TkA04G033310 | RubberDandelionOmics

Gene overview

TkA04G033310

Reference: TK1151 Chr: Chr04 Coordinates: 8909531-8910855 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

354 bp · TkA04G033310|TK1151|cDNA

ATGCTGACGGCCGACATACCACCGAACCAGACAATTTACGTCAAGAATCTCAACGAGAAGGTCAAGAAAGAAGGCCGAAAGAAAAAAGATCCACATGCTCCACAACCTACTAATGGAGCTAGACCCGACACGAATGGCACCCCTGCTGGGTCATATGGAATGGGAGAGGACATGTTGGAGCTTCTGTTCAAACAGTTTCCTGGATTTAAGGAAAGTGAGAATGATAGATGCGAACCGGGAATTGCGTTTGTGGAGTTTGA...

CDS

Download CDS FASTA

354 bp · TkA04G033310|TK1151|CDS

ATGCTGACGGCCGACATACCACCGAACCAGACAATTTACGTCAAGAATCTCAACGAGAAGGTCAAGAAAGAAGGCCGAAAGAAAAAAGATCCACATGCTCCACAACCTACTAATGGAGCTAGACCCGACACGAATGGCACCCCTGCTGGGTCATATGGAATGGGAGAGGACATGTTGGAGCTTCTGTTCAAACAGTTTCCTGGATTTAAGGAAAGTGAGAATGATAGATGCGAACCGGGAATTGCGTTTGTGGAGTTTGA...

Protein

Download Protein FASTA

117 aa · TkA04G033310|TK1151|PROTEIN

MLTADIPPNQTIYVKNLNEKVKKEGRKKKDPHAPQPTNGARPDTNGTPAGSYGMGEDMLELLFKQFPGFKESENDRCEPGIAFVEFDDDNQSSTAMQSLQGFKITPQKLMAISYAKK

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	`TkA04G033310`
TK1151 ID	TkA04G033310
OH-1004 ID	LXL04_018896
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	55.000
Protein coverage (%)	TK1151 51.282 / OH-1004 24.590 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 TkA04G033310

Location Chr04:8909531-8910855 (+)

Description Similar to U1A: U1 small nuclear ribonucleoprotein A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g06960`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release
`At2g30260`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: B8AM21`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release
`Os03g0298800`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release
`UniProt: A2Y0J7`	Involved in nuclear pre-mRNA splicing.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_018896 · 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:0000354 cis assembly of pre-catalytic spliceosome Biological Process

GO:0000398 mRNA splicing, via spliceosome Biological Process

GO:0006397 mRNA processing Biological Process

GO:0008380 RNA splicing Biological Process

GO:0009631 cold acclimation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005681 spliceosomal complex Cellular Component

GO:0005685 U1 snRNP Cellular Component

GO:0005686 U2 snRNP Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G06960

ath:AT2G30260

ath:AT2G47580

dosa:Os05g0154800

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.

Nucleus0.584

Rank 1 · TkA04G033310 · TK1151

Cytoplasm0.342

Rank 2 · TkA04G033310 · TK1151

Extracellular0.193

Rank 3 · TkA04G033310 · TK1151

Cell membrane0.043

Rank 4 · TkA04G033310 · TK1151

Mitochondrion0.039

Rank 5 · TkA04G033310 · 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.

PF00076RRM_112-24 aa

PF00076RRM_152-106 aa

PF29326RRM_MUD2_C80-110 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G033310	`PF00076`	RRM_1	12	24	1.4e-07	32.0
TkA04G033310	`PF00076`	RRM_1	52	106	1.4e-07	32.0
TkA04G033310	`PF29326`	RRM_MUD2_C	80	110	0.24	12.2

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
`Q8H1S6`	Arabidopsis thaliana	sp\|Q8H1S6\|RU2B2_ARATH U2 small nuclear ribonucleoprotein B'' 2	66.700%	Swiss-Prot	Medium
`O22922`	Arabidopsis thaliana	sp\|O22922\|RU2B1_ARATH U2 small nuclear ribonucleoprotein B''	66.700%	Swiss-Prot	Medium
`B8AM21`	Oryza sativa subsp. indica	sp\|B8AM21\|RU2B_ORYSI U2 small nuclear ribonucleoprotein B''	65.000%	Swiss-Prot	Medium
`Q10MR0`	Oryza sativa subsp. japonica	sp\|Q10MR0\|RU2B_ORYSJ U2 small nuclear ribonucleoprotein B''	65.000%	Swiss-Prot	Medium
`A2Y0J7`	Oryza sativa subsp. indica	sp\|A2Y0J7\|RU1A_ORYSI U1 small nuclear ribonucleoprotein A	58.300%	Swiss-Prot	Medium

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