RubberDandelionOmics Rubber Dandelion Multi-omics Website
More
Transcriptome Expression Annotation Rubber Pathway TF Prediction Targets Protein Network Resequencing Tools Downloads
ZH EN

How to use this page

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

TkA05G293950
Reference: TK1151 Chr: Chr05 Coordinates: 72543349-72544602 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

717 bp · TkA05G293950|TK1151|cDNA

TCAGAGCATGGAAGCAAAGGTGTGGAGGTATTTGTTGGGGGTTTGGCTCGTTCTCTCACTGAAGACAAGGTTCACAAGGTATTCGCTGCTTGTGGAGAAATTAAAGACATGCGCTTGATAAAAGATCATATGGGCATACTAAAGGTATTTGGCTTTGTACGCTTTGCAACAAAAGAAGCTGCTGACAAAGCTCTGAAGGAATTATCCGGATCTATGTTAGAATGGAAAAAGATTGGTGTTCTTCCATCAGCTGCACAAGA...

CDS

Download CDS FASTA

717 bp · TkA05G293950|TK1151|CDS

TCAGAGCATGGAAGCAAAGGTGTGGAGGTATTTGTTGGGGGTTTGGCTCGTTCTCTCACTGAAGACAAGGTTCACAAGGTATTCGCTGCTTGTGGAGAAATTAAAGACATGCGCTTGATAAAAGATCATATGGGCATACTAAAGGTATTTGGCTTTGTACGCTTTGCAACAAAAGAAGCTGCTGACAAAGCTCTGAAGGAATTATCCGGATCTATGTTAGAATGGAAAAAGATTGGTGTTCTTCCATCAGCTGCACAAGA...

Protein

Download Protein FASTA

238 aa · TkA05G293950|TK1151|PROTEIN

SEHGSKGVEVFVGGLARSLTEDKVHKVFAACGEIKDMRLIKDHMGILKVFGFVRFATKEAADKALKELSGSMLEWKKIGVLPSAAQDTLFLENLNKGWSVDDFNKVVRQVFPDVVSIHLAMPQSGSEITNKNFKNRGFAFVKFSSHATAARAFRAGTKPDFVLGGTLHPFVKWAEEDPEVDPDELAKIKIAFVRKLHSSTDEEYLKKLFMPFGKVKRVVVSNKGDFSWIYSFFSKITT

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 IDTkA05G293950
TK1151 IDTkA05G293950
OH-1004 IDLXL04_010840
Relationship / confidenceNon Reciprocal Best Hit / Complex relationship
Protein identity (%)31.900
Protein coverage (%)TK1151 94.118 / OH-1004 46.653
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 versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA05G293950
LocationChr05:72543349-72544602 (+)
DescriptionSimilar to LIF2: Heterogeneous nuclear ribonucleoprotein Q
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At4g00830 Transcriptional activator that binds DNA on GAGA-like motif and 5'-(C/G)ACGTG(G/T)C(A/G)-3' consensus motif in the promoters of target genes.
Control of flowering and cell fate by LIF2, an RNA binding partner of the polycomb complex component LHP1.2011 · DOI: 10.1371/journal.pone.0016592
The hnRNP-Q protein LIF2 participates in the plant immune response.2014 · DOI: 10.1371/journal.pone.0099343
The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 Subunit LHP1 Function in Concert to Regulate the Transcription of Stress-Responsive Genes.2016 · DOI: 10.1105/tpc.16.00244

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_010840 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)
GO:0000398 mRNA splicing, via spliceosome Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0006396 RNA processing Biological Process
GO:0006397 mRNA processing Biological Process
GO:0007623 circadian rhythm Biological Process
GO:0008380 RNA splicing Biological Process
GO:0009617 response to bacterium Biological Process
GO:0009909 regulation of flower development Biological Process
GO:0010439 regulation of glucosinolate biosynthetic process Biological Process
GO:0010468 regulation of gene expression Biological Process
GO:0016554 cytidine to uridine editing Biological Process
GO:0016556 mRNA modification Biological Process
KEGG gene cross-reference
ath:AT4G00830
hsa:10492
mmu:56403
pon:100174508
rno:363113
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.

Cytoplasm0.521
Rank 1 · TkA05G293950 · TK1151
Nucleus0.452
Rank 2 · TkA05G293950 · TK1151
Cell membrane0.074
Rank 3 · TkA05G293950 · TK1151
Endoplasmic reticulum0.047
Rank 4 · TkA05G293950 · TK1151
Mitochondrion0.039
Rank 5 · TkA05G293950 · TK1151

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.

PF08777RRM_37-74 aa
PF16367RRM_79-34 aa
PF00076RRM_110-78 aa
PF28976RRM_ACIN110-71 aa
PF16842RRM_occluded19-78 aa
PF14605Nup35_RRM_222-65 aa
PF28441RRM_1136-89 aa
PF26250RRM_RdRP1_246-74 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA05G293950PF08777RRM_37740.01116.5
TkA05G293950PF16367RRM_79340.0116.5
TkA05G293950PF00076RRM_110785.7e-29100.5
TkA05G293950PF28976RRM_ACIN110710.001119.7
TkA05G293950PF16842RRM_occluded19780.07913.5
TkA05G293950PF14605Nup35_RRM_222650.0005820.4
TkA05G293950PF28441RRM_1136890.1912.8
TkA05G293950PF26250RRM_RdRP1_246740.007317.4
TkA05G293950PF29326RRM_MUD2_C48740.001119.7
TkA05G293950PF24572RBD_RDR650670.005817.4
TkA05G293950PF00076RRM_1901545.7e-29100.5
TkA05G293950PF29326RRM_MUD2_C1071570.001119.7
TkA05G293950PF24572RBD_RDR61261650.005817.4
TkA05G293950PF14605Nup35_RRM_21271520.0005820.4
TkA05G293950PF26250RRM_RdRP1_21291530.007317.4
TkA05G293950PF28441RRM_111291540.1912.8

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
Q9ASP6Arabidopsis thalianasp|Q9ASP6|HNRPQ_ARATH Heterogeneous nuclear ribonucleoprotein Q34.900%Swiss-ProtMedium

JBrowse

View in Genome Browser