TkA01G339940 | RubberDandelionOmics

Gene overview

TkA01G339940

Reference: TK1151 Chr: Chr01 Coordinates: 84414376-84419376 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2264 bp · TkA01G339940|TK1151|cDNA

ACTTTACCTACCATACCGACCAGCCTTATGTTTCCCATTCCCAAATTTAAGTTAAAAGATTCGAGATAAGATGAGGTGGTAAAACACGTGTACTTTATCGGTAACCAATTTATACCCTAATCCCCTCAATTGGGTGAGACTCGTACCGCTGAAACCCTAGCCTCCACCCAATCTCTCAACCCCGAAAGAAACCCTAAATCGATTCTCATCGTCCCGACCACCATGGCCAAGAAGCGAAAGTCTCGTGCTTCACAACCTTC...

CDS

Download CDS FASTA

1464 bp · TkA01G339940|TK1151|CDS

ATGGCCAAGAAGCGAAAGTCTCGTGCTTCACAACCTTCGGTGGAAGAACCAGTACCTAAGGAGGAGCCTCAAGTGCAGATCATTGAAGCACAACAGCAACAGGAAATTATTGCCAATGATGATGTCGTAAATGAGGAGCGAGAGCAAGAAGGTGATGAAATCGCTCAAAATATGGAGGATGTTATAGTAAAAGACGAAGCAGAAGAAGAAGATGACGAGGAAGATCCTCAGGACGATGATGAAGAAGAAGAAGAAGAAAG...

Protein

Download Protein FASTA

487 aa · TkA01G339940|TK1151|PROTEIN

MAKKRKSRASQPSVEEPVPKEEPQVQIIEAQQQQEIIANDDVVNEEREQEGDEIAQNMEDVIVKDEAEEEDDEEDPQDDDEEEEEESDEEANISEVKAEANGEGAEETEDLEDEPVENLLEPFSKEQLVLLLKEAVSKHPDLIESVQKIADADPAHRKIFVHGLGWDTNADILTSEFGKYGEIEDCKAVVDKVSGKSKGYAFILFKHRAGAQKALREPQKKIGNRMTSCQLASAGPIPAPPPTAPPVSEYTQRKIFVSNV...

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	`TkA01G339940`
TK1151 ID	TkA01G339940
OH-1004 ID	LXL04_012285
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	51.500
Protein coverage (%)	TK1151 45.791 / OH-1004 41.049 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

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 ID TkA01G339940

Location Chr01:84414376-84419376 (-)

Description Similar to UBA2B: UBP1-associated protein 2B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g41060`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of a complex regulating the turnover of mRNAs in the nucleus.	No verified direct reference in this release
`At3g56860`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of a complex regulating the turnover of mRNAs in the nucleus.	UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants.2002 · DOI: 10.1128/mcb.22.12.4346-4357.2002
`At3g15010`	Heterogeneous nuclear ribonucleoprotein (hnRNP)-like protein that acts as a component of a complex regulating the turnover of mRNAs in the nucleus.	No verified direct reference in this release
`At2g22090`	Acts as a component of a complex regulating the turnover of mRNAs in the nucleus.	UBA1 and UBA2, two proteins that interact with UBP1, a multifunctional effector of pre-mRNA maturation in plants.2002 · DOI: 10.1128/mcb.22.12.4346-4357.2002

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0265800`	RNA-binding protein that binds to a cis-localization element or zipcode, within the 5'-CDS of prolamine RNA.	Characterization of RNA binding protein RBP-P reveals a possible role in rice glutelin gene expression and RNA localization.2014 · DOI: 10.1007/s11103-014-0191-z RNA-Binding Protein RBP-P Is Required for Glutelin and Prolamine mRNA Localization in Rice Endosperm Cells.2018 · DOI: 10.1105/tpc.18.00321 Zipcode RNA-Binding Proteins and Membrane Trafficking Proteins Cooperate to Transport Glutelin mRNAs in Rice Endosperm.2020 · DOI: 10.1105/tpc.20.00111

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012285 · 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:0006952 defense response Biological Process

GO:0009693 ethylene biosynthetic process Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0010150 leaf senescence Biological Process

GO:0012501 programmed cell death Biological Process

GO:0048255 mRNA stabilization Biological Process

GO:0051028 mRNA transport Biological Process

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0035925 mRNA 3'-UTR AU-rich region binding Molecular Function

KEGG gene cross-reference

ath:AT2G22090

ath:AT2G41060

ath:AT3G15010

ath:AT3G56860

dosa:Os01g0265800

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.

Nucleus0.868

Rank 1 · TkA01G339940 · TK1151

Cytoplasm0.260

Rank 2 · TkA01G339940 · TK1151

Cell membrane0.037

Rank 3 · TkA01G339940 · TK1151

Endoplasmic reticulum0.028

Rank 4 · TkA01G339940 · TK1151

Mitochondrion0.024

Rank 5 · TkA01G339940 · 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.

PF10232Med820-114 aa

PF02724CDC4531-109 aa

PF11696DUF329245-121 aa

PF10986ZrgA61-99 aa

PF08559Cut874-150 aa

PF16367RRM_7157-222 aa

PF05172RRM_Nup35158-225 aa

PF00076RRM_1159-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G339940	`PF10232`	Med8	20	114	0.54	10.5
TkA01G339940	`PF02724`	CDC45	31	109	4.8	6.0
TkA01G339940	`PF11696`	DUF3292	45	121	1.1	8.3
TkA01G339940	`PF10986`	ZrgA	61	99	2.4	8.8
TkA01G339940	`PF08559`	Cut8	74	150	0.00038	20.8
TkA01G339940	`PF16367`	RRM_7	157	222	6.8e-11	42.7
TkA01G339940	`PF05172`	RRM_Nup35	158	225	6.6e-05	23.5
TkA01G339940	`PF00076`	RRM_1	159	225	5.4e-27	94.2
TkA01G339940	`PF28441`	RRM_11	162	227	0.00049	21.1
TkA01G339940	`PF16367`	RRM_7	253	313	6.8e-11	42.7
TkA01G339940	`PF00076`	RRM_1	255	322	5.4e-27	94.2
TkA01G339940	`PF28441`	RRM_11	267	312	0.00049	21.1
TkA01G339940	`PF05172`	RRM_Nup35	268	329	6.6e-05	23.5
TkA01G339940	`PF10986`	ZrgA	303	363	2.4	8.8
TkA01G339940	`PF08559`	Cut8	349	355	0.00038	20.8

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
`O80678`	Arabidopsis thaliana	sp\|O80678\|UBA2B_ARATH UBP1-associated protein 2B	56.300%	Swiss-Prot	High
`Q9LES2`	Arabidopsis thaliana	sp\|Q9LES2\|UBA2A_ARATH UBP1-associated protein 2A	54.600%	Swiss-Prot	Medium
`Q9LKA4`	Arabidopsis thaliana	sp\|Q9LKA4\|UBA2C_ARATH UBP1-associated protein 2C	49.300%	Swiss-Prot	Low
`Q9SHZ6`	Arabidopsis thaliana	sp\|Q9SHZ6\|UBA1A_ARATH UBP1-associated proteins 1A	49.600%	Swiss-Prot	Low
`Q9LJ04`	Oryza sativa subsp. japonica	sp\|Q9LJ04\|RBPP_ORYSJ RNA-binding protein P	54.100%	Swiss-Prot	Medium

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