TkA01G060620 | RubberDandelionOmics

Gene overview

TkA01G060620

Reference: TK1151 Chr: Chr01 Coordinates: 15619516-15621100 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1174 bp · TkA01G060620|TK1151|cDNA

CTCCATTCCCCCCATATCCAAATTCAAACCCTAACCATATCGATCCCTCTTCTTATGGATTGATTTCATAACGATCATCACTTTCTCCCTCTACTGAATCTTATCCTTATCCAATCTCTTACCAATTTTATTTTACTCCCAAATTCAGCCATGCTAACTCCATCGAACGAGGTGCAGGAGCACAGCGTCAAGTTTCCTGATTTCGGACATACCCGTAATGATTTAAATCGGAAGACGCATTTTGAGATAAATCGGCAATC...

CDS

Download CDS FASTA

870 bp · TkA01G060620|TK1151|CDS

ATGCTAACTCCATCGAACGAGGTGCAGGAGCACAGCGTCAAGTTTCCTGATTTCGGACATACCCGTAATGATTTAAATCGGAAGACGCATTTTGAGATAAATCGGCAATCGCCATTTTCGATTTCCACAAGCTCGAGCTCTTTCCCTCAATATTTACCTGCTAAACGCAGCTCCTGGAGGTCACTTTCATTTGGAAAATTCTCCGCAAAACCAATCAGACTTTCGATTCTCAAATTAGATGGATCTTCCTTCGAGATTGT...

Protein

Download Protein FASTA

289 aa · TkA01G060620|TK1151|PROTEIN

MLTPSNEVQEHSVKFPDFGHTRNDLNRKTHFEINRQSPFSISTSSSSFPQYLPAKRSSWRSLSFGKFSAKPIRLSILKLDGSSFEIVVSKRATVAKVKKAIEAAFSYLPTQGDDEFSWSYVWGNFCLCFENMKLIRDRDSISRFGIKNGDQLQFVRHTPVYEVTGERFENITIDSNPPKGSSSKSDLNTDIKKDRWNIRSNHNRVRNEVNRSSWACMVRRLFLHRKTGGTVTLGQWFPSIDDDDGDDDDDTDDDGNISCK...

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	`TkA01G060620`
TK1151 ID	TkA01G060620
OH-1004 ID	LXL04_005321
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	99.700
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G060620

Location Chr01:15619516-15621100 (+)

Description Similar to SNRNP25: U11/U12 small nuclear ribonucleoprotein 25 kDa protein

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g07860`	U11/U12 small nuclear ribonucleoprotein 25 kDa protein.	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_005321 · 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:0000388 spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0008380 RNA splicing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005689 U12-type spliceosomal complex Cellular Component

GO:0005829 cytosol Cellular Component

GO:0034693 U11/U12 snRNP Cellular Component

GO:0045171 intercellular bridge Cellular Component

GO:0071016 U12-type precatalytic spliceosome Cellular Component

KEGG gene cross-reference

ath:AT3G07860

bta:513526

hsa:79622

mmu:78372

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.

Cell membrane0.400

Rank 1 · TkA01G060620 · TK1151

Nucleus0.367

Rank 2 · TkA01G060620 · TK1151

Cytoplasm0.298

Rank 3 · TkA01G060620 · TK1151

Endoplasmic reticulum0.082

Rank 4 · TkA01G060620 · TK1151

Plastid0.052

Rank 5 · TkA01G060620 · 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.

PF18036Ubiquitin_470-157 aa

PF00240ubiquitin78-109 aa

PF00240ubiquitin133-158 aa

PF16538FlgT_C145-170 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G060620	`PF18036`	Ubiquitin_4	70	157	2.7e-26	92.3
TkA01G060620	`PF00240`	ubiquitin	78	109	0.00062	20.2
TkA01G060620	`PF00240`	ubiquitin	133	158	0.00062	20.2
TkA01G060620	`PF16538`	FlgT_C	145	170	0.26	12.5

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
`Q84WS8`	Arabidopsis thaliana	sp\|Q84WS8\|U1125_ARATH U11/U12 small nuclear ribonucleoprotein 25 kDa protein	37.200%	Swiss-Prot	Low

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