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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

LXL04_016790
Reference: OH-1004 Chr: Chr03 Coordinates: 133765276-133767555 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

2280 bp · LXL04_016790|LXL04_016790|OH1004|cDNA

ATGTCACATTTGAACGACATTGCACCGAGAATATCTTGCTTCAAACACTTAACACAGCTCCATGCGCAGATCATTCACCATTCAGTCCACAATCATAACTACTGGGTGTCAATCCTCATCAGCCACTGCACGCGCCTCCGTGCACCACCGCCCTACACCCGCCTCATTTTCAATTCCACAGACCAACCAAATGTCTACGCATTCACCAACATGCTCAAGTTCTACTCCAATGTCGGAGCCCATACCGATGTCATCACCCT...

CDS

Download CDS FASTA

2280 bp · LXL04_016790|LXL04_016790|OH1004|CDS

ATGTCACATTTGAACGACATTGCACCGAGAATATCTTGCTTCAAACACTTAACACAGCTCCATGCGCAGATCATTCACCATTCAGTCCACAATCATAACTACTGGGTGTCAATCCTCATCAGCCACTGCACGCGCCTCCGTGCACCACCGCCCTACACCCGCCTCATTTTCAATTCCACAGACCAACCAAATGTCTACGCATTCACCAACATGCTCAAGTTCTACTCCAATGTCGGAGCCCATACCGATGTCATCACCCT...

Protein

Download Protein FASTA

759 aa · LXL04_016790|LXL04_016790|OH1004|PROTEIN

MSHLNDIAPRISCFKHLTQLHAQIIHHSVHNHNYWVSILISHCTRLRAPPPYTRLIFNSTDQPNVYAFTNMLKFYSNVGAHTDVITLFHSLRISGVTPDAFVFPIVIKSSGKDAVVIHGHVLKTGHQNDRYVRNAIMGMYAKYGGIGLARKLFDEMPERMAADWNLMISGYWRCGDESEARNLFDVMPEKNVITWTAMVTGYSNTQDLATARSYFDQMPEKNIVSWNAMLSGYTQNGYAEEAIKLFNKMINSNIQPDETT...

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.

Download Gene (CDS) Download Protein

ID Mapping

Input IDLXL04_016790
TK1151 IDTkA02G102490
OH-1004 IDLXL04_016790
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)73.900
Protein coverage (%)TK1151 97.719 / OH-1004 33.333
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 versionOH-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 IDLXL04_016790
LocationChr03:133765276-133767555 (-)
DescriptionSimilar to PCMP-A4: Pentatricopeptide repeat-containing protein At1g14470
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g14470 Pentatricopeptide repeat-containing protein At1g14470. No verified direct reference in this release
At3g22690 Pentatricopeptide repeat-containing protein At3g22690. No verified direct reference in this release
At4g02750 Pentatricopeptide repeat-containing protein At4g02750. No verified direct reference in this release
At2g29760 Involved in RNA editing event in chloroplasts.
A study of new Arabidopsis chloroplast RNA editing mutants reveals general features of editing factors and their target sites.2009 · DOI: 10.1105/tpc.109.071472
At1g08070 Involved in multiple sites RNA editing events in chloroplasts. 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_016790 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0009409 response to cold Biological Process
GO:0009451 RNA modification Biological Process
GO:0009644 response to high light intensity Biological Process
GO:0010027 thylakoid membrane organization Biological Process
GO:0010207 photosystem II assembly Biological Process
GO:0010214 seed coat development Biological Process
GO:0010380 regulation of chlorophyll biosynthetic process Biological Process
GO:0048564 photosystem I assembly Biological Process
GO:0140547 acquisition of seed longevity Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G14470
ath:AT3G22690
ath:AT4G02750
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.

Mitochondrion0.647
Rank 1 · LXL04_016790 · OH-1004
Plastid0.180
Rank 2 · LXL04_016790 · OH-1004
Nucleus0.063
Rank 3 · LXL04_016790 · OH-1004
Cytoplasm0.033
Rank 4 · LXL04_016790 · OH-1004
Cell membrane0.006
Rank 5 · LXL04_016790 · 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.

PF13041.13PPR_263-108 aa
PF01535.27PPR164-192 aa
PF13041.13PPR_2221-269 aa
PF12854.14PPR_1222-249 aa
PF01535.27PPR224-254 aa
PF29070.1MSC6_N227-317 aa
PF17177.11PPR_long238-322 aa
PF23276.3TPR_24260-382 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_016790PF13041.13PPR_2631081.8e-80265.6
LXL04_016790PF01535.27PPR1641921.8e-78254.1
LXL04_016790PF13041.13PPR_22212691.8e-80265.6
LXL04_016790PF12854.14PPR_12222493.2e-52174.6
LXL04_016790PF01535.27PPR2242541.8e-78254.1
LXL04_016790PF29070.1MSC6_N2273171.9e-1970.7
LXL04_016790PF17177.11PPR_long2383221.2e-1454.9
LXL04_016790PF23276.3TPR_242603821.8e-2073.9
LXL04_016790PF12854.14PPR_13203513.2e-52174.6
LXL04_016790PF13041.13PPR_23233561.8e-80265.6
LXL04_016790PF01535.27PPR3263551.8e-78254.1
LXL04_016790PF13041.13PPR_23554031.8e-80265.6
LXL04_016790PF12854.14PPR_13553823.2e-52174.6
LXL04_016790PF01535.27PPR3573851.8e-78254.1
LXL04_016790PF29070.1MSC6_N3604521.9e-1970.7
LXL04_016790PF13812.13PPR_34194542.4e-45153.2

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

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q9M9R6Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1447055.639%Swiss-Protmoderate database homology
Q9LUJ2Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g2269036.816%Swiss-Protmoderate database homology
Q9SY02Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g0275040.407%Swiss-Protmoderate database homology
O82380Arabidopsis thalianaPentatricopeptide repeat-containing protein At2g29760, chloroplastic36.667%Swiss-Protmoderate database homology
Q9LN01Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g08070, chloroplastic35.958%Swiss-Protmoderate database homology

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