LXL04_038223 | RubberDandelionOmics

Gene overview

LXL04_038223

Reference: OH-1004 Chr: Chr09 Coordinates: 34591659-34594761 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1473 bp · LXL04_038223|LXL04_038223|OH1004|cDNA

ATGGCGGATCAGACGATCGAGAAACGTTCGTCTGAAGTTGGTGATCATGAGAAAGAGCCGAGGAAAAAAAAGGACGTCACCGAGGATCCAGAAACCTTCAGCTGTATGCTTCAGCCTTGTCCTACCGACTCCGATCCTAAATACGTCGGAATTCGCCGCCTTCTTCTCTTTCGGAAGGCTCAATCGGGCGTCCTTCTCCGAAAGGACTGGAGATGCAATTCGAAAGGTTATGTAGCTTACCGCAATTTCATCAACAGGCC...

CDS

Download CDS FASTA

1473 bp · LXL04_038223|LXL04_038223|OH1004|CDS

ATGGCGGATCAGACGATCGAGAAACGTTCGTCTGAAGTTGGTGATCATGAGAAAGAGCCGAGGAAAAAAAAGGACGTCACCGAGGATCCAGAAACCTTCAGCTGTATGCTTCAGCCTTGTCCTACCGACTCCGATCCTAAATACGTCGGAATTCGCCGCCTTCTTCTCTTTCGGAAGGCTCAATCGGGCGTCCTTCTCCGAAAGGACTGGAGATGCAATTCGAAAGGTTATGTAGCTTACCGCAATTTCATCAACAGGCC...

Protein

Download Protein FASTA

490 aa · LXL04_038223|LXL04_038223|OH1004|PROTEIN

MADQTIEKRSSEVGDHEKEPRKKKDVTEDPETFSCMLQPCPTDSDPKYVGIRRLLLFRKAQSGVLLRKDWRCNSKGYVAYRNFINRPDNWLNSQILSRTSTPGTSGRWIPSPNQLSIEVESWAASSWTGMKDLHDSQSQTLSQTVSSIGVNSSEFEHPRRKTEHAYSFVGMHCIFDECKSMVTVIKFGHMSSDVLAYGATDGTLTVCSVSDPPSIMNKLTGHSKDVTDFDFSLNNQYIASSSLDKTVRVWDIPNNLCIRV...

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_038223`
TK1151 ID	TkAUNG028260
OH-1004 ID	LXL04_038223
Relationship / confidence	Rbh High Identity Coverage Local Synteny Minor Chr Pair / Probable
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_038223

Location Chr09:34591659-34594761 (+)

Description Similar to WDR13: WD repeat-containing protein 13

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g49660`	Forms multiple COMPASS-like complexes involved in histone methylation by interacting with different histone H3 'Lys-4' methyltransferases such as ATX1, SDG14 or SDG16.	Establishment of the winter-annual growth habit via FRIGIDA-mediated histone methylation at FLOWERING LOCUS C in Arabidopsis.2009 · DOI: 10.1105/tpc.109.067967

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_038223 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0010228 vegetative to reproductive phase transition of meristem Biological Process

GO:0032259 methylation Biological Process

GO:1904691 negative regulation of type B pancreatic cell proliferation Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0034451 centriolar satellite Cellular Component

GO:0048188 Set1C/COMPASS complex Cellular Component

GO:0042393 histone binding Molecular Function

GO:0140938 histone H3 methyltransferase activity Molecular Function

GO:1990841 promoter-specific chromatin binding Molecular Function

KEGG gene cross-reference

ath:AT3G49660

hsa:64743

mmu:73447

pon:100171581

ptr:449584

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.

Cytoplasm0.468

Rank 1 · LXL04_038223 · OH-1004

Nucleus0.454

Rank 2 · LXL04_038223 · OH-1004

Cell membrane0.092

Rank 3 · LXL04_038223 · OH-1004

Lysosome / Vacuole0.059

Rank 4 · LXL04_038223 · OH-1004

Golgi apparatus0.046

Rank 5 · LXL04_038223 · 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_1st127-350 aa

PF25173.2Beta-prop_WDR3_1st172-267 aa

PF24805.2EIF3I173-254 aa

PF23414.2Beta-prop_EML_2175-254 aa

PF24782.3WD40_MABP1-WDR62_2nd176-321 aa

PF25175.2Beta-prop_WDR5178-485 aa

PF24796.2WDR55178-388 aa

PF25168.2Beta-prop_WDR36-Utp21_2nd181-305 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_038223	`PF24817.2`	WD40_WDHD1_1st	127	350	8.6e-26	91.5
LXL04_038223	`PF25173.2`	Beta-prop_WDR3_1st	172	267	1.1e-27	97.6
LXL04_038223	`PF24805.2`	EIF3I	173	254	1.1e-10	42.0
LXL04_038223	`PF23414.2`	Beta-prop_EML_2	175	254	3.6e-25	89.6
LXL04_038223	`PF24782.3`	WD40_MABP1-WDR62_2nd	176	321	1.1e-07	31.8
LXL04_038223	`PF25175.2`	Beta-prop_WDR5	178	485	1.3e-31	110.7
LXL04_038223	`PF24796.2`	WDR55	178	388	2.9e-15	56.8
LXL04_038223	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	181	305	4.1e-14	53.3
LXL04_038223	`PF24814.2`	WD40_Prp19	182	302	4.5e-24	85.7
LXL04_038223	`PF24807.2`	WD40_CDC20-Fz	188	325	8.3e-25	88.4
LXL04_038223	`PF25174.2`	Beta-prop_THOC3	191	339	1.7e-37	129.6
LXL04_038223	`PF23381.2`	Beta-prop_IFT122_1st	194	441	1.7e-29	103.7
LXL04_038223	`PF24105.2`	Beta-prop_CAF1B_HIR1	216	306	1.1e-11	45.0
LXL04_038223	`PF00400.39`	WD40	217	251	6.8e-22	77.7
LXL04_038223	`PF25391.2`	WD40_Gbeta	217	343	2.6e-07	30.7
LXL04_038223	`PF23409.2`	Beta-prop_EML	220	363	1.9e-06	28.3

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
`Q9M2Z2`	Arabidopsis thaliana	COMPASS-like H3K4 histone methylase component WDR5A	28.076%	Swiss-Prot	weak database homology

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