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

TkA08G426420
Reference: TK1151 Chr: Chr08 Coordinates: 108327142-108333301 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1644 bp · TkA08G426420|TK1151|cDNA

AAAACGGTAAAAGTGAAGGTTTTTGCGCCTTTCTTACGTCGTGCCCCCCTCGAATCCCGATCTCTGTTTGACCTTTTTCCATCTCTCTAGGGTTTCGCTATGCACCCAGGAACAACGGCGGTCATGGATCCTAGGTACCAACAGCAATGGATGATGATGAATCAACAAGCACCCCCACCACAGCAACAGTTCCATCAACAACAGCCGCAACAAATGTATACCTACAACCAGCAACCGCCACCGGCTGCGGCAGTACCAGC...

CDS

Download CDS FASTA

1245 bp · TkA08G426420|TK1151|CDS

ATGCACCCAGGAACAACGGCGGTCATGGATCCTAGGTACCAACAGCAATGGATGATGATGAATCAACAAGCACCCCCACCACAGCAACAGTTCCATCAACAACAGCCGCAACAAATGTATACCTACAACCAGCAACCGCCACCGGCTGCGGCAGTACCAGCGGTTTTACCTCATTACTCGGTAGCAGCAGCAACTTCGGGTACTGGCCCATCTCATCAACCAACTAGCGCCGATGAAGTCCGTACGCTATGGATCGGCGA...

Protein

Download Protein FASTA

414 aa · TkA08G426420|TK1151|PROTEIN

MHPGTTAVMDPRYQQQWMMMNQQAPPPQQQFHQQQPQQMYTYNQQPPPAAAVPAVLPHYSVAAATSGTGPSHQPTSADEVRTLWIGDLQYWMDEQYLVSCFAQSGEVISAKVIRNKQTGQSEGYGFIEFANRGAAERHLQTYNGSLMPNVEQNFRLNWASFGVGEKRADGSPDFTIFVGDLAADVTDYTLQETFRAHYQSVRSAKVVTDRMTGRTKGYGFVKFGDETEQIRAMTEMNGSLCSTRPMRIGPAANKNTTGGQ...

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 IDTkA08G426420
TK1151 IDTkA08G426420
OH-1004 IDLXL04_027086
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)75.800
Protein coverage (%)TK1151 95.169 / OH-1004 95.146
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 IDTkA08G426420
LocationChr08:108327142-108333301 (+)
DescriptionSimilar to RBP45: Polyadenylate-binding protein RBP45
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g11650 Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation.
Phylogenetic and expression analysis of RNA-binding proteins with triple RNA recognition motifs in plants.2011 · DOI: 10.1007/s10059-011-0001-2
At4g27000 Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation. No verified direct reference in this release
At5g54900 Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation. No verified direct reference in this release
At5g19350 Heterogeneous nuclear ribonucleoprotein (hnRNP)-protein binding the poly(A) tail of mRNA and probably involved in some steps of pre-mRNA maturation. No verified direct reference in this release

Rice

Reference gene IDPossible functionPapers / DOI
Os04g0625800 RNA-binding protein that binds to a cis-localization element or zipcode, within the 5'-CDS of prolamine RNA.
Targeted Endoplasmic Reticulum Localization of Storage Protein mRNAs Requires the RNA-Binding Protein RBP-L.2019 · DOI: 10.1104/pp.18.01434
Zipcode RNA-Binding Proteins and Membrane Trafficking Proteins Cooperate to Transport Glutelin mRNAs in Rice Endosperm.2020 · DOI: 10.1105/tpc.20.00111
Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_027086 · 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:0010193 response to ozone Biological Process
GO:0051028 mRNA transport Biological Process
GO:0005576 extracellular region Cellular Component
GO:0005634 nucleus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005829 cytosol Cellular Component
GO:0010494 cytoplasmic stress granule Cellular Component
GO:0003723 RNA binding Molecular Function
GO:0003729 mRNA binding Molecular Function
GO:0008143 poly(A) binding Molecular Function
KEGG gene cross-reference
ath:AT1G11650
ath:AT4G27000
ath:AT5G54900
dosa:Os04g0625800
osa:4337064
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.

Nucleus0.762
Rank 1 · TkA08G426420 · TK1151
Cytoplasm0.435
Rank 2 · TkA08G426420 · TK1151
Cell membrane0.042
Rank 3 · TkA08G426420 · TK1151
Endoplasmic reticulum0.026
Rank 4 · TkA08G426420 · TK1151
Mitochondrion0.019
Rank 5 · TkA08G426420 · 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.

PF16367RRM_782-135 aa
PF00076RRM_183-147 aa
PF23085RRM_PARP14_387-117 aa
PF22976RRM_1092-154 aa
PF13893RRM_592-146 aa
PF05172RRM_Nup3596-147 aa
PF28442DUF8400109-144 aa
PF14605Nup35_RRM_2115-137 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA08G426420PF16367RRM_7821351.3e-0732.2
TkA08G426420PF00076RRM_1831472.1e-47159.6
TkA08G426420PF23085RRM_PARP14_3871170.1213.1
TkA08G426420PF22976RRM_10921542.8e-0628.1
TkA08G426420PF13893RRM_5921466.5e-0626.6
TkA08G426420PF05172RRM_Nup35961470.0004320.9
TkA08G426420PF28442DUF84001091440.00617.5
TkA08G426420PF14605Nup35_RRM_21151370.04114.5
TkA08G426420PF29326RRM_MUD2_C1231440.02815.2
TkA08G426420PF11767SET_assoc1261470.02614.9
TkA08G426420PF00076RRM_11762412.1e-47159.6
TkA08G426420PF16367RRM_71762261.3e-0732.2
TkA08G426420PF23085RRM_PARP14_31762050.1213.1
TkA08G426420PF22976RRM_101832372.8e-0628.1
TkA08G426420PF28442DUF84002022500.00617.5
TkA08G426420PF13893RRM_52162506.5e-0626.6

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
Q9SAB3Arabidopsis thalianasp|Q9SAB3|RB45B_ARATH Polyadenylate-binding protein RBP45B66.300%Swiss-ProtHigh
Q93W34Arabidopsis thalianasp|Q93W34|RP45C_ARATH Polyadenylate-binding protein RBP45C65.300%Swiss-ProtHigh
Q9FPJ8Arabidopsis thalianasp|Q9FPJ8|RB45A_ARATH Polyadenylate-binding protein RBP45A66.800%Swiss-ProtHigh
Q8VXZ9Arabidopsis thalianasp|Q8VXZ9|R47BP_ARATH Polyadenylate-binding protein RBP47B'69.100%Swiss-ProtMedium
Q0J9Y2Oryza sativa subsp. japonicasp|Q0J9Y2|RBPL_ORYSJ RNA-binding protein L64.700%Swiss-ProtHigh

JBrowse

View in Genome Browser