LXL04_028537 | RubberDandelionOmics

Gene overview

LXL04_028537

Reference: OH-1004 Chr: Chr06 Coordinates: 44808523-44810763 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2241 bp · LXL04_028537|LXL04_028537|OH1004|cDNA

ATGTTGTTAAGGAAGTTGAGATATGGGAACTCAAACGCTCTTTATGCAATTCAAGCCATGTTTTGCAGTAATCTTAACGCTATCAGAGTACCCAGATGCCACCTCGCAAGGTATTCTTCTTCCATGGCAGTTAATAACACATTTAGATGGCAATCTTTTTCAACTATGGGCAGCACAATCTTGGTCCAAGCTAGAGACCCTGGTAAGCTAAGTGAGGAGTTGCAAACTGCACTTGATGAACATAGGCTTAATGATGCTTG...

CDS

Download CDS FASTA

2241 bp · LXL04_028537|LXL04_028537|OH1004|CDS

ATGTTGTTAAGGAAGTTGAGATATGGGAACTCAAACGCTCTTTATGCAATTCAAGCCATGTTTTGCAGTAATCTTAACGCTATCAGAGTACCCAGATGCCACCTCGCAAGGTATTCTTCTTCCATGGCAGTTAATAACACATTTAGATGGCAATCTTTTTCAACTATGGGCAGCACAATCTTGGTCCAAGCTAGAGACCCTGGTAAGCTAAGTGAGGAGTTGCAAACTGCACTTGATGAACATAGGCTTAATGATGCTTG...

Protein

Download Protein FASTA

746 aa · LXL04_028537|LXL04_028537|OH1004|PROTEIN

MLLRKLRYGNSNALYAIQAMFCSNLNAIRVPRCHLARYSSSMAVNNTFRWQSFSTMGSTILVQARDPGKLSEELQTALDEHRLNDAWNLHEQHMNMEGFPRKSIVNNLLTTSAQSLQLEWLNNAYHLVQKAIDEHKQNLLEKQTLIYLSLCLSIHGLPINAAVILRKLLETQQFPPVTAWSAILAYMSQTPSGAYLAAELVLEIGFIFQDGRVDPRKKSNEDLICMKPNTTAVNIALGGCLLFGTNRKAEQLLDMIPRIG...

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_028537`
TK1151 ID	TkA07G166690
OH-1004 ID	LXL04_028537
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.300
Protein coverage (%)	TK1151 100.000 / OH-1004 92.627 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_028537

Location Chr06:44808523-44810763 (+)

Description Similar to At1g03100: Pentatricopeptide repeat-containing protein At1g03100, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g03100`	Pentatricopeptide repeat-containing protein At1g03100, mitochondrial.	No verified direct reference in this release
`At4g17616`	Pentatricopeptide repeat-containing protein At4g17616.	No verified direct reference in this release
`At1g69290`	Pentatricopeptide repeat-containing protein At1g69290.	No verified direct reference in this release
`At1g68980`	Pentatricopeptide repeat-containing protein At1g68980, mitochondrial.	No verified direct reference in this release
`At3g09650`	Involved in the processing of polycistronic chloroplast psbB- psbT-psbH-petB-petD transcript.	The nucleus-encoded HCF107 gene of Arabidopsis provides a link between intercistronic RNA processing and the accumulation of translation-competent psbH transcripts in chloroplasts.2001 · DOI: 10.1105/tpc.010090 HCF152, an Arabidopsis RNA binding pentatricopeptide repeat protein involved in the processing of chloroplast psbB-psbT-psbH-petB-petD RNAs.2003 · DOI: 10.1105/tpc.010397

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028537 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0005739 mitochondrion Cellular Component

GO:0009507 chloroplast Cellular Component

KEGG gene cross-reference

ath:AT1G03100

ath:AT1G68980

ath:AT1G69290

ath:AT4G17616

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.

Mitochondrion0.842

Rank 1 · LXL04_028537 · OH-1004

Plastid0.092

Rank 2 · LXL04_028537 · OH-1004

Nucleus0.063

Rank 3 · LXL04_028537 · OH-1004

Cytoplasm0.046

Rank 4 · LXL04_028537 · OH-1004

Cell membrane0.014

Rank 5 · LXL04_028537 · 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.

PF25245.1TPR_At1g6898068-190 aa

PF13041.13PPR_2495-537 aa

PF13812.13PPR_3515-560 aa

PF13041.13PPR_2595-638 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028537	`PF25245.1`	TPR_At1g68980	68	190	4.2e-08	34.1
LXL04_028537	`PF13041.13`	PPR_2	495	537	7.9e-27	93.8
LXL04_028537	`PF13812.13`	PPR_3	515	560	1.6e-11	44.8
LXL04_028537	`PF13041.13`	PPR_2	595	638	7.9e-27	93.8

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
`Q9SA60`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g03100, mitochondrial	60.027%	Swiss-Prot	strong database homology
`B3H672`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g17616	26.579%	Swiss-Prot	weak database homology
`P0C7R4`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g69290	35.015%	Swiss-Prot	weak database homology
`Q9CAA5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At1g68980, mitochondrial	31.928%	Swiss-Prot	weak database homology
`Q9SF38`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g09650, chloroplastic	26.761%	Swiss-Prot	weak database homology

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