LXL04_008567 | RubberDandelionOmics

Gene overview

LXL04_008567

Reference: OH-1004 Chr: Chr02 Coordinates: 102881705-102884595 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1806 bp · LXL04_008567|LXL04_008567|OH1004|cDNA

ATGACAACTGCAACCACTGCACTGACTTCCACAACTACATCGGGACTCGGCGGTGGTAAACTTTGCTCCCAGAAGAGAATTGCCAATGATTTCGCCCTCAATACGGCGGTGAGCAGCTCTAATGGCTTCAATTGCTGGAGTGCTGCTACGAATCATCCTCGCAGACGCTTGGTGTTTACAAGGGCTTCTTCTTCGTCCCCTCCTCCGGAAACCGGCAACGATAAGCAGAAACAGGATCAGAGTGATGATGAGAGTGGTAT...

CDS

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1806 bp · LXL04_008567|LXL04_008567|OH1004|CDS

ATGACAACTGCAACCACTGCACTGACTTCCACAACTACATCGGGACTCGGCGGTGGTAAACTTTGCTCCCAGAAGAGAATTGCCAATGATTTCGCCCTCAATACGGCGGTGAGCAGCTCTAATGGCTTCAATTGCTGGAGTGCTGCTACGAATCATCCTCGCAGACGCTTGGTGTTTACAAGGGCTTCTTCTTCGTCCCCTCCTCCGGAAACCGGCAACGATAAGCAGAAACAGGATCAGAGTGATGATGAGAGTGGTAT...

Protein

Download Protein FASTA

601 aa · LXL04_008567|LXL04_008567|OH1004|PROTEIN

MTTATTALTSTTTSGLGGGKLCSQKRIANDFALNTAVSSSNGFNCWSAATNHPRRRLVFTRASSSSPPPETGNDKQKQDQSDDESGIDDDVEGNQKASSVSVMKRLVDANPVGLGRRSRQIFDEAWRKFSELGQISRTTRTNDESSLLIQEGGPMCEFAIPEAQNTTVLVVGATSRVGRIVVRKLMLRGYSVKALVRKADQEVVDMLPTSVKIVIGDVGDPATLRLAVEGCSKIIYCATARSSITVDLNRVDYQGVYNLS...

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_008567`
TK1151 ID	TkA03G358440
OH-1004 ID	LXL04_008567
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	97.600
Protein coverage (%)	TK1151 99.043 / OH-1004 68.885 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_008567

Location Chr02:102881705-102884595 (-)

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
`At5g02240`	Uncharacterized protein At5g02240.	No verified direct reference in this release
`At2g37660`	Uncharacterized protein At2g37660, chloroplastic.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_008567 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006413 translational initiation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0010207 photosystem II assembly Biological Process

GO:0015979 photosynthesis Biological Process

GO:0015995 chlorophyll biosynthetic process Biological Process

GO:0000325 plant-type vacuole 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

GO:0009535 chloroplast thylakoid membrane Cellular Component

KEGG gene cross-reference

ath:AT1G16720

ath:AT2G37660

ath:AT5G02240

syn:slr0399

zma:100281890

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.

Plastid0.974

Rank 1 · LXL04_008567 · OH-1004

Mitochondrion0.034

Rank 2 · LXL04_008567 · OH-1004

Nucleus0.022

Rank 3 · LXL04_008567 · OH-1004

Cytoplasm0.020

Rank 4 · LXL04_008567 · OH-1004

Cell membrane0.014

Rank 5 · LXL04_008567 · 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.

PF05368.20NmrA165-241 aa

PF13460.13NAD_binding_10172-262 aa

PF08547.19CIA30315-417 aa

PF13460.13NAD_binding_10468-553 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_008567	`PF05368.20`	NmrA	165	241	5.6e-09	36.7
LXL04_008567	`PF13460.13`	NAD_binding_10	172	262	1.3e-25	91.1
LXL04_008567	`PF08547.19`	CIA30	315	417	4.9e-09	37.1
LXL04_008567	`PF13460.13`	NAD_binding_10	468	553	1.3e-25	91.1

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	81.400%	Swiss-Prot	strong database homology
`Q94EG6`	Arabidopsis thaliana	Uncharacterized protein At5g02240	34.000%	Swiss-Prot	weak database homology
`O80934`	Arabidopsis thaliana	Uncharacterized protein At2g37660, chloroplastic	33.010%	Swiss-Prot	weak database homology

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