LXL04_032088 | RubberDandelionOmics

Gene overview

LXL04_032088

Reference: OH-1004 Chr: Chr07 Coordinates: 16626360-16629541 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2724 bp · LXL04_032088|LXL04_032088|OH1004|cDNA

CTACTAGGGTTTAAGAGCAGCGCCCCATTACTTTGGGAAGCGCCGGGAAGCATTTGAGCGTCGTCAACCTCTCGACGCGTTACCATGAACTACAGGTTTCAAAATCTCCTCGGAGCTCCCTACAGAGGCGGTAATGCCATTGTTGTCAACAACACACTTCTTATATCACCAGTTGGCAACCGTATCTCTGTCACAGACCTCGTGAAATCAGAAACCATAACTCTTCCCTGTCAAGCCTCATCAAACATATCCAGAATTGC...

CDS

Download CDS FASTA

2640 bp · LXL04_032088|LXL04_032088|OH1004|CDS

ATGAACTACAGGTTTCAAAATCTCCTCGGAGCTCCCTACAGAGGCGGTAATGCCATTGTTGTCAACAACACACTTCTTATATCACCAGTTGGCAACCGTATCTCTGTCACAGACCTCGTGAAATCAGAAACCATAACTCTTCCCTGTCAAGCCTCATCAAACATATCCAGAATTGCCGCCTCTCCTGACGGCGTATTCCTCCTCGCCATTGACGACAACTCCCGCTGCCTCTTCATCAACCTACCTCGCCGTGCCGTACT...

Protein

Download Protein FASTA

879 aa · LXL04_032088|LXL04_032088|OH1004|PROTEIN

MNYRFQNLLGAPYRGGNAIVVNNTLLISPVGNRISVTDLVKSETITLPCQASSNISRIAASPDGVFLLAIDDNSRCLFINLPRRAVLHRINFKKPVASAKFSPDGSFIAVAAGKLVQVWRSPGFKKEFFPFELVKTFANCNDKVTALDWSPDSDYLLAGSKDLTVRLFCLKKLSGSHKPFMFLGHRDVIKGVFFGVEKKTKQVSRVYTVSRDGAIFTWNYTARDETPDEIPSPGTPEQTMEVDQTSNFKKRKSSDLISNE...

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	`LXL04_032088`
TK1151 ID	TkA02G360160
OH-1004 ID	LXL04_032088
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	22.300
Protein coverage (%)	TK1151 31.090 / OH-1004 20.250 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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_032088

Location Chr07:16626360-16629541 (-)

Description Similar to PWP2: Periodic tryptophan protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g15440`	Involved in nucleolar processing of pre-18S ribosomal RNA.	A comparative study of the Arabidopsis thaliana guard-cell transcriptome and its modulation by sucrose.2012 · DOI: 10.1371/journal.pone.0049641 40S ribosome biogenesis co-factors are essential for gametophyte and embryo development.2013 · DOI: 10.1371/journal.pone.0054084

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_032088 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000028 ribosomal small subunit assembly 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:0000462 maturation of SSU-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:0000920 septum digestion after cytokinesis Biological Process

GO:0006364 rRNA processing Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009744 response to sucrose Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0030010 establishment of cell polarity Biological Process

GO:0030490 maturation of SSU-rRNA Biological Process

KEGG gene cross-reference

ath:AT1G15440

hsa:5822

pon:100190840

sce:YCR057C

spo:2541182

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.

Nucleus0.799

Rank 1 · LXL04_032088 · OH-1004

Cytoplasm0.205

Rank 2 · LXL04_032088 · OH-1004

Lysosome / Vacuole0.044

Rank 3 · LXL04_032088 · OH-1004

Golgi apparatus0.034

Rank 4 · LXL04_032088 · OH-1004

Cell membrane0.031

Rank 5 · LXL04_032088 · OH-1004

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.

PF24807.2WD40_CDC20-Fz23-169 aa

PF25174.2Beta-prop_THOC343-126 aa

PF24814.2WD40_Prp1949-175 aa

PF23414.2Beta-prop_EML_266-199 aa

PF25172.2Beta-prop_WDR3_2nd89-219 aa

PF25047.1Beta-prop_TEP1_2nd91-226 aa

PF25175.2Beta-prop_WDR593-222 aa

PF25173.2Beta-prop_WDR3_1st93-221 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_032088	`PF24807.2`	WD40_CDC20-Fz	23	169	1.5e-49	169.6
LXL04_032088	`PF25174.2`	Beta-prop_THOC3	43	126	2.2e-57	194.9
LXL04_032088	`PF24814.2`	WD40_Prp19	49	175	1.6e-48	165.9
LXL04_032088	`PF23414.2`	Beta-prop_EML_2	66	199	1.1e-41	143.7
LXL04_032088	`PF25172.2`	Beta-prop_WDR3_2nd	89	219	3.4e-29	102.7
LXL04_032088	`PF25047.1`	Beta-prop_TEP1_2nd	91	226	2.3e-27	96.5
LXL04_032088	`PF25175.2`	Beta-prop_WDR5	93	222	1.8e-60	205.4
LXL04_032088	`PF25173.2`	Beta-prop_WDR3_1st	93	221	9.3e-56	189.2
LXL04_032088	`PF23381.2`	Beta-prop_IFT122_1st	96	194	1.1e-53	183.0
LXL04_032088	`PF00400.39`	WD40	132	168	1.8e-51	171.1
LXL04_032088	`PF25174.2`	Beta-prop_THOC3	141	404	2.2e-57	194.9
LXL04_032088	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	257	396	2.1e-22	80.6
LXL04_032088	`PF24807.2`	WD40_CDC20-Fz	282	523	1.5e-49	169.6
LXL04_032088	`PF24814.2`	WD40_Prp19	284	473	1.6e-48	165.9
LXL04_032088	`PF24796.2`	WDR55	285	566	7.8e-25	88.2
LXL04_032088	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	296	485	4.3e-27	96.0

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
`Q8VYZ5`	Arabidopsis thaliana	Periodic tryptophan protein 2	68.380%	Swiss-Prot	strong database homology

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