08 Coordinates: 51219277-51223768 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2274 bp · LXL04_036984|LXL04_036984|OH1004|cDNA

ATGAAGTTCCAAATCGAAGATGTAACAGTCTACTTCCCATACGATCACATATACCCCGAACAGTACTCCTACATGATCGAACTCAAACGAGCCCTAGACGCCAAAGGACATTGCCTCCTTGAAATGCCCACCGGTACCGGAAAAACCATCGCCCTTCTCTCATTGATCACCAGCTACACTCTCTCCAAACCATCTAACCCCGTTAAGCTACTCTACTGTACTCGCACGGTTCACGAGATGGAAAAAACCCTAGCTGAGCT...

CDS

Download CDS FASTA

2274 bp · LXL04_036984|LXL04_036984|OH1004|CDS

ATGAAGTTCCAAATCGAAGATGTAACAGTCTACTTCCCATACGATCACATATACCCCGAACAGTACTCCTACATGATCGAACTCAAACGAGCCCTAGACGCCAAAGGACATTGCCTCCTTGAAATGCCCACCGGTACCGGAAAAACCATCGCCCTTCTCTCATTGATCACCAGCTACACTCTCTCCAAACCATCTAACCCCGTTAAGCTACTCTACTGTACTCGCACGGTTCACGAGATGGAAAAAACCCTAGCTGAGCT...

Protein

Download Protein FASTA

757 aa · LXL04_036984|LXL04_036984|OH1004|PROTEIN

MKFQIEDVTVYFPYDHIYPEQYSYMIELKRALDAKGHCLLEMPTGTGKTIALLSLITSYTLSKPSNPVKLLYCTRTVHEMEKTLAELKLLHKYQLENIGPSARMLALGLSSRKNLCINPEVVSAENRDSVDAGCRKLTASWVRALAIENPNIPTCSFYERYEKAGSDAVLPPGVYTLQDLRIFGKDKGWCPYFLARHMVQFANVVVYSYQYLLDPKVAGIISKEMQRESVVVFDEAHNIDNVCIEALSVSVRKQTLEGAT...

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_036984`
TK1151 ID	TkA04G012240
OH-1004 ID	LXL04_036984
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.900
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

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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_036984

Location Chr08:51219277-51223768 (+)

Description Similar to XPD: General transcription and DNA repair factor IIH helicase subunit XPD

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g03190`	ATP-dependent 5'-3' DNA helicase, component of the general transcription and DNA repair factor IIH (TFIIH) core complex, which is involved in general and transcription-coupled nucleotide excision repair (NER) of damaged DNA and, when complexed to CDK-activating kinase (CAK), involved in transcription by RNA polymerase II.	Arabidopsis UVH6, a homolog of human XPD and yeast RAD3 DNA repair genes, functions in DNA repair and is essential for plant growth.2003 · DOI: 10.1104/pp.103.021808 Evidence that heat and ultraviolet radiation activate a common stress-response program in plants that is altered in the uvh6 mutant of Arabidopsis thaliana.1997 · DOI: 10.1104/pp.115.4.1351

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_036984 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006281 DNA repair Biological Process

GO:0006283 transcription-coupled nucleotide-excision repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006362 transcription elongation by RNA polymerase I Biological Process

GO:0006366 transcription by RNA polymerase II Biological Process

GO:0006367 transcription initiation at RNA polymerase II promoter Biological Process

GO:0006979 response to oxidative stress Biological Process

GO:0007059 chromosome segregation Biological Process

GO:0008283 cell population proliferation Biological Process

GO:0008340 determination of adult lifespan Biological Process

KEGG gene cross-reference

ath:AT1G03190

bta:100125238

hsa:2068

mmu:13871

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.

Nucleus0.662

Rank 1 · LXL04_036984 · OH-1004

Cytoplasm0.355

Rank 2 · LXL04_036984 · OH-1004

Cell membrane0.041

Rank 3 · LXL04_036984 · OH-1004

Golgi apparatus0.041

Rank 4 · LXL04_036984 · OH-1004

Endoplasmic reticulum0.039

Rank 5 · LXL04_036984 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF04851.22ResIII24-77 aa

PF06733.22DEAD_272-256 aa

PF06777.18HBB270-413 aa

PF13307.13Helicase_C_2524-697 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036984	`PF04851.22`	ResIII	24	77	7.2e-07	30.0
LXL04_036984	`PF06733.22`	DEAD_2	72	256	4.3e-51	173.7
LXL04_036984	`PF06777.18`	HBB	270	413	1.9e-41	142.1
LXL04_036984	`PF13307.13`	Helicase_C_2	524	697	9.8e-39	133.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8W4M7`	Arabidopsis thaliana	General transcription and DNA repair factor IIH helicase subunit XPD	83.773%	Swiss-Prot	strong database homology

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