LXL04_025409 | RubberDandelionOmics

Gene overview

LXL04_025409

Reference: OH-1004 Chr: Chr05 Coordinates: 111208664-111211060 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1530 bp · LXL04_025409|LXL04_025409|OH1004|cDNA

ATGGAGCATGCCCTACACTTAGGTGGTCTATCCCCAACTATGCTCGGATCATTTTCCACACCAAATCAGCATATCCCAAACCCTATTGCATATAATTGGAGTAATCAGTCTCATAACCTGCGTACTAATGACAGAATTTCATCCGTCTTCTTTCACAAATGCCGCCAGAGCACATATGAACAACACCGGCCACAAAAACCCAGAACCTCCATTATCGCGTGTCATCCTCCTACCCGCGATTATCATAGAAACAAGAAGCG...

CDS

Download CDS FASTA

1530 bp · LXL04_025409|LXL04_025409|OH1004|CDS

ATGGAGCATGCCCTACACTTAGGTGGTCTATCCCCAACTATGCTCGGATCATTTTCCACACCAAATCAGCATATCCCAAACCCTATTGCATATAATTGGAGTAATCAGTCTCATAACCTGCGTACTAATGACAGAATTTCATCCGTCTTCTTTCACAAATGCCGCCAGAGCACATATGAACAACACCGGCCACAAAAACCCAGAACCTCCATTATCGCGTGTCATCCTCCTACCCGCGATTATCATAGAAACAAGAAGCG...

Protein

Download Protein FASTA

509 aa · LXL04_025409|LXL04_025409|OH1004|PROTEIN

MEHALHLGGLSPTMLGSFSTPNQHIPNPIAYNWSNQSHNLRTNDRISSVFFHKCRQSTYEQHRPQKPRTSIIACHPPTRDYHRNKKRLTPPQNTDLPPQLPKQKKKPFPIPLKKILQTARADKKLAEKGIEKPLDPPKNGLLVPELVPIAYEVLDAWKLLIKGLSQLLHVIPVHACSECGEIHVGPTGHNIQTCHGPNSANRRSFHLWVKGTITDVLLPIESYHQFDPFGTRIKHETRFKYDRIPAVVELCIQAGVELPE...

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_025409`
TK1151 ID	TkA06G061050
OH-1004 ID	LXL04_025409
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.600
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_025409

Location Chr05:111208664-111211060 (-)

Description Similar to APO1: APO protein 1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g64810`	Involved in the stable assembly of several 4Fe-4S cluster- containing complexes of chloroplasts.	ACCUMULATION OF PHOTOSYSTEM ONE1, a member of a novel gene family, is required for accumulation of [4Fe-4S] cluster-containing chloroplast complexes and antenna proteins.2004 · DOI: 10.1105/tpc.104.024935
`At5g57930`	May be involved in the stable assembly of several 4Fe-4S cluster-containing complexes of chloroplasts.	No verified direct reference in this release
`At5g61930`	May be involved in the stable assembly of several 4Fe-4S cluster-containing complexes of mitochondria.	No verified direct reference in this release
`At3g21740`	May be involved in the stable assembly of several 4Fe-4S cluster-containing complexes of mitochondria.	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_025409 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000373 Group II intron splicing Biological Process

GO:0009615 response to virus Biological Process

GO:0009658 chloroplast organization Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0015979 photosynthesis Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

KEGG gene cross-reference

ath:AT1G64810

ath:AT3G21740

ath:AT5G57930

ath:AT5G61930

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Plastid0.924

Rank 1 · LXL04_025409 · OH-1004

Nucleus0.055

Rank 2 · LXL04_025409 · OH-1004

Mitochondrion0.053

Rank 3 · LXL04_025409 · OH-1004

Cytoplasm0.037

Rank 4 · LXL04_025409 · OH-1004

Cell membrane0.028

Rank 5 · LXL04_025409 · 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.

PF05634.17APO_RNA-bind84-279 aa

PF05634.17APO_RNA-bind307-430 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025409	`PF05634.17`	APO_RNA-bind	84	279	5.4e-123	408.6
LXL04_025409	`PF05634.17`	APO_RNA-bind	307	430	5.4e-123	408.6

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
`Q9XIR4`	Arabidopsis thaliana	APO protein 1, chloroplastic	65.608%	Swiss-Prot	strong database homology
`Q8W4A5`	Arabidopsis thaliana	APO protein 2, chloroplastic	49.157%	Swiss-Prot	moderate database homology
`Q9FH50`	Arabidopsis thaliana	APO protein 3, mitochondrial	43.132%	Swiss-Prot	moderate database homology
`Q9LSZ0`	Arabidopsis thaliana	APO protein 4, mitochondrial	37.542%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card