LXL04_026451 | RubberDandelionOmics

Gene overview

LXL04_026451

Reference: OH-1004 Chr: Chr05 Coordinates: 126467001-126475083 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5487 bp · LXL04_026451|LXL04_026451|OH1004|cDNA

ATGGGTAAAAGTAGACCTAGGGCTGCAGAAAAGAGGGTTTTAGGGCAAGGGTCAATTGTGTTAACATCAGCCTCATCGTTAGCTATACCACCTGCACCTGTTTACACTCCTACCGAAGAGGAGTTTAAGGACCCATTAgcatatatttataaaatcagaCCAGAAGCTGAGTCATATGGGATCTGTAAAATAATTCCTCCAAAGAATTGGAAACCCCCTTTTGCCCTAGATTTGAATACGTTTACATTTCCCACAAAAAC...

CDS

Download CDS FASTA

5487 bp · LXL04_026451|LXL04_026451|OH1004|CDS

ATGGGTAAAAGTAGACCTAGGGCTGCAGAAAAGAGGGTTTTAGGGCAAGGGTCAATTGTGTTAACATCAGCCTCATCGTTAGCTATACCACCTGCACCTGTTTACACTCCTACCGAAGAGGAGTTTAAGGACCCATTAGCATATATTTATAAAATCAGACCAGAAGCTGAGTCATATGGGATCTGTAAAATAATTCCTCCAAAGAATTGGAAACCCCCTTTTGCCCTAGATTTGAATACGTTTACATTTCCCACAAAAAC...

Protein

Download Protein FASTA

1828 aa · LXL04_026451|LXL04_026451|OH1004|PROTEIN

MGKSRPRAAEKRVLGQGSIVLTSASSLAIPPAPVYTPTEEEFKDPLAYIYKIRPEAESYGICKIIPPKNWKPPFALDLNTFTFPTKTQAIHQLQARPPACNSKTFELEYNRFLEDQCGKKAVKKKVVFEGKELDLCKLFNGVKRFGGYDNVVKEKKWGEVFRFVRSGGKISACSKYVLCQLYKEHLYDYENYYSKLDQVKEKSSKRGLQSDKKTGNQSSKRSRINEAGENIKKVKEEEYDQICEQCRSGLHAEVMLLCDR...

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_026451`
TK1151 ID	TkA06G010730
OH-1004 ID	LXL04_026451
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.000
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_026451

Location Chr05:126467001-126475083 (+)

Description Similar to Kdm5a: Lysine-specific demethylase 5A

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g63490`	Functions as a histone H3 'Lys-4' (H3K4me) demethylase involved in the regulation of gene expression.	Arabidopsis histone H3K4 demethylase JMJ17 functions in dehydration stress response.2019 · DOI: 10.1111/nph.15874

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_026451 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000122 negative regulation of transcription by RNA polymerase II Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0008340 determination of adult lifespan Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0010468 regulation of gene expression Biological Process

GO:0032922 circadian regulation of gene expression Biological Process

GO:0045814 negative regulation of gene expression, epigenetic Biological Process

KEGG gene cross-reference

ath:AT1G63490

cel:CELE_ZK593.4

hsa:5927

mmu:214899

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.

Nucleus0.823

Rank 1 · LXL04_026451 · OH-1004

Cytoplasm0.208

Rank 2 · LXL04_026451 · OH-1004

Cell membrane0.035

Rank 3 · LXL04_026451 · OH-1004

Mitochondrion0.023

Rank 4 · LXL04_026451 · OH-1004

Endoplasmic reticulum0.020

Rank 5 · LXL04_026451 · 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.

PF02375.24JmjN33-66 aa

PF01388.28ARID103-190 aa

PF00628.36PHD243-287 aa

PF02373.29JmjC413-520 aa

PF02928.22zf-C5HC2651-703 aa

PF08429.17PLU-1786-1062 aa

PF08429.17PLU-1922-1231 aa

PF08429.17PLU-11247-1439 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_026451	`PF02375.24`	JmjN	33	66	7.7e-17	61.5
LXL04_026451	`PF01388.28`	ARID	103	190	9.9e-13	49.0
LXL04_026451	`PF00628.36`	PHD	243	287	3e-13	50.3
LXL04_026451	`PF02373.29`	JmjC	413	520	1.4e-38	132.5
LXL04_026451	`PF02928.22`	zf-C5HC2	651	703	2e-17	63.9
LXL04_026451	`PF08429.17`	PLU-1	786	1062	2.9e-37	129.3
LXL04_026451	`PF08429.17`	PLU-1	922	1231	2.9e-37	129.3
LXL04_026451	`PF08429.17`	PLU-1	1247	1439	2.9e-37	129.3
LXL04_026451	`PF08429.17`	PLU-1	1541	1723	2.9e-37	129.3
LXL04_026451	`PF00628.36`	PHD	1732	1766	3e-13	50.3

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
`F4I240`	Arabidopsis thaliana	Lysine-specific demethylase JMJ17	50.899%	Swiss-Prot	moderate database homology

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