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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_025234
Reference: OH-1004 Chr: Chr05 Coordinates: 108307407-108328505 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

6732 bp · LXL04_025234|LXL04_025234|OH1004|cDNA

ATGGATATTTTCAAATATTATAAATATGAGCAAacATTTAAATTCATTAAGTTGGTTATCTTGATAAAAAAAGATGCTTTAATATCACCAGTCGAAAAATTCGATGGCGAATTTTGCGAATTTAAAGCAAACTTGAAGAACGAGAAGATCTTACGGTGCTCCAAGAGGATGAAACGGTCtagagatgatgatgatgccTACAGCAGCTCCCAACTCAAGCGACCACTGATCTCTGAACACTCAAAGCACCCCCAAATGAT...

CDS

Download CDS FASTA

6732 bp · LXL04_025234|LXL04_025234|OH1004|CDS

ATGGATATTTTCAAATATTATAAATATGAGCAAACATTTAAATTCATTAAGTTGGTTATCTTGATAAAAAAAGATGCTTTAATATCACCAGTCGAAAAATTCGATGGCGAATTTTGCGAATTTAAAGCAAACTTGAAGAACGAGAAGATCTTACGGTGCTCCAAGAGGATGAAACGGTCTAGAGATGATGATGATGCCTACAGCAGCTCCCAACTCAAGCGACCACTGATCTCTGAACACTCAAAGCACCCCCAAATGAT...

Protein

Download Protein FASTA

2243 aa · LXL04_025234|LXL04_025234|OH1004|PROTEIN

MDIFKYYKYEQTFKFIKLVILIKKDALISPVEKFDGEFCEFKANLKNEKILRCSKRMKRSRDDDDAYSSSQLKRPLISEHSKHPQMMDKGTAQKLTANDALTYLEKVKDIFQNEKEKYDEFLKIMKDFKAQRIDTTGVITMVKELFKGHQELLLGFNPFLPKGFQITLPLDNHQQHHVIKKPLEMEEAVLFVNKIKMRFQGQDHVYKYFLDTLNKYKKENKSIKEVHQEVAALLNDQQDLLKEFINFLPNPSHTECKVNL...

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_025234
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_025234
LocationChr05:108307407-108328505 (+)
DescriptionSimilar to ISE2: DExH-box ATP-dependent RNA helicase DExH15 chloroplastic
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g70070 RNA helicase involved in group II intron splicing.
Identification of a developmental transition in plasmodesmatal function during embryogenesis in Arabidopsis thaliana.2002 · DOI: 10.1242/dev.129.5.1261
INCREASED SIZE EXCLUSION LIMIT 2 encodes a putative DEVH box RNA helicase involved in plasmodesmata function during Arabidopsis embryogenesis.2007 · DOI: 10.1105/tpc.106.045666
Loss of INCREASED SIZE EXCLUSION LIMIT (ISE)1 or ISE2 increases the formation of secondary plasmodesmata.2010 · DOI: 10.1016/j.cub.2010.03.064
The chloroplastic DEVH-box RNA helicase INCREASED SIZE EXCLUSION LIMIT 2 involved in plasmodesmata regulation is required for group II intron splicing.2016 · DOI: 10.1111/pce.12603
At1g24190 Acts as a transcriptional repressor.
Role of an Arabidopsis AP2/EREBP-type transcriptional repressor in abscisic acid and drought stress responses.2005 · DOI: 10.1105/tpc.105.033043
At1g70060 Acts as a transcriptional repressor. No verified direct reference in this release
At5g15020 Acts as a transcriptional repressor. No verified direct reference in this release
At3g01320 Acts as a transcriptional repressor.
PAH-domain-specific interactions of the Arabidopsis transcription coregulator SIN3-LIKE1 (SNL1) with telomere-binding protein 1 and ALWAYS EARLY2 Myb-DNA binding factors.2010 · DOI: 10.1016/j.jmb.2009.11.065

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_025234 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)
GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process
GO:0000373 Group II intron splicing Biological Process
GO:0000712 resolution of meiotic recombination intermediates Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006397 mRNA processing Biological Process
GO:0009737 response to abscisic acid Biological Process
GO:0009793 embryo development ending in seed dormancy Biological Process
GO:0010497 plasmodesmata-mediated intercellular transport Biological Process
GO:0016441 post-transcriptional gene silencing Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0031047 regulatory ncRNA-mediated gene silencing Biological Process
GO:0045892 negative regulation of DNA-templated transcription Biological Process
KEGG gene cross-reference
ath:AT1G24190
ath:AT1G70060
ath:AT1G70070
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.

Nucleus0.628
Rank 1 · LXL04_025234 · OH-1004
Cytoplasm0.284
Rank 2 · LXL04_025234 · OH-1004
Cell membrane0.049
Rank 3 · LXL04_025234 · OH-1004
Mitochondrion0.044
Rank 4 · LXL04_025234 · OH-1004
Plastid0.030
Rank 5 · LXL04_025234 · 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.

PF23202.2PAH_ZNF598103-149 aa
PF02671.27PAH116-160 aa
PF02671.27PAH204-248 aa
PF02671.27PAH361-403 aa
PF08295.18Sin3_corepress472-563 aa
PF16879.11Sin3a_C863-1102 aa
PF00270.36DEAD1206-1360 aa
PF04851.22ResIII1207-1356 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
LXL04_025234PF23202.2PAH_ZNF5981031498.4e-1658.7
LXL04_025234PF02671.27PAH1161604.5e-42142.2
LXL04_025234PF02671.27PAH2042484.5e-42142.2
LXL04_025234PF02671.27PAH3614034.5e-42142.2
LXL04_025234PF08295.18Sin3_corepress4725634e-35120.5
LXL04_025234PF16879.11Sin3a_C86311021.4e-38133.7
LXL04_025234PF00270.36DEAD120613601e-2487.9
LXL04_025234PF04851.22ResIII120713568.1e-0729.8
LXL04_025234PF22527.3DEXQc_Suv3122413542.4e-0731.2
LXL04_025234PF25446.2SH3_ISE2178819705.7e-84281.0
LXL04_025234PF08148.18DSHCT205922156.1e-31108.2

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
B9DFG3Arabidopsis thalianaDExH-box ATP-dependent RNA helicase DExH15 chloroplastic66.792%Swiss-Protweak database homology
O48686Arabidopsis thalianaPaired amphipathic helix protein Sin3-like 351.560%Swiss-Protweak database homology
O04539Arabidopsis thalianaPaired amphipathic helix protein Sin3-like 449.100%Swiss-Protweak database homology
Q9LFQ3Arabidopsis thalianaPaired amphipathic helix protein Sin3-like 248.148%Swiss-Protweak database homology
Q9SRH9Arabidopsis thalianaPaired amphipathic helix protein Sin3-like 147.650%Swiss-Protweak database homology

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