TkA07G173180 | RubberDandelionOmics

Gene overview

TkA07G173180

Reference: TK1151 Chr: Chr07 Coordinates: 44422159-44426349 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1733 bp · TkA07G173180|TK1151|cDNA

AAAATTTGAGAGCATATAAATGGGCCTAGATTTATTTTGGGCCAGTACCCACAAGCTATCATCAACGTAACATTGAATTCCCACTCCAATTCTTAGCTAGGGTTTGTCTGAAGGGGTTTCCGATCCGAAACTGAGCTCTCTCCTGCGCATGGCGAAACCAGGACGTGGTCGTCCGTCGGCTCCTGCGGGGTCTGGTTCAGGCTCATCCTCCCGCTCTCGTTCTCGCTCCATCTCCGGTTCTTCTCGTTCAAGTTCTCGTT...

CDS

Download CDS FASTA

1275 bp · TkA07G173180|TK1151|CDS

ATGGCGAAACCAGGACGTGGTCGTCCGTCGGCTCCTGCGGGGTCTGGTTCAGGCTCATCCTCCCGCTCTCGTTCTCGCTCCATCTCCGGTTCTTCTCGTTCAAGTTCTCGTTCTAGGTCGCGCTCCAGATCCTACACTTCTTCATCATCTCCATCTCGCAGCGTCAGTTCTCGTAGCCGTAGTCCCCCTCCGAAGAAAAGTTCTGGTGATGGACCAAGGCGAGGTCGCTCTCCACCACATCAATCTAAGAGGTCTTCTCC...

Protein

Download Protein FASTA

424 aa · TkA07G173180|TK1151|PROTEIN

MAKPGRGRPSAPAGSGSGSSSRSRSRSISGSSRSSSRSRSRSRSYTSSSSPSRSVSSRSRSPPPKKSSGDGPRRGRSPPHQSKRSSPPPRKASPVPESLVLHIGQLTRNVNENHLKEIFGNFGEVVHVQLAMDHVVNLPKGSGYVEFKLRADAEKAQLHMDGAQIDGRVVQAKFTLPERKKATSPPPKPLPTASRRDTAKNDISSADVEKDGPKRVPPASPRRRPPSPSRRRSPAARRASPLPPPPPRRRGDSPPPPRRR...

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.

ID Mapping

Input ID	`TkA07G173180`
TK1151 ID	TkA07G173180
OH-1004 ID	LXL04_028587
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.200
Protein coverage (%)	TK1151 93.632 / OH-1004 93.647 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 version	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA07G173180

Location Chr07:44422159-44426349 (-)

Description Similar to SR45: Serine/arginine-rich splicing factor SR45

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g16610`	Involved in 5' and 3' splicing site selection of introns, and may bridge the 5' and 3' components of the spliceosome.	Two alternatively spliced isoforms of the Arabidopsis SR45 protein have distinct roles during normal plant development.2009 · DOI: 10.1104/pp.109.138180 The plant-specific SR45 protein negatively regulates glucose and ABA signaling during early seedling development in Arabidopsis.2010 · DOI: 10.1104/pp.110.155523 The splicing factor SR45 affects the RNA-directed DNA methylation pathway in Arabidopsis.2012 · DOI: 10.4161/epi.7.1.18782 The Arabidopsis SR45 Splicing Factor, a Negative Regulator of Sugar Signaling, Modulates SNF1-Related Protein Kinase 1 Stability.2016 · DOI: 10.1105/tpc.16.00301
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028587 · 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:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0010182 sugar mediated signaling pathway Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0016607 nuclear speck Cellular Component

KEGG gene cross-reference

ath:AT1G16610

dre:327020

xla:495230

xla:735191

xtr:548710

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

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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.

Nucleus0.981

Rank 1 · TkA07G173180 · TK1151

Cytoplasm0.096

Rank 2 · TkA07G173180 · TK1151

Cell membrane0.015

Rank 3 · TkA07G173180 · TK1151

Endoplasmic reticulum0.008

Rank 4 · TkA07G173180 · TK1151

Mitochondrion0.007

Rank 5 · TkA07G173180 · 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.

PF30126YHR127W_C100-173 aa

PF28976RRM_ACIN1100-164 aa

PF00076RRM_1103-170 aa

PF16842RRM_occluded105-170 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA07G173180	`PF30126`	YHR127W_C	100	173	0.00014	22.5
TkA07G173180	`PF28976`	RRM_ACIN1	100	164	0.0016	19.2
TkA07G173180	`PF00076`	RRM_1	103	170	4.2e-15	56.1
TkA07G173180	`PF16842`	RRM_occluded	105	170	0.00019	21.9

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SEE9`	Arabidopsis thaliana	sp\|Q9SEE9\|SR45_ARATH Serine/arginine-rich splicing factor SR45	69.100%	Swiss-Prot	Low
`Q9SAB3`	Arabidopsis thaliana	sp\|Q9SAB3\|RB45B_ARATH Polyadenylate-binding protein RBP45B	29.700%	Swiss-Prot	Low

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