LXL04_034446 | RubberDandelionOmics

Gene overview

LXL04_034446

Reference: OH-1004 Chr: Chr07 Coordinates: 101011481-101016852 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1734 bp · LXL04_034446|LXL04_034446|OH1004|cDNA

ATGTTGAATGGTGATTTGCAGAGCGTTTCGTCTACAAGATTATGTAGGAGTAAGTTATCATCAAGACTTAATAATCCATTTCTTAAAGTAAATGACAAAATTAAGCCCATCTCTCATCAACATAATACATATTATTTGAGAACCTACAAGAAGACCATCTATGCGGAATCTCGAAATCAGGGTTGGGACTTTGGAAGATTTGTGAAGACATTGTATTTCTTTAATGGGCCTCCATCACCTATTAAgATGTTTGAAAGCCT...

CDS

Download CDS FASTA

1734 bp · LXL04_034446|LXL04_034446|OH1004|CDS

ATGTTGAATGGTGATTTGCAGAGCGTTTCGTCTACAAGATTATGTAGGAGTAAGTTATCATCAAGACTTAATAATCCATTTCTTAAAGTAAATGACAAAATTAAGCCCATCTCTCATCAACATAATACATATTATTTGAGAACCTACAAGAAGACCATCTATGCGGAATCTCGAAATCAGGGTTGGGACTTTGGAAGATTTGTGAAGACATTGTATTTCTTTAATGGGCCTCCATCACCTATTAAGATGTTTGAAAGCCT...

Protein

Download Protein FASTA

577 aa · LXL04_034446|LXL04_034446|OH1004|PROTEIN

MLNGDLQSVSSTRLCRSKLSSRLNNPFLKVNDKIKPISHQHNTYYLRTYKKTIYAESRNQGWDFGRFVKTLYFFNGPPSPIKMFESLIASFSGPSSSEPEKSMEASGIVLVAGATGGVGRRVVDVLRNKGLPVRVLVRNKEKAEKMLGPDIDMVVGDITKASTLLPDYFKGVTKVINAVSVIVGPKEGDTPDRAKYNQGIKFFEPEIKGDSPEMVEYIGMQNLIKALKDNVGLKSGKLVYGFEDGSSRILPWGALDDVVM...

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_034446`
TK1151 ID	TkA08G393400
OH-1004 ID	LXL04_034446
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	97.400
Protein coverage (%)	TK1151 100.000 / OH-1004 85.789 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

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Basic Information and Functional Annotation

Gene ID LXL04_034446

Location Chr07:101011481-101016852 (+)

Description Similar to HCF173: Protein HIGH CHLOROPHYLL FLUORESCENCE PHENOTYPE 173, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g16720`	Auxiliary factor required, together with HCF244, for the biogenesis of photosystem II (PSII), especially for the synthesis of the reaction center proteins (e.g. D1), via the regulation of the corresponding mRNA (e.g. psbA) translation initiation (ribosomal loading) and stabilization.	The nuclear-encoded factor HCF173 is involved in the initiation of translation of the psbA mRNA in Arabidopsis thaliana.2007 · DOI: 10.1105/tpc.106.042895 The Arabidopsis pentatricopeptide repeat protein LPE1 and its maize ortholog are required for translation of the chloroplast psbJ RNA.2019 · DOI: 10.1111/tpj.14308
`At1g17350`	Chaperone protein involved in the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex (complex I).	No verified direct reference in this release
`At5g02240`	Uncharacterized protein At5g02240.	No verified direct reference in this release
`At2g34460`	Uncharacterized protein At2g34460, chloroplastic.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_034446 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006120 mitochondrial electron transport, NADH to ubiquinone Biological Process

GO:0006413 translational initiation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0010207 photosystem II assembly Biological Process

GO:0032981 mitochondrial respiratory chain complex I assembly Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009523 photosystem II Cellular Component

KEGG gene cross-reference

ath:AT1G16720

ath:AT1G17350

ath:AT2G34460

ath:AT5G02240

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.

Plastid0.972

Rank 1 · LXL04_034446 · OH-1004

Mitochondrion0.044

Rank 2 · LXL04_034446 · OH-1004

Cytoplasm0.028

Rank 3 · LXL04_034446 · OH-1004

Peroxisome0.017

Rank 4 · LXL04_034446 · OH-1004

Nucleus0.016

Rank 5 · LXL04_034446 · 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.

PF05368.20NmrA108-180 aa

PF01370.28Epimerase109-182 aa

PF13460.13NAD_binding_10113-227 aa

PF08547.19CIA30248-407 aa

PF13460.13NAD_binding_10422-521 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_034446	`PF05368.20`	NmrA	108	180	1.1e-08	35.7
LXL04_034446	`PF01370.28`	Epimerase	109	182	6.3e-07	29.8
LXL04_034446	`PF13460.13`	NAD_binding_10	113	227	8e-27	95.0
LXL04_034446	`PF08547.19`	CIA30	248	407	1.3e-35	123.5
LXL04_034446	`PF13460.13`	NAD_binding_10	422	521	8e-27	95.0

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
`Q8W4D6`	Arabidopsis thaliana	Protein HIGH CHLOROPHYLL FLUORESCENCE PHENOTYPE 173, chloroplastic	28.571%	Swiss-Prot	weak database homology
`Q9LQI7`	Arabidopsis thaliana	Probable complex I intermediate-associated protein 30	25.967%	Swiss-Prot	weak database homology
`Q94EG6`	Arabidopsis thaliana	Uncharacterized protein At5g02240	31.858%	Swiss-Prot	weak database homology
`Q8H124`	Arabidopsis thaliana	Uncharacterized protein At2g34460, chloroplastic	32.759%	Swiss-Prot	weak database homology

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