LXL04_011629 | RubberDandelionOmics

Gene overview

LXL04_011629

Reference: OH-1004 Chr: Chr02 Coordinates: 168541416-168543552 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1542 bp · LXL04_011629|LXL04_011629|OH1004|cDNA

ATGATGAAAGGTAAAAAGTTCAATAACAATAACAAGAGTCAAAATGGGCACAGAAGCAAACGGTTTAAATCCGACAAGCCAGACCCGTTCTTCGACGGCGATTCAAAACACCGAAAGAAATTTGCAAATCGAGACAATGATGAGGACAGCATTAAGAGCAGTGATTCTGAAGATTATGACGACAGAGATGTGGCGGCGGCGGTGGAGGATGACGGCGAGGAAAATGAATTGGTTGAAGAGGACGCAGGTGAGAAACGGAA...

CDS

Download CDS FASTA

1542 bp · LXL04_011629|LXL04_011629|OH1004|CDS

ATGATGAAAGGTAAAAAGTTCAATAACAATAACAAGAGTCAAAATGGGCACAGAAGCAAACGGTTTAAATCCGACAAGCCAGACCCGTTCTTCGACGGCGATTCAAAACACCGAAAGAAATTTGCAAATCGAGACAATGATGAGGACAGCATTAAGAGCAGTGATTCTGAAGATTATGACGACAGAGATGTGGCGGCGGCGGTGGAGGATGACGGCGAGGAAAATGAATTGGTTGAAGAGGACGCAGGTGAGAAACGGAA...

Protein

Download Protein FASTA

513 aa · LXL04_011629|LXL04_011629|OH1004|PROTEIN

MMKGKKFNNNNKSQNGHRSKRFKSDKPDPFFDGDSKHRKKFANRDNDEDSIKSSDSEDYDDRDVAAAVEDDGEENELVEEDAGEKRKRVAEAYVEKIRAGLRKQEEEGDDEVDERGGKEGGDRDSLVARMLQAQQLEDSGRVRKLIASRVQKPTTADGFKVLVKHRQSVTSVVLSEDDSKGFSASKDGYIVQWDVESGKAEAYTWPSEEVLKSHGAKEPQGRAKKRSKHVLALAVSSDGRYLASGGFDRHVHLWDTRTRE...

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_011629`
TK1151 ID	TkA03G606970
OH-1004 ID	LXL04_011629
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 100.000 / OH-1004 99.805 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011629

Location Chr02:168541416-168543552 (-)

Description Similar to YAO: U3 snoRNP-associated protein-like YAO

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g05410`	Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA (By similarity).	No verified direct reference in this release
`At4g21130`	Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA (By similarity).	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0625900`	Component of a nucleolar small nuclear ribonucleoprotein particle (snoRNP) thought to participate in the processing and modification of pre-ribosomal RNA (By similarity).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_011629 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006364 rRNA processing Biological Process

GO:0009553 embryo sac development Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0030490 maturation of SSU-rRNA Biological Process

GO:0042274 ribosomal small subunit biogenesis Biological Process

GO:0060321 acceptance of pollen Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0031428 box C/D methylation guide snoRNP complex Cellular Component

GO:0032040 small-subunit processome Cellular Component

GO:0080008 Cul4-RING E3 ubiquitin ligase complex Cellular Component

KEGG gene cross-reference

ath:AT4G05410

ath:AT4G21130

dosa:Os03g0625900

hsa:9136

mmu:27966

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.

Nucleus0.954

Rank 1 · LXL04_011629 · OH-1004

Cytoplasm0.105

Rank 2 · LXL04_011629 · OH-1004

Mitochondrion0.018

Rank 3 · LXL04_011629 · OH-1004

Cell membrane0.017

Rank 4 · LXL04_011629 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_011629 · OH-1004

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.

PF24105.2Beta-prop_CAF1B_HIR1159-301 aa

PF24796.2WDR55162-390 aa

PF23098.2Beta-prop_NOL10_N167-308 aa

PF25171.2Beta-prop_WDR36-Utp21_1st186-337 aa

PF25047.1Beta-prop_TEP1_2nd205-339 aa

PF24782.3WD40_MABP1-WDR62_2nd218-340 aa

PF24807.2WD40_CDC20-Fz221-340 aa

PF25173.2Beta-prop_WDR3_1st223-379 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011629	`PF24105.2`	Beta-prop_CAF1B_HIR1	159	301	1.4e-11	44.7
LXL04_011629	`PF24796.2`	WDR55	162	390	1.9e-20	73.8
LXL04_011629	`PF23098.2`	Beta-prop_NOL10_N	167	308	1.6e-06	28.2
LXL04_011629	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	186	337	6.2e-12	46.2
LXL04_011629	`PF25047.1`	Beta-prop_TEP1_2nd	205	339	1.8e-25	90.3
LXL04_011629	`PF24782.3`	WD40_MABP1-WDR62_2nd	218	340	1.5e-12	47.9
LXL04_011629	`PF24807.2`	WD40_CDC20-Fz	221	340	1.7e-23	84.1
LXL04_011629	`PF25173.2`	Beta-prop_WDR3_1st	223	379	4.6e-38	131.5
LXL04_011629	`PF23381.2`	Beta-prop_IFT122_1st	223	301	1.1e-32	114.2
LXL04_011629	`PF24817.2`	WD40_WDHD1_1st	224	266	2.7e-23	83.3
LXL04_011629	`PF23414.2`	Beta-prop_EML_2	224	319	9.1e-20	71.9
LXL04_011629	`PF25391.2`	WD40_Gbeta	225	377	2.8e-16	60.2
LXL04_011629	`PF24780.2`	WD40_MABP1-WDR62_1st	225	305	6.4e-09	36.2
LXL04_011629	`PF23798.2`	Beta-prop_SPT8	225	379	2e-07	31.0
LXL04_011629	`PF24814.2`	WD40_Prp19	226	318	6.4e-27	95.0
LXL04_011629	`PF25174.2`	Beta-prop_THOC3	227	312	2e-41	142.5

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
`Q9M0V4`	Arabidopsis thaliana	U3 snoRNP-associated protein-like YAO	55.361%	Swiss-Prot	strong database homology
`Q3MKM6`	Arabidopsis thaliana	U3 snoRNP-associated protein-like EMB2271	56.584%	Swiss-Prot	strong database homology
`Q75LV5`	Oryza sativa subsp. japonica	U3 snoRNP-associated protein-like YAOH	56.478%	Swiss-Prot	strong database homology

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