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

TkA03G558090
Reference: TK1151 Chr: Chr03 Coordinates: 141289626-141291468 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1354 bp · TkA03G558090|TK1151|cDNA

GGTAATGATTTGGGGAATTATGTGGTGATGTCGAATATTTATGCGGGAAAAGGTAAGTGGGAGGAAGTGATGGAAATAAGGCGGTTGATGAAGACGAAGGATTTGAAAAAACCCGCGGGGTGTAGTTGGATTGAAATTGATGGGAGGAAAAATGTGTTTATAGCGGGGGATAGTTCTCATCCGTTGAGATTGAGGATTGCTGACGTATTGGGGAAGTTGGATATACAAGTTAAAGAGCGGTTTCAGTTATGATAATACTT...

CDS

Download CDS FASTA

666 bp · TkA03G558090|TK1151|CDS

ATGGAGGAAACGGAGGGAGGTATAAGCTTCGATTTCGAAGGCGGCTTAGAAACAGGACCAACCCAACCTACCGCTTCCGTACCCGTAATCCACCGATCCACTGATCTCAACAGTAATAATGATAACGATCCATCATCCGCCTCTGCAGTCAACGTGAATTCAGCCTCCGGCGATACTCCTGCTGCTGTCACAGCTCCAAACTTTTCCGGCAGGAGGAGCAACAGCTACCGTCAGACCGTATGCCGCCACTGGCTCCGCGG...

Protein

Download Protein FASTA

221 aa · TkA03G558090|TK1151|PROTEIN

MEETEGGISFDFEGGLETGPTQPTASVPVIHRSTDLNSNNDNDPSSASAVNVNSASGDTPAAVTAPNFSGRRSNSYRQTVCRHWLRGLCMKGETCGFLHQYDKSRMPICRFFRLYGECREQDCVYKHTTEDIKECNMYKLGFCPNGPDCRYRHAKLPGPPPPVQEILQKVHQLNSNRFFQNRNFNHSQQSEKPQLPHGVNSFNQVVIIPTTTDSTTFRQIA

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 IDTkA03G558090
TK1151 IDTkA03G558090
OH-1004 IDLXL04_010954
Relationship / confidenceSequence Supported Annotation Or Model Conflict / Review
Protein identity (%)100.000
Protein coverage (%)TK1151 100.000 / OH-1004 20.674
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 IDTkA03G558090
LocationChr03:141289626-141291468 (-)
DescriptionSimilar to PCMP-E32: Putative pentatricopeptide repeat-containing protein At5g08490
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g30460 Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation.
Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit.2006 · DOI: 10.1104/pp.105.070672
A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor.2007 · DOI: 10.1093/nar/gkm457
A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana.2008 · DOI: 10.1371/journal.pone.0002410
The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein.2010 · DOI: 10.1016/j.febslet.2010.03.007
Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis.2012 · DOI: 10.1105/tpc.112.096107
The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis.2014 · DOI: 10.1104/pp.114.236083

Rice

Reference gene IDPossible functionPapers / DOI
Os06g0677700 Zinc finger CCCH domain-containing protein 45. No verified direct reference in this release
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_010954 · 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:0006397 mRNA processing Biological Process
GO:0009414 response to water deprivation Biological Process
GO:0009451 RNA modification Biological Process
GO:0009737 response to abscisic acid Biological Process
GO:0031425 chloroplast RNA processing Biological Process
GO:0080156 mitochondrial mRNA modification Biological Process
GO:0005739 mitochondrion Cellular Component
GO:0009507 chloroplast Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008270 zinc ion binding Molecular Function
KEGG gene cross-reference
ath:AT2G40720
ath:AT3G63370
ath:AT5G08490
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.

Nucleus0.543
Rank 1 · TkA03G558090 · TK1151
Cytoplasm0.494
Rank 2 · TkA03G558090 · TK1151
Mitochondrion0.040
Rank 3 · TkA03G558090 · TK1151
Cell membrane0.035
Rank 4 · TkA03G558090 · TK1151
Endoplasmic reticulum0.032
Rank 5 · TkA03G558090 · 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.

PF16131Torus43-100 aa
PF00642zf-CCCH76-99 aa
PF25584zf-CCCH_RBM2277-97 aa
PF15663zf-CCCH_378-130 aa
PF25586zf-CCCH_PAN378-83 aa
PF25427zf-CCCH_UNK79-108 aa
PF18044zf-CCCH_480-99 aa
PF29102Su_sable_N80-128 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G558090PF16131Torus431009.1e-0730.1
TkA03G558090PF00642zf-CCCH76995.4e-0626.9
TkA03G558090PF25584zf-CCCH_RBM2277970.001119.7
TkA03G558090PF15663zf-CCCH_3781300.03315.1
TkA03G558090PF25586zf-CCCH_PAN378830.09113.2
TkA03G558090PF25427zf-CCCH_UNK791080.09613.3
TkA03G558090PF18044zf-CCCH_480990.02315.2
TkA03G558090PF29102Su_sable_N801280.1113.5
TkA03G558090PF18345zf_CCCH_481999.6e-0935.8
TkA03G558090PF14608zf-CCCH_281991.8e-0629.0
TkA03G558090PF25543zf-CCCH_tandem811026.87.6
TkA03G558090PF25542zf-CCCH_12831014e-0523.9
TkA03G558090PF22623zf-CCCH_987990.01915.4
TkA03G558090PF25585zf-CCCH_DUS3L87992.88.7
TkA03G558090PF16131Torus1041289.1e-0730.1
TkA03G558090PF00642zf-CCCH1051275.4e-0626.9

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
A9LNK9Arabidopsis thalianasp|A9LNK9|CPSF_ARATH 30-kDa cleavage and polyadenylation specificity factor 3065.400%Swiss-ProtHigh
Q0DA50Oryza sativa subsp. japonicasp|Q0DA50|C3H45_ORYSJ Zinc finger CCCH domain-containing protein 4565.700%Swiss-ProtLow

JBrowse

View in Genome Browser