LXL04_019422 | RubberDandelionOmics

Gene overview

LXL04_019422

Reference: OH-1004 Chr: Chr04 Coordinates: 31010985-31013626 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1074 bp · LXL04_019422|LXL04_019422|OH1004|cDNA

ATGGAGATTAATTTGAAGAATATAGCATTCGACCTTGATTTTCATCCTTCAAATCAGCTAGTTGCTGCTGGTTTAATCACTGGCAACCTTTTTGTATATCGATATGCTGAAGATTCTGAACCAAAAAGGGTGTTGAAGGTTCGTGCCCATGGTGAATCTTGTAGAGCTGCTAGATTCATCAATGAAGGACGTGTAATTCTCACGGGGTCTCCAGACTGTTCAATCCTGGCCACTGATATTGAAACAGGATCTCCAGTTGC...

CDS

Download CDS FASTA

1074 bp · LXL04_019422|LXL04_019422|OH1004|CDS

ATGGAGATTAATTTGAAGAATATAGCATTCGACCTTGATTTTCATCCTTCAAATCAGCTAGTTGCTGCTGGTTTAATCACTGGCAACCTTTTTGTATATCGATATGCTGAAGATTCTGAACCAAAAAGGGTGTTGAAGGTTCGTGCCCATGGTGAATCTTGTAGAGCTGCTAGATTCATCAATGAAGGACGTGTAATTCTCACGGGGTCTCCAGACTGTTCAATCCTGGCCACTGATATTGAAACAGGATCTCCAGTTGC...

Protein

Download Protein FASTA

357 aa · LXL04_019422|LXL04_019422|OH1004|PROTEIN

MEINLKNIAFDLDFHPSNQLVAAGLITGNLFVYRYAEDSEPKRVLKVRAHGESCRAARFINEGRVILTGSPDCSILATDIETGSPVARLENCHEKAVNRLVNLTETTVASGGDEGCIKVWDTRQQTCCNTFQVHEEYITDMTLEPDSMKLLGTSGDGTLSVCNLRSNKVQTQSEFSEDEPLSIVIMKNGRKVICGTESGTMLLYSWGFFKDCSDRFTGLSPNPVNTLLKLDEERVIAGTENGLISLVGILPNRIIQPIAE...

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_019422`
TK1151 ID	TkA05G050660
OH-1004 ID	LXL04_019422
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.300
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_019422

Location Chr04:31010985-31013626 (+)

Description Similar to WDR55: WD repeat-containing protein 55

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g34260`	Required for male and female gametogenesis, seed development, and embryo and endosperm development at early stages.	Arabidopsis WD repeat domain55 Interacts with DNA damaged binding protein1 and is required for apical patterning in the embryo.2012 · DOI: 10.1105/tpc.111.089425 The Arabidopsis DDB1 interacting protein WDR55 is required for vegetative development.2013 · DOI: 10.4161/psb.25347

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019422 · 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:0009855 determination of bilateral symmetry Biological Process

GO:0009960 endosperm development Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0080186 developmental vegetative growth Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT2G34260

bta:508709

ddi:DDB_G0282573

hsa:54853

rno:307494

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.

Nucleus0.884

Rank 1 · LXL04_019422 · OH-1004

Cytoplasm0.206

Rank 2 · LXL04_019422 · OH-1004

Mitochondrion0.024

Rank 3 · LXL04_019422 · OH-1004

Cell membrane0.023

Rank 4 · LXL04_019422 · OH-1004

Endoplasmic reticulum0.013

Rank 5 · LXL04_019422 · 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.

PF24796.2WDR552-295 aa

PF23414.2Beta-prop_EML_211-92 aa

PF25173.2Beta-prop_WDR3_1st12-161 aa

PF25175.2Beta-prop_WDR512-262 aa

PF24807.2WD40_CDC20-Fz12-169 aa

PF25391.2WD40_Gbeta14-179 aa

PF25171.2Beta-prop_WDR36-Utp21_1st16-120 aa

PF24817.2WD40_WDHD1_1st20-170 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019422	`PF24796.2`	WDR55	2	295	3.3e-95	319.2
LXL04_019422	`PF23414.2`	Beta-prop_EML_2	11	92	1.4e-17	64.7
LXL04_019422	`PF25173.2`	Beta-prop_WDR3_1st	12	161	5.2e-28	98.7
LXL04_019422	`PF25175.2`	Beta-prop_WDR5	12	262	2.3e-24	86.9
LXL04_019422	`PF24807.2`	WD40_CDC20-Fz	12	169	1.1e-19	71.6
LXL04_019422	`PF25391.2`	WD40_Gbeta	14	179	2.4e-12	47.3
LXL04_019422	`PF25171.2`	Beta-prop_WDR36-Utp21_1st	16	120	1.9e-12	47.9
LXL04_019422	`PF24817.2`	WD40_WDHD1_1st	20	170	7.2e-17	62.2
LXL04_019422	`PF25047.1`	Beta-prop_TEP1_2nd	42	167	1.9e-14	54.2
LXL04_019422	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	44	169	5.6e-14	52.9
LXL04_019422	`PF25174.2`	Beta-prop_THOC3	50	294	1.2e-28	100.6
LXL04_019422	`PF23098.2`	Beta-prop_NOL10_N	53	203	8.9e-08	32.4
LXL04_019422	`PF23381.2`	Beta-prop_IFT122_1st	59	204	4.4e-22	79.4
LXL04_019422	`PF24814.2`	WD40_Prp19	62	176	7.4e-20	71.9
LXL04_019422	`PF23393.3`	Beta-prop_WDR90_POC16_2nd	70	152	4.2e-09	36.8
LXL04_019422	`PF24805.2`	EIF3I	82	184	2.7e-14	53.7

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
`O80775`	Arabidopsis thaliana	WD repeat-containing protein 55	62.117%	Swiss-Prot	strong database homology

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