TkA04G017650 | RubberDandelionOmics

Gene overview

TkA04G017650

Reference: TK1151 Chr: Chr04 Coordinates: 4402226-4403850 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1323 bp · TkA04G017650|TK1151|cDNA

ATGGCTACTTTAATTTCCCAAAATGCGTGTCCTATCTGCATACGATGGTGCACCATCAGGCGAAATCGTGACCACGGACAATCCCGGCCAAAAAAACCCGTGTGGGTAGACGAAGAGGAACAAAAAACCACCATAAACATCTCCAAAATCAACCGGTTAAGAAAGATCCGGAACACAGAAGACGAAACGATAATATCCGGATCCGAATACATCTCGAGACTCCGGGCCCACCACACGAAACTCAACCCGGGCACAAACTG...

CDS

Download CDS FASTA

1323 bp · TkA04G017650|TK1151|CDS

ATGGCTACTTTAATTTCCCAAAATGCGTGTCCTATCTGCATACGATGGTGCACCATCAGGCGAAATCGTGACCACGGACAATCCCGGCCAAAAAAACCCGTGTGGGTAGACGAAGAGGAACAAAAAACCACCATAAACATCTCCAAAATCAACCGGTTAAGAAAGATCCGGAACACAGAAGACGAAACGATAATATCCGGATCCGAATACATCTCGAGACTCCGGGCCCACCACACGAAACTCAACCCGGGCACAAACTG...

Protein

Download Protein FASTA

440 aa · TkA04G017650|TK1151|PROTEIN

MATLISQNACPICIRWCTIRRNRDHGQSRPKKPVWVDEEEQKTTINISKINRLRKIRNTEDETIISGSEYISRLRAHHTKLNPGTNWAHPESKTYNSDDEDTILQTTEDLVVSGSSKLLPGVLEYSRLIDGNAQDPSSGPVNSVHFHRNGQLLLTGGLDKKLRFFQIDGKRNLKIQSVFIDDCPIRKAAFTPDGSQVIVSGRRKFFYTFDLVKSEASKIGPLVGREEKSLENFEISPDSKTIAFIGNEGYVLLVSTKTKE...

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	`TkA04G017650`
TK1151 ID	TkA04G017650
OH-1004 ID	LXL04_036918
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.800
Protein coverage (%)	TK1151 93.409 / OH-1004 71.107 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 TkA04G017650

Location Chr04:4402226-4403850 (+)

Description Similar to At5g14050: U3 small nucleolar RNA-associated protein 18 homolog

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g14050`	Involved in nucleolar processing of pre-18S ribosomal RNA.	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_036918 · 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:0000292 RNA fragment catabolic process Biological Process

GO:0000447 endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0000472 endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0000480 endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Biological Process

GO:0006364 rRNA processing Biological Process

GO:0030490 maturation of SSU-rRNA Biological Process

GO:0042274 ribosomal small subunit biogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0030686 90S preribosome Cellular Component

GO:0031965 nuclear membrane Cellular Component

KEGG gene cross-reference

ath:AT5G14050

hsa:51096

mmu:217109

sce:YJL069C

spo:2540529

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.

Nucleus0.944

Rank 1 · TkA04G017650 · TK1151

Cytoplasm0.123

Rank 2 · TkA04G017650 · TK1151

Mitochondrion0.023

Rank 3 · TkA04G017650 · TK1151

Cell membrane0.015

Rank 4 · TkA04G017650 · TK1151

Endoplasmic reticulum0.007

Rank 5 · TkA04G017650 · 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.

PF23098Beta-prop_NOL10_N29-89 aa

PF23409Beta-prop_EML49-89 aa

PF24805EIF3I69-103 aa

PF23393Beta-prop_WDR90_POC16_2nd116-205 aa

PF12894ANAPC4_WD40134-169 aa

PF25171Beta-prop_WDR36-Utp21_1st136-168 aa

PF23342WDR90_beta-prop_4th136-159 aa

PF24807WD40_CDC20-Fz137-303 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G017650	`PF23098`	Beta-prop_NOL10_N	29	89	3.5e-06	27.1
TkA04G017650	`PF23409`	Beta-prop_EML	49	89	0.0008	19.7
TkA04G017650	`PF24805`	EIF3I	69	103	9.5e-05	22.4
TkA04G017650	`PF23393`	Beta-prop_WDR90_POC16_2nd	116	205	1.1e-07	32.1
TkA04G017650	`PF12894`	ANAPC4_WD40	134	169	8.3e-10	39.5
TkA04G017650	`PF25171`	Beta-prop_WDR36-Utp21_1st	136	168	3.8e-07	30.5
TkA04G017650	`PF23342`	WDR90_beta-prop_4th	136	159	0.19	11.5
TkA04G017650	`PF24807`	WD40_CDC20-Fz	137	303	8.5e-13	49.0
TkA04G017650	`PF25172`	Beta-prop_WDR3_2nd	137	171	1.9e-05	24.8
TkA04G017650	`PF23775`	Beta-prop_RIG_2nd	137	201	0.0062	16.7
TkA04G017650	`PF00400`	WD40	138	165	3.8e-17	62.7
TkA04G017650	`PF24814`	WD40_Prp19	138	305	2.4e-16	60.3
TkA04G017650	`PF25175`	Beta-prop_WDR5	138	211	7.5e-15	55.7
TkA04G017650	`PF25168`	Beta-prop_WDR36-Utp21_2nd	138	285	0.00053	20.1
TkA04G017650	`PF25047`	Beta-prop_TEP1_2nd	138	167	0.0077	16.1
TkA04G017650	`PF25174`	Beta-prop_THOC3	139	421	2.8e-24	86.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9FMU5`	Arabidopsis thaliana	sp\|Q9FMU5\|UTP18_ARATH U3 small nucleolar RNA-associated protein 18 homolog	67.600%	Swiss-Prot	High

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