TkA03G400070 | RubberDandelionOmics

Gene overview

TkA03G400070

Reference: TK1151 Chr: Chr03 Coordinates: 99481147-99482717 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

838 bp · TkA03G400070|TK1151|cDNA

GCCAAATCGTCCCCCCTCCCAAAAAAAATCTCCCTCTCTGATTCTCTCTCGCTATTCCGCCATTTTTCTTCATTCACCTGTGTTTGACTATAAAAAGCTAGGGTTTCTTTATTTCCAGGATCATTAAAACATACATATGATGGAGATAATGTCGAGCTTCGATCACGATAATCGGAATCCAAGGGTTTTGATTCACAACGCGCTCCTTGTTCGAGGCTTATCGTTTTCGTATCACAAGCTTCCTAAACAACTTCTCAAGC...

CDS

Download CDS FASTA

609 bp · TkA03G400070|TK1151|CDS

ATGATGGAGATAATGTCGAGCTTCGATCACGATAATCGGAATCCAAGGGTTTTGATTCACAACGCGCTCCTTGTTCGAGGCTTATCGTTTTCGTATCACAAGCTTCCTAAACAACTTCTCAAGCTATCTGTTCTGAAATTAGATGGTTCTTCCTTTGGCGTCGAGGTTTCTATGAATGCTACCGTAGCAGATCTTAAACTTGTATTAGAGAAGTTTTTTCGCTTCTTGCCTAAGGAGGAGAGACGCATTGTTTCCTGGTC...

Protein

Download Protein FASTA

202 aa · TkA03G400070|TK1151|PROTEIN

MMEIMSSFDHDNRNPRVLIHNALLVRGLSFSYHKLPKQLLKLSVLKLDGSSFGVEVSMNATVADLKLVLEKFFRFLPKEERRIVSWSHVWGHFCLCYKGKKLLNDKAYIRRLGIKDGDQIKFVRHVTINYRPARQQMIKNQSDDELKQCSMSSYDEDGDLNDVRNCESVEDEQVESVFIHGSKVANFLKGWFSYRKFRNGIV

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	`TkA03G400070`
TK1151 ID	TkA03G400070
OH-1004 ID	LXL04_009166
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.600
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 TkA03G400070

Location Chr03:99481147-99482717 (-)

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_009166 · 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.

Nucleus0.403

Rank 1 · TkA03G400070 · TK1151

Cytoplasm0.317

Rank 2 · TkA03G400070 · TK1151

Cell membrane0.306

Rank 3 · TkA03G400070 · TK1151

Endoplasmic reticulum0.099

Rank 4 · TkA03G400070 · TK1151

Lysosome / Vacuole0.064

Rank 5 · TkA03G400070 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF18036Ubiquitin_430-127 aa

PF00240ubiquitin46-79 aa

PF14461Prok-E2_B52-98 aa

PF23603Ubiquitin_TPR152-76 aa

PF25565Ubiquitin_At1g3342054-74 aa

PF00240ubiquitin93-125 aa

PF23603Ubiquitin_TPR195-115 aa

PF08595RXT2_N99-172 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G400070	`PF18036`	Ubiquitin_4	30	127	1.1e-28	100.0
TkA03G400070	`PF00240`	ubiquitin	46	79	2.5e-07	31.1
TkA03G400070	`PF14461`	Prok-E2_B	52	98	0.12	13.1
TkA03G400070	`PF23603`	Ubiquitin_TPR1	52	76	0.17	12.3
TkA03G400070	`PF25565`	Ubiquitin_At1g33420	54	74	0.09	13.4
TkA03G400070	`PF00240`	ubiquitin	93	125	2.5e-07	31.1
TkA03G400070	`PF23603`	Ubiquitin_TPR1	95	115	0.17	12.3
TkA03G400070	`PF08595`	RXT2_N	99	172	0.31	11.8
TkA03G400070	`PF25565`	Ubiquitin_At1g33420	162	183	0.09	13.4
TkA03G400070	`PF23603`	Ubiquitin_TPR1	176	185	0.17	12.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q84WS8`	Arabidopsis thaliana	sp\|Q84WS8\|U1125_ARATH U11/U12 small nuclear ribonucleoprotein 25 kDa protein	41.600%	Swiss-Prot	Low

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