LXL04_021716 | RubberDandelionOmics

Gene overview

LXL04_021716

Reference: OH-1004 Chr: Chr04 Coordinates: 135820249-135832253 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2148 bp · LXL04_021716|LXL04_021716|OH1004|cDNA

ATGGCGATTCTTGTCTACCCCAGCATTCCAACTGCCTTGCTCTTGCAAAATCGTCGTCGATCAGTTCTACCAACTCCGGTCCGGTGTTCTTCTTCCGGCACTGTAAAATCCCCCACGTCTAAGGTAATAACAAGTTCCAATGGCGGAAAAAGCACGGGCGCTGCAGTTCTCTGGTACAAGAATGATCTTCGTGTCGATGACCATCCAGGTTTAATTGCTGCCTCCAAACATACTGTGGTTGTTCCTCTTTATGTCTACGA...

CDS

Download CDS FASTA

2148 bp · LXL04_021716|LXL04_021716|OH1004|CDS

ATGGCGATTCTTGTCTACCCCAGCATTCCAACTGCCTTGCTCTTGCAAAATCGTCGTCGATCAGTTCTACCAACTCCGGTCCGGTGTTCTTCTTCCGGCACTGTAAAATCCCCCACGTCTAAGGTAATAACAAGTTCCAATGGCGGAAAAAGCACGGGCGCTGCAGTTCTCTGGTACAAGAATGATCTTCGTGTCGATGACCATCCAGGTTTAATTGCTGCCTCCAAACATACTGTGGTTGTTCCTCTTTATGTCTACGA...

Protein

Download Protein FASTA

715 aa · LXL04_021716|LXL04_021716|OH1004|PROTEIN

MAILVYPSIPTALLLQNRRRSVLPTPVRCSSSGTVKSPTSKVITSSNGGKSTGAAVLWYKNDLRVDDHPGLIAASKHTVVVPLYVYDHRILRYFTEEMLELLLFAVKDLRKSLKDVGSDLMIRSGRTESVIHDLVKEVRAANIYTEAEVEYDLQLVIEKVKDNLGDIKSPKLSLWSTPFYDIKNIMEIPLSYDKFQQIKLSVNSPLSSPKLHGTSTDLTWGTLPTLNDLKKLINDNPYKSKDSWTSIKNNSAESILQNAR...

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_021716`
TK1151 ID	TkA05G417310
OH-1004 ID	LXL04_021716
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.900
Protein coverage (%)	TK1151 99.860 / OH-1004 99.021 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_021716

Location Chr04:135820249-135832253 (+)

Description Similar to PPH: Pheophytinase, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g13800`	Alpha/beta hydrolase dephytylating specifically the Mg-free chlorophyll pigment (pheophytin), yielding pheophorbide.	Reverse genetic identification of CRN1 and its distinctive role in chlorophyll degradation in Arabidopsis.2010 · DOI: 10.1111/j.1744-7909.2010.00945.x
`At5g24850`	May have a photoreceptor function.	No verified direct reference in this release
`At2g47590`	Blue-light photoreceptor PHR2.	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_021716 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000719 photoreactive repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0015996 chlorophyll catabolic process Biological Process

GO:0005634 nucleus Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009536 plastid Cellular Component

GO:0009570 chloroplast stroma Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0003904 deoxyribodipyrimidine photo-lyase activity Molecular Function

KEGG gene cross-reference

ath:AT2G47590

ath:AT5G13800

ath:AT5G24850

gvi:glr0835

nph:NP_3456A

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.

Plastid0.926

Rank 1 · LXL04_021716 · OH-1004

Mitochondrion0.050

Rank 2 · LXL04_021716 · OH-1004

Cytoplasm0.036

Rank 3 · LXL04_021716 · OH-1004

Nucleus0.031

Rank 4 · LXL04_021716 · OH-1004

Cell membrane0.027

Rank 5 · LXL04_021716 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF00875.25DNA_photolyase55-185 aa

PF00561.27Abhydrolase_1432-538 aa

PF12146.16Hydrolase_4433-549 aa

PF12697.14Abhydrolase_6434-676 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_021716	`PF00875.25`	DNA_photolyase	55	185	5.3e-19	69.5
LXL04_021716	`PF00561.27`	Abhydrolase_1	432	538	7e-18	65.9
LXL04_021716	`PF12146.16`	Hydrolase_4	433	549	1e-07	32.2
LXL04_021716	`PF12697.14`	Abhydrolase_6	434	676	6.2e-17	63.7

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
`Q9FFZ1`	Arabidopsis thaliana	Pheophytinase, chloroplastic	27.157%	Swiss-Prot	weak database homology
`Q84KJ5`	Arabidopsis thaliana	Cryptochrome DASH, chloroplastic/mitochondrial	29.187%	Swiss-Prot	weak database homology
`Q8LB72`	Arabidopsis thaliana	Blue-light photoreceptor PHR2	26.400%	Swiss-Prot	weak database homology

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