LXL04_006087 | RubberDandelionOmics

Gene overview

LXL04_006087

Reference: OH-1004 Chr: Chr02 Coordinates: 1545304-1549132 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1344 bp · LXL04_006087|LXL04_006087|OH1004|cDNA

ATGAAGTTCCTCCGTTCTATCTCCGCGAATCGCCAGCCATTGCTTGCAGCTCTCGGCCGTCGTCAATTTGCCGTCTCCGCCGACGATTACGCCAAGAGAAACTACGCCAACAATGTCTCTGAATACAATACAGTCATTGGATCTCTCACTTCTCAAAGAAGGATTTACTTGTTGAGAGATGTATACGATGATATGATGCTGGATGGAGTTAAACCAGAGAAAGACACATTTCGCGCGCTGATTGCTGGTAGCATGAAAGG...

CDS

Download CDS FASTA

1344 bp · LXL04_006087|LXL04_006087|OH1004|CDS

ATGAAGTTCCTCCGTTCTATCTCCGCGAATCGCCAGCCATTGCTTGCAGCTCTCGGCCGTCGTCAATTTGCCGTCTCCGCCGACGATTACGCCAAGAGAAACTACGCCAACAATGTCTCTGAATACAATACAGTCATTGGATCTCTCACTTCTCAAAGAAGGATTTACTTGTTGAGAGATGTATACGATGATATGATGCTGGATGGAGTTAAACCAGAGAAAGACACATTTCGCGCGCTGATTGCTGGTAGCATGAAAGG...

Protein

Download Protein FASTA

447 aa · LXL04_006087|LXL04_006087|OH1004|PROTEIN

MKFLRSISANRQPLLAALGRRQFAVSADDYAKRNYANNVSEYNTVIGSLTSQRRIYLLRDVYDDMMLDGVKPEKDTFRALIAGSMKGVRLQDCFYFRDQMKSMGLIPDVVLYNFMISTCGKCKNSTEATRIFEEMKKLEVKPTGQTFICLINACAATGRLDQVYAIIRDMTAAGLGLNKFCYAGLIAAHKNKTPLPKDTSTKILELVEQSKGWSSLEQTRDSAENVMMGISEEELYDIPTANYIHRRGGFVQRFLTVYHV...

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_006087`
TK1151 ID	TkA03G008860
OH-1004 ID	LXL04_006087
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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_006087

Location Chr02:1545304-1549132 (-)

Description Similar to At4g35850: Pentatricopeptide repeat-containing protein At4g35850, mitochondrial

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g35850`	Pentatricopeptide repeat-containing protein At4g35850, mitochondrial.	No verified direct reference in this release
`At5g25630`	Pentatricopeptide repeat-containing protein At5g25630.	No verified direct reference in this release
`At3g53700`	May be involved in female gametophyte development.	No verified direct reference in this release
`At2g37230`	Large ribosomal subunit protein mL102 (rPPR5).	No verified direct reference in this release
`At4g19440`	Pentatricopeptide repeat-containing protein At4g19440, chloroplastic.	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_006087 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009409 response to cold Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0010239 chloroplast mRNA processing Biological Process

GO:0005739 mitochondrion Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005840 ribosome Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0009534 chloroplast thylakoid Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0042644 chloroplast nucleoid Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT2G37230

ath:AT3G53700

ath:AT4G35850

ath:AT5G25630

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.

Mitochondrion0.937

Rank 1 · LXL04_006087 · OH-1004

Nucleus0.040

Rank 2 · LXL04_006087 · OH-1004

Cytoplasm0.036

Rank 3 · LXL04_006087 · OH-1004

Plastid0.022

Rank 4 · LXL04_006087 · OH-1004

Cell membrane0.014

Rank 5 · LXL04_006087 · 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.

PF29070.1MSC6_N21-167 aa

PF13041.13PPR_238-83 aa

PF17177.11PPR_long55-171 aa

PF13812.13PPR_361-121 aa

PF13812.13PPR_398-154 aa

PF12854.14PPR_1103-136 aa

PF13041.13PPR_2107-155 aa

PF01535.27PPR110-138 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_006087	`PF29070.1`	MSC6_N	21	167	3.4e-11	43.6
LXL04_006087	`PF13041.13`	PPR_2	38	83	3e-25	88.8
LXL04_006087	`PF17177.11`	PPR_long	55	171	1.9e-09	38.0
LXL04_006087	`PF13812.13`	PPR_3	61	121	4.6e-19	69.0
LXL04_006087	`PF13812.13`	PPR_3	98	154	4.6e-19	69.0
LXL04_006087	`PF12854.14`	PPR_1	103	136	2.5e-07	31.0
LXL04_006087	`PF13041.13`	PPR_2	107	155	3e-25	88.8
LXL04_006087	`PF01535.27`	PPR	110	138	6.3e-13	48.7

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
`Q8VYR5`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g35850, mitochondrial	63.514%	Swiss-Prot	strong database homology
`Q8GZ63`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At5g25630	20.701%	Swiss-Prot	weak database homology
`Q9LFF1`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g53700, chloroplastic	20.352%	Swiss-Prot	weak database homology
`Q9ZUU3`	Arabidopsis thaliana	Large ribosomal subunit protein mL102 (rPPR5)	26.842%	Swiss-Prot	weak database homology
`Q940A6`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At4g19440, chloroplastic	30.345%	Swiss-Prot	weak database homology

JBrowse

View in Genome Browser

Gene Card