LXL04_002546 | RubberDandelionOmics

Gene overview

LXL04_002546

Reference: OH-1004 Chr: Chr01 Coordinates: 51364040-51369043 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1740 bp · LXL04_002546|LXL04_002546|OH1004|cDNA

ATGGCCACGGTGGCCAAATTTCACATGGTTCCGGCTGTCTTCCACCACAGAACCACCCAACTGGGCTTCTGCCGGACCTCAGTCTCGTGGGACTCAATTCCGCCGCTTTCTCGACGGAGGGTGTTTCTGCAGCCGTGTAGGTCGTTTAGAACCGAAAATGGAGGTGCAAAAGATAATAAAAGTACGAAGAAGCTAGCGAATtctgataaaaataaaagaaaaaatttACTGGGAGCTATCAAATCTTTCATCTTTTCGAA...

CDS

Download CDS FASTA

1740 bp · LXL04_002546|LXL04_002546|OH1004|CDS

ATGGCCACGGTGGCCAAATTTCACATGGTTCCGGCTGTCTTCCACCACAGAACCACCCAACTGGGCTTCTGCCGGACCTCAGTCTCGTGGGACTCAATTCCGCCGCTTTCTCGACGGAGGGTGTTTCTGCAGCCGTGTAGGTCGTTTAGAACCGAAAATGGAGGTGCAAAAGATAATAAAAGTACGAAGAAGCTAGCGAATTCTGATAAAAATAAAAGAAAAAATTTACTGGGAGCTATCAAATCTTTCATCTTTTCGAA...

Protein

Download Protein FASTA

579 aa · LXL04_002546|LXL04_002546|OH1004|PROTEIN

MATVAKFHMVPAVFHHRTTQLGFCRTSVSWDSIPPLSRRRVFLQPCRSFRTENGGAKDNKSTKKLANSDKNKRKNLLGAIKSFIFSKDNSMEKLEENLSKIALHLGRYIVTMMSTGVILVIGFNLSGGDGQMNDLIWYSWVGGIIIGTMIGSNMVLDEVSRAGPRNVVITGSTRGLGKALAREFLLSGDRVVIASRSEESVDMTIKELEENLQEGIATAPSSCRKNLAHAKVVGTSCDVCDPNDVRNLANFAVNELGSID...

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_002546`
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_002546

Location Chr01:51364040-51369043 (+)

Description Similar to NYC1: Probable chlorophyll(ide) b reductase NYC1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g13250`	Involved in chlorophyll b degradation.	Participation of chlorophyll b reductase in the initial step of the degradation of light-harvesting chlorophyll a/b-protein complexes in Arabidopsis.2009 · DOI: 10.1074/jbc.m109.008912
`At5g04900`	Required for chlorophyll b degradation.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0227100`	Required for proper chloroplast degradation.	No verified direct reference in this release
`Os03g0654600`	Required for chlorophyll b degradation.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002546 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010304 PSII associated light-harvesting complex II catabolic process Biological Process

GO:0015996 chlorophyll catabolic process Biological Process

GO:0005886 plasma membrane Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0009536 plastid Cellular Component

GO:0016491 oxidoreductase activity Molecular Function

GO:0034256 chlorophyll(ide) b reductase activity Molecular Function

KEGG gene cross-reference

ath:AT4G13250

ath:AT5G04900

dosa:Os01g0227100

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.

Plastid0.905

Rank 1 · LXL04_002546 · OH-1004

Mitochondrion0.071

Rank 2 · LXL04_002546 · OH-1004

Nucleus0.039

Rank 3 · LXL04_002546 · OH-1004

Cytoplasm0.031

Rank 4 · LXL04_002546 · OH-1004

Golgi apparatus0.017

Rank 5 · LXL04_002546 · 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.

PF00106.32adh_short166-285 aa

PF13561.13adh_short_C2173-286 aa

PF00106.32adh_short347-444 aa

PF13561.13adh_short_C2351-445 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002546	`PF00106.32`	adh_short	166	285	2.2e-32	112.8
LXL04_002546	`PF13561.13`	adh_short_C2	173	286	3.3e-20	73.4
LXL04_002546	`PF00106.32`	adh_short	347	444	2.2e-32	112.8
LXL04_002546	`PF13561.13`	adh_short_C2	351	445	3.3e-20	73.4

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
`Q93ZA0`	Arabidopsis thaliana	Probable chlorophyll(ide) b reductase NYC1, chloroplastic	83.796%	Swiss-Prot	weak database homology
`Q8LEU3`	Arabidopsis thaliana	Chlorophyll(ide) b reductase NOL, chloroplastic	48.031%	Swiss-Prot	weak database homology
`Q5N800`	Oryza sativa subsp. japonica	Probable chlorophyll(ide) b reductase NYC1, chloroplastic	73.432%	Swiss-Prot	weak database homology
`Q84ST4`	Oryza sativa subsp. japonica	Chlorophyll(ide) b reductase NOL, chloroplastic	44.275%	Swiss-Prot	weak database homology

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