LXL04_027158 | RubberDandelionOmics

Gene overview

LXL04_027158

Reference: OH-1004 Chr: Chr06 Coordinates: 9807327-9808457 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1131 bp · LXL04_027158|LXL04_027158|OH1004|cDNA

ATGTCTACCATTTCTCGCATCTTCCGCTCCTTCTCCACTTCCGTCTCCACCCCACCGGCGAAATCGATCTACGAAGACCTCTACAAGGAACGGAATCTCAAAAGAGTAGTAGAGAAATTCAAAAAAGCATCGGAATCGCATTTGTTCCGTAAACAAGCGAATGTTTACGGCAGCACAGTCCGCCGCCTCGCTTCCGCCAAGAAATTCAAATGGGTGGAGGAGATTCTCGAGGACCAGAAACAGTATCATGAGATTTCCAA...

CDS

Download CDS FASTA

1131 bp · LXL04_027158|LXL04_027158|OH1004|CDS

ATGTCTACCATTTCTCGCATCTTCCGCTCCTTCTCCACTTCCGTCTCCACCCCACCGGCGAAATCGATCTACGAAGACCTCTACAAGGAACGGAATCTCAAAAGAGTAGTAGAGAAATTCAAAAAAGCATCGGAATCGCATTTGTTCCGTAAACAAGCGAATGTTTACGGCAGCACAGTCCGCCGCCTCGCTTCCGCCAAGAAATTCAAATGGGTGGAGGAGATTCTCGAGGACCAGAAACAGTATCATGAGATTTCCAA...

Protein

Download Protein FASTA

376 aa · LXL04_027158|LXL04_027158|OH1004|PROTEIN

MSTISRIFRSFSTSVSTPPAKSIYEDLYKERNLKRVVEKFKKASESHLFRKQANVYGSTVRRLASAKKFKWVEEILEDQKQYHEISKEGFAVRLISLYGKSGMFDHASKVFDEMPERNCPQTIKSFNALLGACVNAKKFDKLEGFFRELPEKLSLKPDIVSYNTAIKAFCDMGSFDSAATLFDEIEKNGMEPDLITFNTLLIGCYGNGRFLDGEKFLAKMMNTNLSPDIRTYNAKLVGLVSEKKLDEAIDIFNKLASKNL...

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_027158`
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_027158

Location Chr06:9807327-9808457 (-)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

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
`At2g18520`	Pentatricopeptide repeat-containing protein At2g18520, mitochondrial.	No verified direct reference in this release
`At4g36680`	Small ribosomal subunit protein mL103 (rPPR7).	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_027158 · 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:0005886 plasma membrane Cellular Component

GO:1990904 ribonucleoprotein complex Cellular Component

GO:0003729 mRNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G55890

ath:AT2G18520

ath:AT3G13150

ath:AT3G13160

ath:AT4G36680

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.

Mitochondrion0.873

Rank 1 · LXL04_027158 · OH-1004

Plastid0.066

Rank 2 · LXL04_027158 · OH-1004

Nucleus0.048

Rank 3 · LXL04_027158 · OH-1004

Cytoplasm0.037

Rank 4 · LXL04_027158 · OH-1004

Cell membrane0.011

Rank 5 · LXL04_027158 · 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_N3-183 aa

PF13041.13PPR_294-135 aa

PF01535.27PPR94-119 aa

PF13812.13PPR_394-135 aa

PF13812.13PPR_3153-207 aa

PF12854.14PPR_1155-185 aa

PF13041.13PPR_2157-204 aa

PF01535.27PPR160-189 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_027158	`PF29070.1`	MSC6_N	3	183	2.8e-15	57.0
LXL04_027158	`PF13041.13`	PPR_2	94	135	1.6e-46	156.9
LXL04_027158	`PF01535.27`	PPR	94	119	4.5e-37	124.4
LXL04_027158	`PF13812.13`	PPR_3	94	135	3.4e-25	88.6
LXL04_027158	`PF13812.13`	PPR_3	153	207	3.4e-25	88.6
LXL04_027158	`PF12854.14`	PPR_1	155	185	7.4e-35	119.1
LXL04_027158	`PF13041.13`	PPR_2	157	204	1.6e-46	156.9
LXL04_027158	`PF01535.27`	PPR	160	189	4.5e-37	124.4
LXL04_027158	`PF17177.11`	PPR_long	190	279	3.5e-15	56.7
LXL04_027158	`PF13041.13`	PPR_2	195	236	1.6e-46	156.9
LXL04_027158	`PF13812.13`	PPR_3	217	276	3.4e-25	88.6
LXL04_027158	`PF13041.13`	PPR_2	227	276	1.6e-46	156.9
LXL04_027158	`PF23276.3`	TPR_24	248	353	3.8e-10	40.5
LXL04_027158	`PF12854.14`	PPR_1	258	284	7.4e-35	119.1
LXL04_027158	`PF13041.13`	PPR_2	262	311	1.6e-46	156.9
LXL04_027158	`PF01535.27`	PPR	265	289	4.5e-37	124.4

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
`Q9LG23`	Arabidopsis thaliana	Small ribosomal subunit protein mS78 (rPPR3a)	48.111%	Swiss-Prot	moderate database homology
`Q9LK57`	Arabidopsis thaliana	Small ribosomal subunit protein mS79 (rPPR3b)	47.297%	Swiss-Prot	moderate database homology
`Q9LK58`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At3g13150	41.765%	Swiss-Prot	moderate database homology
`Q9ZU67`	Arabidopsis thaliana	Pentatricopeptide repeat-containing protein At2g18520, mitochondrial	34.437%	Swiss-Prot	moderate database homology
`Q9M065`	Arabidopsis thaliana	Small ribosomal subunit protein mL103 (rPPR7)	33.887%	Swiss-Prot	moderate database homology

JBrowse

View in Genome Browser

Gene Card