LXL04_017791 | RubberDandelionOmics

Gene overview

LXL04_017791

Reference: OH-1004 Chr: Chr04 Coordinates: 1300132-1300798 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

618 bp · LXL04_017791|LXL04_017791|OH1004|cDNA

ATGCCTGAGAGAAATTGCCCGCAGACTATCAAGTCGTTCAATGCACTTCTCGGGGAGTGTGTTGAAGGGTTTTTCCGGGAGCTGTTTGAGAAACTATATTTGAAACCGGATATCGTCTCGTATAACACCGCGATCAAAGCTTTCTGCGATATGGGTTCATTTGATTCAGCTGCGACTCTATTTGGTGAAATCGAAAAGAACGGTATGGAACCTGATTTGATCACTTTCAATACTCTCCTCATCGGGTATTACGGAAACGG...

CDS

Download CDS FASTA

618 bp · LXL04_017791|LXL04_017791|OH1004|CDS

ATGCCTGAGAGAAATTGCCCGCAGACTATCAAGTCGTTCAATGCACTTCTCGGGGAGTGTGTTGAAGGGTTTTTCCGGGAGCTGTTTGAGAAACTATATTTGAAACCGGATATCGTCTCGTATAACACCGCGATCAAAGCTTTCTGCGATATGGGTTCATTTGATTCAGCTGCGACTCTATTTGGTGAAATCGAAAAGAACGGTATGGAACCTGATTTGATCACTTTCAATACTCTCCTCATCGGGTATTACGGAAACGG...

Protein

Download Protein FASTA

205 aa · LXL04_017791|LXL04_017791|OH1004|PROTEIN

MPERNCPQTIKSFNALLGECVEGFFRELFEKLYLKPDIVSYNTAIKAFCDMGSFDSAATLFGEIEKNGMEPDLITFNTLLIGYYGNGRFLDGEKLWAKMMNTNLTPDIRTYSAKLVGLLCFCNNGDLTEAKNWYAKLGQSDSSTNKATFAALIRLACKLNDYDWSIEHFQQTIEEKCIVDRNVVQLMIDGLVKEKKIEIASSFHP

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_017791`
TK1151 ID	TkA08G050620
OH-1004 ID	LXL04_017791
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	98.500
Protein coverage (%)	TK1151 47.518 / OH-1004 32.683 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

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Basic Information and Functional Annotation

Gene ID LXL04_017791

Location Chr04:1300132-1300798 (-)

Description Similar to At1g55890: Pentatricopeptide repeat-containing protein At1g55890, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g55890`	Small ribosomal subunit protein mS78 (rPPR3a).	No verified direct reference in this release
`At3g13160`	Small ribosomal subunit protein mS79 (rPPR3b).	No verified direct reference in this release
`At3g13150`	Pentatricopeptide repeat-containing protein At3g13150.	No verified direct reference in this release
`At1g62680`	Pentatricopeptide repeat-containing protein At1g62680, mitochondrial.	No verified direct reference in this release
`At1g09680`	Putative pentatricopeptide repeat-containing protein At1g09680.	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_017791 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006396 RNA processing Biological Process

GO:0007005 mitochondrion organization Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005829 cytosol Cellular Component

GO:0005840 ribosome Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G55890

ath:AT1G62680

ath:AT3G13150

ath:AT3G13160

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.

Mitochondrion0.805

Rank 1 · LXL04_017791 · OH-1004

Plastid0.069

Rank 2 · LXL04_017791 · OH-1004

Nucleus0.047

Rank 3 · LXL04_017791 · OH-1004

Cytoplasm0.044

Rank 4 · LXL04_017791 · OH-1004

Cell membrane0.010

Rank 5 · LXL04_017791 · 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.

PF12854.14PPR_134-64 aa

PF13812.13PPR_334-86 aa

PF13041.13PPR_236-83 aa

PF01535.27PPR39-68 aa

PF13041.13PPR_271-113 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017791	`PF12854.14`	PPR_1	34	64	2.3e-16	60.0
LXL04_017791	`PF13812.13`	PPR_3	34	86	3.6e-12	46.9
LXL04_017791	`PF13041.13`	PPR_2	36	83	1.1e-25	90.1
LXL04_017791	`PF01535.27`	PPR	39	68	1.3e-16	60.2
LXL04_017791	`PF13041.13`	PPR_2	71	113	1.1e-25	90.1

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
`Q9LG23`	Arabidopsis thaliana	Small ribosomal subunit protein mS78 (rPPR3a)	38.750%	Swiss-Prot	moderate database homology
`Q9LK57`	Arabidopsis thaliana	Small ribosomal subunit protein mS79 (rPPR3b)	37.288%	Swiss-Prot	moderate database homology
`Q9LK58`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g13150	33.333%	Swiss-Prot	moderate database homology
`Q3ECK2`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g62680, mitochondrial	29.016%	Swiss-Prot	weak database homology
`O04491`	Arabidopsis thaliana	Putative pentatricopeptide repeat-containing protein At1g09680	29.703%	Swiss-Prot	weak database homology

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