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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_030552
Reference: OH-1004 Chr: Chr06 Coordinates: 118458965-118466651 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

4596 bp · LXL04_030552|LXL04_030552|OH1004|cDNA

ATGTCTAGATTTCTCACCACCACCGTCCACATTTCCGCTGCTATCCTCACCAAATCCCGATCGCCGCTTCATCTCTCCGCTTCTCAGTTCTCCTTTCCACATGTCACTTCAACTAAGTTTCATCATCTGAAACCTCATCGGAGCATCTCAATTCGAGCTGTCAATTCATCGTCTGACACCAAAAGTGAGGACGTTTCGTCAGAGAAACAAGAGGATAAAAGTGAATCCAAGTCCGAATTGGATAATAATGGCAGTTTTAG...

CDS

Download CDS FASTA

4596 bp · LXL04_030552|LXL04_030552|OH1004|CDS

ATGTCTAGATTTCTCACCACCACCGTCCACATTTCCGCTGCTATCCTCACCAAATCCCGATCGCCGCTTCATCTCTCCGCTTCTCAGTTCTCCTTTCCACATGTCACTTCAACTAAGTTTCATCATCTGAAACCTCATCGGAGCATCTCAATTCGAGCTGTCAATTCATCGTCTGACACCAAAAGTGAGGACGTTTCGTCAGAGAAACAAGAGGATAAAAGTGAATCCAAGTCCGAATTGGATAATAATGGCAGTTTTAG...

Protein

Download Protein FASTA

1531 aa · LXL04_030552|LXL04_030552|OH1004|PROTEIN

MSRFLTTTVHISAAILTKSRSPLHLSASQFSFPHVTSTKFHHLKPHRSISIRAVNSSSDTKSEDVSSEKQEDKSESKSELDNNGSFRGDDAYPSGEFEFQSPGAWKSFVVKLRMLIAYPWQRVRKGSVLNLKLRGQISDQVKTRFSSGLSLPQICENLIKAAYDPRISGVYLHIETLNCGWGKIEEIRRHILDFRKSGKFIIGYAPLWSEKEYYLGCACEELYAPPSAYFSLYGLTASASFLGGVLEKIGVEPQVQRIGK...

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.

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ID Mapping

Input IDLXL04_030552
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_030552
LocationChr06:118458965-118466651 (+)
DescriptionSimilar to SPPA: Serine protease SPPA, chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g73990 Serine protease that may be involved in the light-dependent degradation of antenna and photosystem II in chloroplasts.
Identification and characterization of SppA, a novel light-inducible chloroplast protease complex associated with thylakoid membranes.2001 · DOI: 10.1074/jbc.m100506200
Loss of chloroplast protease SPPA function alters high light acclimation processes in Arabidopsis thaliana L. (Heynh.).2009 · DOI: 10.1093/jxb/erp051
At1g18485 Pentatricopeptide repeat-containing protein At1g18485. No verified direct reference in this release
At4g21300 Pentatricopeptide repeat-containing protein At4g21300. No verified direct reference in this release
At3g63370 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
At3g03580 Pentatricopeptide repeat-containing protein At3g03580. 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_030552 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0006397 mRNA processing Biological Process
GO:0006465 signal peptide processing Biological Process
GO:0009451 RNA modification Biological Process
GO:0009642 response to light intensity Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0009534 chloroplast thylakoid Cellular Component
GO:0009535 chloroplast thylakoid membrane Cellular Component
GO:0009570 chloroplast stroma Cellular Component
GO:0009941 chloroplast envelope Cellular Component
GO:0003723 RNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G18485
ath:AT1G73990
ath:AT3G03580
ath:AT3G63370
ath:AT4G21300
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.

Plastid0.689
Rank 1 · LXL04_030552 · OH-1004
Mitochondrion0.276
Rank 2 · LXL04_030552 · OH-1004
Nucleus0.026
Rank 3 · LXL04_030552 · OH-1004
Cytoplasm0.019
Rank 4 · LXL04_030552 · OH-1004
Cell membrane0.009
Rank 5 · LXL04_030552 · 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.

PF01343.24Peptidase_S49195-344 aa
PF01343.24Peptidase_S49445-596 aa
PF01535.27PPR901-927 aa
PF13041.13PPR_21029-1076 aa
PF01535.27PPR1032-1062 aa
PF13041.13PPR_21131-1178 aa
PF01535.27PPR1135-1164 aa
PF13041.13PPR_21233-1279 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_030552PF01343.24Peptidase_S491953444.5e-61206.1
LXL04_030552PF01343.24Peptidase_S494455964.5e-61206.1
LXL04_030552PF01535.27PPR9019274.2e-69224.8
LXL04_030552PF13041.13PPR_2102910764.8e-65216.2
LXL04_030552PF01535.27PPR103210624.2e-69224.8
LXL04_030552PF13041.13PPR_2113111784.8e-65216.2
LXL04_030552PF01535.27PPR113511644.2e-69224.8
LXL04_030552PF13041.13PPR_2123312794.8e-65216.2
LXL04_030552PF12854.14PPR_1123312615.8e-37125.8
LXL04_030552PF01535.27PPR123512644.2e-69224.8
LXL04_030552PF13041.13PPR_2133513804.8e-65216.2
LXL04_030552PF01535.27PPR133813654.2e-69224.8
LXL04_030552PF20431.5E_motif145115136e-2072.0

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
Q9C9C0Arabidopsis thalianaSerine protease SPPA, chloroplastic67.773%Swiss-Protweak database homology
Q0WN60Arabidopsis thalianaPentatricopeptide repeat-containing protein At1g1848548.335%Swiss-Protmoderate database homology
Q9STE1Arabidopsis thalianaPentatricopeptide repeat-containing protein At4g2130033.163%Swiss-Protmoderate database homology
Q9M1V3Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g63370, chloroplastic32.987%Swiss-Protmoderate database homology
Q9SS60Arabidopsis thalianaPentatricopeptide repeat-containing protein At3g0358031.783%Swiss-Protmoderate database homology

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