LXL04_017303 | RubberDandelionOmics

Gene overview

LXL04_017303

Reference: OH-1004 Chr: Chr03 Coordinates: 145957006-145961049 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1149 bp · LXL04_017303|LXL04_017303|OH1004|cDNA

ATGCGTGGTTTAGCAGCTAGATTCAGCTCCTATTTGTGCAGAAGAAGACCAGTGAATGTTCGATCACGCCAGTATTCGTCATCATATGAAAGAGGGTTTCCAGATGAACGAGATATTGAAGAGGAAGCCGAAAGAAAATTCGGATGGCTCTTTAAACTCCTCTTTGTTGGAACTGTAACAATCGGGAGAATGTTTCAAGACTATCACCAACCACTGTCTTTCAAAGTGCAACTTCAGTACAGATGGATGACCAAGGTTAT...

CDS

Download CDS FASTA

1149 bp · LXL04_017303|LXL04_017303|OH1004|CDS

ATGCGTGGTTTAGCAGCTAGATTCAGCTCCTATTTGTGCAGAAGAAGACCAGTGAATGTTCGATCACGCCAGTATTCGTCATCATATGAAAGAGGGTTTCCAGATGAACGAGATATTGAAGAGGAAGCCGAAAGAAAATTCGGATGGCTCTTTAAACTCCTCTTTGTTGGAACTGTAACAATCGGGAGAATGTTTCAAGACTATCACCAACCACTGTCTTTCAAAGTGCAACTTCAGTACAGATGGATGACCAAGGTTAT...

Protein

Download Protein FASTA

382 aa · LXL04_017303|LXL04_017303|OH1004|PROTEIN

MRGLAARFSSYLCRRRPVNVRSRQYSSSYERGFPDERDIEEEAERKFGWLFKLLFVGTVTIGRMFQDYHQPLSFKVQLQYRWMTKVMFVSEKLVIGVGYDCNPMVFAVIGVGLWATSCTLCSETNLLWEVELKLFVYVTMSKRITGGLAFNMNTLDEIQRITVKDLAELGLIKRQQGRKALVICVVEKVPSVPENVTDQIRLWESDLNRVEMTPAHFFDDFPSRDVFEAACDHARDYSCLLWDDSKKMRLVVKTEIYAHM...

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_017303`
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_017303

Location Chr03:145957006-145961049 (-)

Description Similar to TFB2: General transcription and DNA repair factor IIH subunit TFB2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g17020`	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.	No verified direct reference in this release
`At5g67380`	Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates.	Cloning and characterization of two cDNAs encoding casein kinase II catalytic subunits in Arabidopsis thaliana.1993 · DOI: 10.1007/bf00019944 Reconstitution of Arabidopsis casein kinase II from recombinant subunits and phosphorylation of transcription factor GBF1.1995 · DOI: 10.1105/tpc.7.1.105
`At3g50000`	Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates (By similarity).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: B6F107`	Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates.	No verified direct reference in this release
`UniProt: Q9AR27`	Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017303 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006468 protein phosphorylation Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007623 circadian rhythm Biological Process

GO:0009648 photoperiodism Biological Process

GO:0009908 flower development Biological Process

GO:0010225 response to UV-C Biological Process

GO:0010229 inflorescence development Biological Process

GO:0010332 response to gamma radiation Biological Process

KEGG gene cross-reference

ath:AT3G50000

ath:AT4G17020

ath:AT5G67380

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.

Mitochondrion0.846

Rank 1 · LXL04_017303 · OH-1004

Cytoplasm0.104

Rank 2 · LXL04_017303 · OH-1004

Nucleus0.087

Rank 3 · LXL04_017303 · OH-1004

Plastid0.046

Rank 4 · LXL04_017303 · OH-1004

Cell membrane0.035

Rank 5 · LXL04_017303 · 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.

PF18307.7Tfb2_C198-263 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017303	`PF18307.7`	Tfb2_C	198	263	4.2e-21	75.8

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
`Q680U9`	Arabidopsis thaliana	General transcription and DNA repair factor IIH subunit TFB2	67.949%	Swiss-Prot	weak database homology
`Q08467`	Arabidopsis thaliana	Casein kinase II subunit alpha-1	49.505%	Swiss-Prot	weak database homology
`Q08466`	Arabidopsis thaliana	Casein kinase II subunit alpha-2	48.980%	Swiss-Prot	weak database homology
`B6F107`	Oryza sativa subsp. japonica	Casein kinase II subunit alpha-2	46.939%	Swiss-Prot	weak database homology
`Q9AR27`	Oryza sativa subsp. indica	Casein kinase II subunit alpha-2	46.939%	Swiss-Prot	weak database homology

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