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

TkA01G551180
Reference: TK1151 Chr: Chr01 Coordinates: 138542141-138545818 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

1383 bp · TkA01G551180|TK1151|cDNA

GTTTTAATGACGATCCAAATAATTTGTTCGCCCGAAGTAGTGGTCTTGTTGTCCACTGCTTAAAGGAACTCGAACCTTCCAGGCTTCCACGACTGCGTTTTCTACTTTTCTTATTTGTCGCTCCTAAATTTCCGAAGGTATCTCCTTATGCACTAGTAGCGCAGTCGATCGATTTCAGCCTAATATCTTTTTAGATCAAATGCTCTGCACCTTTGATTTCATTGCGTATTTATTTGGATTACTCCCTAACTAGCATTTGA...

CDS

Download CDS FASTA

966 bp · TkA01G551180|TK1151|CDS

GATCCAAATAATTTGTTCGCCCGAAGTAGTGGTCTTGTTGTCCACTGCTTAAAGGAACTCGAACCTTCCAGGCTTCCACGACTGCGTTTTCTACTTTTCTTATTTGTCGCTCCTAAATTTCCGAAGATCATCACATTTTTTTCCTTTTTCAAAAACATGGGCCGCTCAAGTCGCACTCTCTATGTGGGTAATCTCCCTGGTGATATTCGTGAAAGAGAAATTGAAGATTTGTTTTACAAGTATGGTCCAATTGTTGAAAT...

Protein

Download Protein FASTA

321 aa · TkA01G551180|TK1151|PROTEIN

DPNNLFARSSGLVVHCLKELEPSRLPRLRFLLFLFVAPKFPKIITFFSFFKNMGRSSRTLYVGNLPGDIREREIEDLFYKYGPIVEIELKIPPRPPSFAFVEFEDSRDAEDAIHGRDGYKFDGHRLRVELAHGGRVSSSSIDRHTSSHRESSRRSDYRVYVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRDGMRGIVDYTNYDDMKYAIRKLDDSLFRNQFSKAYIRVEEYDRRSRSPSPYYSRSRSPTHSRSRSYSP...

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 IDTkA01G551180
TK1151 IDTkA01G551180
OH-1004 IDLXL04_001257
Relationship / confidenceRbh Sequence Supported / Probable
Protein identity (%)99.100
Protein coverage (%)TK1151 71.028 / OH-1004 77.027
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 IDTkA01G551180
LocationChr01:138542141-138545818 (+)
DescriptionSimilar to SR30: Serine/arginine-rich splicing factor SR30
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g09140 Regulatory splicing factor that modulates alternative splicing and gene expression in specific cell types.
atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
At1g02840 General splicing factor.
atSRp30, one of two SF2/ASF-like proteins from Arabidopsis thaliana, regulates splicing of specific plant genes.1999 · DOI: 10.1101/gad.13.8.987
At4g02430 Probably involved in intron recognition and spliceosome assembly. No verified direct reference in this release
At3g49430 Probably involved in intron recognition and spliceosome assembly. 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_001257 · 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:0000381 regulation of alternative mRNA splicing, via spliceosome Biological Process
GO:0006397 mRNA processing Biological Process
GO:0008380 RNA splicing Biological Process
GO:0005634 nucleus Cellular Component
GO:0005681 spliceosomal complex Cellular Component
GO:0005730 nucleolus Cellular Component
GO:0005737 cytoplasm Cellular Component
GO:0005829 cytosol Cellular Component
GO:0016607 nuclear speck Cellular Component
GO:0035061 interchromatin granule Cellular Component
GO:0003729 mRNA binding Molecular Function
KEGG gene cross-reference
ath:AT1G02840
ath:AT1G09140
ath:AT3G49430
ath:AT4G02430
gga:772264
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.

Nucleus0.930
Rank 1 · TkA01G551180 · TK1151
Cytoplasm0.234
Rank 2 · TkA01G551180 · TK1151
Cell membrane0.020
Rank 3 · TkA01G551180 · TK1151
Endoplasmic reticulum0.015
Rank 4 · TkA01G551180 · TK1151
Mitochondrion0.010
Rank 5 · TkA01G551180 · 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_757-85 aa
PF14703PHM7_cyt57-85 aa
PF16842RRM_occluded58-128 aa
PF25701RRM_YTH159-126 aa
PF00076RRM_160-127 aa
PF08777RRM_368-130 aa
PF14605Nup35_RRM_278-112 aa
PF14703PHM7_cyt94-113 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA01G551180PF16367RRM_757850.001319.4
TkA01G551180PF14703PHM7_cyt57850.1413.1
TkA01G551180PF16842RRM_occluded581286.5e-0523.4
TkA01G551180PF25701RRM_YTH1591260.00218.7
TkA01G551180PF00076RRM_1601279.5e-32109.4
TkA01G551180PF08777RRM_3681300.1612.7
TkA01G551180PF14605Nup35_RRM_2781120.04814.3
TkA01G551180PF14703PHM7_cyt941130.1413.1
TkA01G551180PF25701RRM_YTH11552210.00218.7
TkA01G551180PF14703PHM7_cyt1571990.1413.1
TkA01G551180PF16367RRM_71581840.001319.4
TkA01G551180PF00076RRM_11592229.5e-32109.4
TkA01G551180PF08777RRM_31602200.1612.7

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
Q9XFR5Arabidopsis thalianasp|Q9XFR5|SR30_ARATH Serine/arginine-rich splicing factor SR3075.400%Swiss-ProtHigh
O22315Arabidopsis thalianasp|O22315|SR34_ARATH Serine/arginine-rich-splicing factor SR3467.700%Swiss-ProtHigh
F4JHI7Arabidopsis thalianasp|F4JHI7|SR34B_ARATH Serine/arginine-rich splicing factor SR34B67.800%Swiss-ProtHigh
A2RVS6Arabidopsis thalianasp|A2RVS6|SR34A_ARATH Serine/arginine-rich splicing factor SR34A66.000%Swiss-ProtHigh

JBrowse

View in Genome Browser