LXL04_000887 | RubberDandelionOmics

Gene overview

LXL04_000887

Reference: OH-1004 Chr: Chr01 Coordinates: 16266561-16269220 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2018 bp · LXL04_000887|LXL04_000887|OH1004|cDNA

ATTTTACAAAATTGATTCGACGTAAATTGCAAAAATAGAACCCCCGTCGGGGACGGCGACATCGATATTGCTTTGAGAAAGAAGAACGAAGTCACACGCACAAATCAATGGAGGGTGATTCAGGATACGACGACGAAATTAGGGCTCATTTTCCCCTTTCTTTCGGCAAAAAATCCAAATCACAAACCCCAGTTGAATCAATTCACAACGCCACTCGCCGCCCCACCACCGGCGCCGACGGCTCACCATCTTCTACTAAC...

CDS

Download CDS FASTA

1911 bp · LXL04_000887|LXL04_000887|OH1004|CDS

ATGGAGGGTGATTCAGGATACGACGACGAAATTAGGGCTCATTTTCCCCTTTCTTTCGGCAAAAAATCCAAATCACAAACCCCAGTTGAATCAATTCACAACGCCACTCGCCGCCCCACCACCGGCGCCGACGGCTCACCATCTTCTACTAACAACAAGAACAAAGACAGCCCCTTTCCATCATTATCCTCATCCTCCAAGTCATGGTTAAATTCCCTCCAAAAAAACCCTAAACCCAGTACTGTTTCTGCGGGTGATGT...

Protein

Download Protein FASTA

636 aa · LXL04_000887|LXL04_000887|OH1004|PROTEIN

MEGDSGYDDEIRAHFPLSFGKKSKSQTPVESIHNATRRPTTGADGSPSSTNNKNKDSPFPSLSSSSKSWLNSLQKNPKPSTVSAGDVVIGPPRPPPSSESVDEEDDAMIGPPRPMPTEDDDDDDDDDEPIIGPPRPPVASDSDDDFPGSEPGIQHRIPLSNEIVLKGHTKVVSTLAIDHSGSRVLSGSFDYTIRMYDFQGMNARLESFRQLEPSEGHQVRSLSWSPSADRFLCVTGSATAKIFDRDGLTLGEFVKGDMYI...

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_000887`
TK1151 ID	TkA01G578730
OH-1004 ID	LXL04_000887
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID	`LXL04_000887`
Location	Chr01:16266561-16269220 (-)
Description	Similar to Wdr70: WD repeat-containing protein 70
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_000887` · GCA_047496595.1_OSU_TarKok_2.0.
GO annotations (OH1004 source)	GO:0000398 mRNA splicing, via spliceosome Biological Process GO:0005634 nucleus Cellular Component GO:0005654 nucleoplasm Cellular Component GO:0005681 spliceosomal complex Cellular Component GO:0035861 site of double-strand break Cellular Component GO:0071006 U2-type catalytic step 1 spliceosome Cellular Component GO:0019899 enzyme binding Molecular Function
KEGG gene cross-reference	bta:540724 hsa:55100 mmu:545085 rno:294783 xtr:780253 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.

Nucleus0.948

Rank 1 · LXL04_000887 · OH-1004

Cytoplasm0.142

Rank 2 · LXL04_000887 · OH-1004

Cell membrane0.016

Rank 3 · LXL04_000887 · OH-1004

Mitochondrion0.016

Rank 4 · LXL04_000887 · OH-1004

Endoplasmic reticulum0.009

Rank 5 · LXL04_000887 · 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.

PF24817.2WD40_WDHD1_1st160-246 aa

PF25173.2Beta-prop_WDR3_1st161-200 aa

PF24807.2WD40_CDC20-Fz162-239 aa

PF00400.39WD40164-197 aa

PF25175.2Beta-prop_WDR5164-244 aa

PF23381.2Beta-prop_IFT122_1st165-245 aa

PF24814.2WD40_Prp19165-244 aa

PF24805.2EIF3I165-308 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_000887	`PF24817.2`	WD40_WDHD1_1st	160	246	1e-21	78.1
LXL04_000887	`PF25173.2`	Beta-prop_WDR3_1st	161	200	1.2e-25	91.0
LXL04_000887	`PF24807.2`	WD40_CDC20-Fz	162	239	1.8e-22	80.8
LXL04_000887	`PF00400.39`	WD40	164	197	1.1e-31	108.7
LXL04_000887	`PF25175.2`	Beta-prop_WDR5	164	244	1.3e-30	107.4
LXL04_000887	`PF23381.2`	Beta-prop_IFT122_1st	165	245	2.3e-26	93.5
LXL04_000887	`PF24814.2`	WD40_Prp19	165	244	4e-24	85.9
LXL04_000887	`PF24805.2`	EIF3I	165	308	2.9e-12	47.1
LXL04_000887	`PF23409.2`	Beta-prop_EML	167	430	6.5e-13	49.5
LXL04_000887	`PF25174.2`	Beta-prop_THOC3	168	244	2.9e-32	112.5
LXL04_000887	`PF25174.2`	Beta-prop_THOC3	217	308	2.9e-32	112.5
LXL04_000887	`PF25047.1`	Beta-prop_TEP1_2nd	220	415	3.8e-22	79.4
LXL04_000887	`PF24807.2`	WD40_CDC20-Fz	263	348	1.8e-22	80.8
LXL04_000887	`PF25175.2`	Beta-prop_WDR5	264	429	1.3e-30	107.4
LXL04_000887	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	265	427	9.4e-15	55.4
LXL04_000887	`PF25173.2`	Beta-prop_WDR3_1st	267	430	1.2e-25	91.0

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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