LXL04_002419 | RubberDandelionOmics

Gene overview

LXL04_002419

Reference: OH-1004 Chr: Chr01 Coordinates: 48220545-48222818 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1617 bp · LXL04_002419|LXL04_002419|OH1004|cDNA

ATGAATAATACGAATTCAATCTACTTAACATGCGGATGCTTACTTTGGTTTCAGGATTTTTCCGATGACATCGATGTGAAAGTTAAAAAATACCAGAGAGGTGAAAGTGCCGACCTAGAGGCCTTGAAAGACAAAAAATTGAAAGGCCAGCTTGCTAATAGAGAAGAATTATATAAAAGGTCTGCTAATGCTGCTGCTAAAGCTGAAAAGtGGCTTATGCAAACTGAGAGTGGCCTTTTGGAAGCTGAAGGTATTGAAAA...

CDS

Download CDS FASTA

1617 bp · LXL04_002419|LXL04_002419|OH1004|CDS

ATGAATAATACGAATTCAATCTACTTAACATGCGGATGCTTACTTTGGTTTCAGGATTTTTCCGATGACATCGATGTGAAAGTTAAAAAATACCAGAGAGGTGAAAGTGCCGACCTAGAGGCCTTGAAAGACAAAAAATTGAAAGGCCAGCTTGCTAATAGAGAAGAATTATATAAAAGGTCTGCTAATGCTGCTGCTAAAGCTGAAAAGTGGCTTATGCAAACTGAGAGTGGCCTTTTGGAAGCTGAAGGTATTGAAAA...

Protein

Download Protein FASTA

538 aa · LXL04_002419|LXL04_002419|OH1004|PROTEIN

MNNTNSIYLTCGCLLWFQDFSDDIDVKVKKYQRGESADLEALKDKKLKGQLANREELYKRSANAAAKAEKWLMQTESGLLEAEGIEKTWRFSQQAIAQEVDIASRKNQFDIVLPDLGPYTIDYTASGRYMLTAGRKGHLAIMDLHTLKPVKDFQVRETVRDAVFLHNELFFAAAQKKYTYIYSREGTELHCLKEHGAVMKLQFLKNHFLLSSINKSGHLHYQDITTGQIVGSYRTALGRSDVLQLNPYNSVIASGHSGGT...

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_002419`
TK1151 ID	TkA04G261770
OH-1004 ID	LXL04_002419
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	84.200
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_002419`
Location	Chr01:48220545-48222818 (+)
Description	Similar to utp7: Probable U3 small nucleolar RNA-associated protein 7 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)
Arabidopsis / Rice Reference Genes and Papers	Download references for this gene Arabidopsis No hit for this species in the current source table. Rice No hit for this species in the current source table.
Functional annotation source	View annotation sources Functional annotation source: OH1004 · `LXL04_002419` · GCA_047496595.1_OSU_TarKok_2.0.
GO annotations (OH1004 source)	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:0030490 maturation of SSU-rRNA Biological Process GO:0042274 ribosomal small subunit biogenesis Biological Process GO:0005654 nucleoplasm Cellular Component GO:0005730 nucleolus Cellular Component GO:0005732 sno(s)RNA-containing ribonucleoprotein complex Cellular Component GO:0030686 90S preribosome Cellular Component GO:0030688 preribosome, small subunit precursor Cellular Component GO:0032040 small-subunit processome Cellular Component
KEGG gene cross-reference	hsa:9277 mmu:57315 sce:YER082C spo:2543484 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.

Nucleus0.950

Rank 1 · LXL04_002419 · OH-1004

Cytoplasm0.104

Rank 2 · LXL04_002419 · OH-1004

Mitochondrion0.019

Rank 3 · LXL04_002419 · OH-1004

Cell membrane0.011

Rank 4 · LXL04_002419 · OH-1004

Endoplasmic reticulum0.006

Rank 5 · LXL04_002419 · 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.

PF24817.2WD40_WDHD1_1st118-269 aa

PF23414.2Beta-prop_EML_2119-231 aa

PF25391.2WD40_Gbeta119-317 aa

PF23381.2Beta-prop_IFT122_1st120-264 aa

PF24814.2WD40_Prp19124-345 aa

PF25174.2Beta-prop_THOC3168-378 aa

PF24807.2WD40_CDC20-Fz172-388 aa

PF25175.2Beta-prop_WDR5175-328 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002419	`PF24817.2`	WD40_WDHD1_1st	118	269	8.2e-15	55.5
LXL04_002419	`PF23414.2`	Beta-prop_EML_2	119	231	3.7e-14	53.5
LXL04_002419	`PF25391.2`	WD40_Gbeta	119	317	3.6e-08	33.5
LXL04_002419	`PF23381.2`	Beta-prop_IFT122_1st	120	264	8.7e-16	58.8
LXL04_002419	`PF24814.2`	WD40_Prp19	124	345	1.7e-22	80.5
LXL04_002419	`PF25174.2`	Beta-prop_THOC3	168	378	1.8e-21	77.1
LXL04_002419	`PF24807.2`	WD40_CDC20-Fz	172	388	5.5e-16	59.4
LXL04_002419	`PF25175.2`	Beta-prop_WDR5	175	328	7.7e-17	62.2
LXL04_002419	`PF24796.2`	WDR55	178	312	1.9e-08	34.4
LXL04_002419	`PF25173.2`	Beta-prop_WDR3_1st	184	322	9.6e-15	55.5
LXL04_002419	`PF25047.1`	Beta-prop_TEP1_2nd	198	313	7.5e-08	32.6
LXL04_002419	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	214	318	7.6e-10	39.4
LXL04_002419	`PF23414.2`	Beta-prop_EML_2	242	325	3.7e-14	53.5
LXL04_002419	`PF23393.3`	Beta-prop_WDR90_POC16_2nd	244	308	1.1e-07	32.1
LXL04_002419	`PF23381.2`	Beta-prop_IFT122_1st	246	336	8.7e-16	58.8
LXL04_002419	`PF23409.2`	Beta-prop_EML	252	316	1.6e-07	31.8

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

No result was found for this query.

JBrowse

View in Genome Browser

Gene Card