LXL04_004459 | RubberDandelionOmics

Gene overview

LXL04_004459

Reference: OH-1004 Chr: Chr01 Coordinates: 136727399-136730214 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1293 bp · LXL04_004459|LXL04_004459|OH1004|cDNA

ATGAGCAACTTCGGCAACGGCAAAGGGAAGCCGATGAACGGGGACGACGACGACGACGAAGATGAAGGAAACGAGAGAGACCTCGAAGCTTGGGAGAGAGCATACGCAGACGAGCGGTCCTGGGAATCATTACAAGAAGATGAATCTGGACTCCTTCGGCCAATCGATAACCAAGCTTTACATCACGCTCAATATCGCCGCCGTCTCCGTTCACTCTCCTCGGCATCCGCCGCCTCACGTATTCAAAAAGGCCTCATTCG...

CDS

Download CDS FASTA

1293 bp · LXL04_004459|LXL04_004459|OH1004|CDS

ATGAGCAACTTCGGCAACGGCAAAGGGAAGCCGATGAACGGGGACGACGACGACGACGAAGATGAAGGAAACGAGAGAGACCTCGAAGCTTGGGAGAGAGCATACGCAGACGAGCGGTCCTGGGAATCATTACAAGAAGATGAATCTGGACTCCTTCGGCCAATCGATAACCAAGCTTTACATCACGCTCAATATCGCCGCCGTCTCCGTTCACTCTCCTCGGCATCCGCCGCCTCACGTATTCAAAAAGGCCTCATTCG...

Protein

Download Protein FASTA

430 aa · LXL04_004459|LXL04_004459|OH1004|PROTEIN

MSNFGNGKGKPMNGDDDDDEDEGNERDLEAWERAYADERSWESLQEDESGLLRPIDNQALHHAQYRRRLRSLSSASAASRIQKGLIRYLYLVIDLSRAAGEMDLRPSRMVVVAKQVEAFVREFFDQNPLSQIGLITIKNGVAQCLTDLGGSPESHIKALMGKLGCAGEASLQNALELVHEQLDKIPSYGHREVIILYSALSTCDPGDVLETIQKCKKSKIRCSVIGLSAEIYICKYLCQETGGLYSVALDEVSPKKEISN...

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_004459`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004459

Location Chr01:136727399-136730214 (+)

Description Similar to GTF2H2: General transcription factor IIH subunit 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g05055`	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 CAK, in RNA transcription by RNA polymerase II.	Arabidopsis homologue of human transcription factor IIH/nucleotide excision repair factor p44 can function in transcription and DNA repair and interacts with AtXPD.2006 · DOI: 10.1111/j.1365-313x.2006.02705.x

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_004459 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0002031 G protein-coupled receptor internalization Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

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

GO:0006366 transcription by RNA polymerase II Biological Process

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

GO:0009411 response to UV Biological Process

GO:0000438 core TFIIH complex portion of holo TFIIH complex Cellular Component

GO:0000439 transcription factor TFIIH core complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005669 transcription factor TFIID complex Cellular Component

KEGG gene cross-reference

ath:AT1G05055

bta:511829

ddi:DDB_G0272362

hsa:2966

rno:294693

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.

Cytoplasm0.443

Rank 1 · LXL04_004459 · OH-1004

Nucleus0.401

Rank 2 · LXL04_004459 · OH-1004

Golgi apparatus0.152

Rank 3 · LXL04_004459 · OH-1004

Lysosome / Vacuole0.136

Rank 4 · LXL04_004459 · OH-1004

Cell membrane0.109

Rank 5 · LXL04_004459 · 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.

PF13519.13VWA_290-197 aa

PF04056.21Ssl192-293 aa

PF27618.1Zn_ribbon_GTF2H2317-347 aa

PF07975.19C1_4374-422 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004459	`PF13519.13`	VWA_2	90	197	9.1e-10	39.8
LXL04_004459	`PF04056.21`	Ssl1	92	293	1.6e-81	273.5
LXL04_004459	`PF27618.1`	Zn_ribbon_GTF2H2	317	347	3.3e-07	30.5
LXL04_004459	`PF07975.19`	C1_4	374	422	7e-18	65.3

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
`Q9ZVN9`	Arabidopsis thaliana	General transcription factor IIH subunit 2	77.171%	Swiss-Prot	strong database homology

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