TkA04G388560 | RubberDandelionOmics

Gene overview

TkA04G388560

Reference: TK1151 Chr: Chr04 Coordinates: 97738097-97742173 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1052 bp · TkA04G388560|TK1151|cDNA

CTAAATCCCATTTATGCTCTGAATTCGATAGTTTTCTAGTGAAGATACGGCCCCTTCCCGCCGGTGACGCATCCCGTTATCAAGCTGCACATTCACCACTTGTGAAGAAATGGTTGAAGTAAACAAGCCAGGACAATTGGTTCCTGAATCTGTATTGAAGAAACAAAAGAGAAATGAAGAATGGGCTTTAGCAAAGAAGCAAGAAACTGAATCATTGAAGAAGAAGAATGCTGCTAACAGGAAGTTGATCTTCAACAGAG...

CDS

Download CDS FASTA

738 bp · TkA04G388560|TK1151|CDS

ATGGTTGAAGTAAACAAGCCAGGACAATTGGTTCCTGAATCTGTATTGAAGAAACAAAAGAGAAATGAAGAATGGGCTTTAGCAAAGAAGCAAGAAACTGAATCATTGAAGAAGAAGAATGCTGCTAACAGGAAGTTGATCTTCAACAGAGCCAAACAGTACACCAAAGAATATGAAGACCAGCAAAAGGAGCTAATCCAATTGAAACGTGAAGCAAGATTGAAAGGTGGATTCTATGTGAACCCAGAAGCCAAGATGTT...

Protein

Download Protein FASTA

245 aa · TkA04G388560|TK1151|PROTEIN

MVEVNKPGQLVPESVLKKQKRNEEWALAKKQETESLKKKNAANRKLIFNRAKQYTKEYEDQQKELIQLKREARLKGGFYVNPEAKMLFIIRIRGINAMDPKSKKILQLLRLRQIFNGVFLKVNKATLNMLHRVEPYVTYGYPNLKSVKELIYKRGYGKLNKQRIALTDNSIVEQGLGKFGLICVEDLIHEILTAGPHFKEANNFLWPFKLKAPLGGMKKKRNHYVEGGDAGNREDYINELIRRMN

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	`TkA04G388560`
TK1151 ID	TkA04G388560
OH-1004 ID	LXL04_038097
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 71.014 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 TkA04G388560

Location Chr04:97738097-97742173 (-)

Description Similar to RPL7D: 60S ribosomal protein L7-4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g13580`	Large ribosomal subunit protein uL30w.	No verified direct reference in this release
`At2g01250`	Large ribosomal subunit protein uL30y.	No verified direct reference in this release
`At2g44120`	Large ribosomal subunit protein uL30x.	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_038097 · 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:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0002181 cytoplasmic translation Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006412 translation Biological Process

GO:0006941 striated muscle contraction Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0042273 ribosomal large subunit biogenesis Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0005773 vacuole Cellular Component

KEGG gene cross-reference

ath:AT2G01250

ath:AT2G44120

ath:AT3G13580

mmu:19989

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.

Cytoplasm0.462

Rank 1 · TkA04G388560 · TK1151

Nucleus0.198

Rank 2 · TkA04G388560 · TK1151

Mitochondrion0.189

Rank 3 · TkA04G388560 · TK1151

Endoplasmic reticulum0.018

Rank 4 · TkA04G388560 · TK1151

Cell membrane0.010

Rank 5 · TkA04G388560 · 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.

PF08079Ribosomal_L30_N11-81 aa

PF16753Tipalpha52-96 aa

PF00327Ribosomal_L3087-137 aa

PF16753Tipalpha112-161 aa

PF08079Ribosomal_L30_N218-225 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G388560	`PF08079`	Ribosomal_L30_N	11	81	3.3e-25	88.9
TkA04G388560	`PF16753`	Tipalpha	52	96	0.052	14.1
TkA04G388560	`PF00327`	Ribosomal_L30	87	137	1.1e-17	64.2
TkA04G388560	`PF16753`	Tipalpha	112	161	0.052	14.1
TkA04G388560	`PF08079`	Ribosomal_L30_N	218	225	3.3e-25	88.9

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
`Q9LHP1`	Arabidopsis thaliana	sp\|Q9LHP1\|RL74_ARATH Large ribosomal subunit protein uL30w	85.600%	Swiss-Prot	High
`P60040`	Arabidopsis thaliana	sp\|P60040\|RL72_ARATH Large ribosomal subunit protein uL30y	85.200%	Swiss-Prot	High
`P60039`	Arabidopsis thaliana	sp\|P60039\|RL73_ARATH Large ribosomal subunit protein uL30x	83.100%	Swiss-Prot	High

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