LXL04_035172 | RubberDandelionOmics

Gene overview

LXL04_035172

Reference: OH-1004 Chr: Chr08 Coordinates: 16372134-16376895 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3168 bp · LXL04_035172|LXL04_035172|OH1004|cDNA

ATGATAATCAAGCGGAAGTTGAAATCGGCAATGCCGAGATTGAAGCGTTGTCGAGTTAGTGAGTCGGGAGGCGGAGACGACGAAGAATGGTCGGGGAAATTGAAATCTCGGAAGAAGCGAAAGACTAAAAACGGGTATTACCCTCTGCATCTGCTCGGAGAGGTTGCCGCCGGGATCATTACGTTGAGTGAATTGGGATTCCACTTCACCGCCGGCGTTATCCCTAGCTTTTTCTGCAGCGACACAGGCGCAGTGGTGAT...

CDS

Download CDS FASTA

3168 bp · LXL04_035172|LXL04_035172|OH1004|CDS

ATGATAATCAAGCGGAAGTTGAAATCGGCAATGCCGAGATTGAAGCGTTGTCGAGTTAGTGAGTCGGGAGGCGGAGACGACGAAGAATGGTCGGGGAAATTGAAATCTCGGAAGAAGCGAAAGACTAAAAACGGGTATTACCCTCTGCATCTGCTCGGAGAGGTTGCCGCCGGGATCATTACGTTGAGTGAATTGGGATTCCACTTCACCGCCGGCGTTATCCCTAGCTTTTTCTGCAGCGACACAGGCGCAGTGGTGAT...

Protein

Download Protein FASTA

1055 aa · LXL04_035172|LXL04_035172|OH1004|PROTEIN

MIIKRKLKSAMPRLKRCRVSESGGGDDEEWSGKLKSRKKRKTKNGYYPLHLLGEVAAGIITLSELGFHFTAGVIPSFFCSDTGAVVIVDSKPNAPKTELVDNSNATNNDTVPPAKPRPPLVRTSRGRVQVLPSRFNDSILDNWKKEKTKLDVNQCSHLDPEFAPIKEKPILKIPKPRDQIQTKKHNADKVSYKYRKSLPKFEEFEDDEYKSFDMIKYSGLNSQHNKDDDTNIKAPDEFSPGDIVWAKSGKHYPAWPAIVL...

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_035172`
TK1151 ID	TkA04G160260
OH-1004 ID	LXL04_035172
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_035172

Location Chr08:16372134-16376895 (+)

Description Similar to ATX4: Histone-lysine N-methyltransferase ATX4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g27910`	Histone methyltransferase.	No verified direct reference in this release
`At5g53430`	Histone methyltransferase.	No verified direct reference in this release
`At3g61740`	Histone methyltransferase.	No verified direct reference in this release
`At2g31650`	May participate in target-gene transcriptional regulation and associated histone methylation.	Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation.2014 · DOI: 10.1111/nph.12493 Arabidopsis homolog of trithorax1 (ATX1) is required for cell production, patterning, and morphogenesis in root development.2014 · DOI: 10.1093/jxb/eru355
`At1g05830`	Histone methyltransferase.	The highly similar Arabidopsis homologs of trithorax ATX1 and ATX2 encode proteins with divergent biochemical functions.2008 · DOI: 10.1105/tpc.107.056614 Combinatorial functions of diverse histone methylations in Arabidopsis thaliana flowering time regulation.2014 · DOI: 10.1111/nph.12493

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_035172 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0009294 DNA-mediated transformation Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009909 regulation of flower development Biological Process

GO:0009910 negative regulation of flower development Biological Process

GO:0010093 specification of floral organ identity Biological Process

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

GO:0018022 peptidyl-lysine methylation Biological Process

KEGG gene cross-reference

ath:AT1G05830

ath:AT2G31650

ath:AT3G61740

ath:AT4G27910

ath:AT5G53430

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.

Nucleus0.931

Rank 1 · LXL04_035172 · OH-1004

Cytoplasm0.111

Rank 2 · LXL04_035172 · OH-1004

Cell membrane0.030

Rank 3 · LXL04_035172 · OH-1004

Plastid0.015

Rank 4 · LXL04_035172 · OH-1004

Endoplasmic reticulum0.014

Rank 5 · LXL04_035172 · 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.

PF00855.24PWWP241-335 aa

PF00628.36PHD428-478 aa

PF00628.36PHD623-668 aa

PF13831.13PHD_2635-669 aa

PF13832.13zf-HC5HC2H_2676-788 aa

PF13771.13zf-HC5HC2H698-789 aa

PF00856.34SET924-1029 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_035172	`PF00855.24`	PWWP	241	335	5e-13	50.1
LXL04_035172	`PF00628.36`	PHD	428	478	3.9e-08	33.9
LXL04_035172	`PF00628.36`	PHD	623	668	3.9e-08	33.9
LXL04_035172	`PF13831.13`	PHD_2	635	669	2.8e-11	43.4
LXL04_035172	`PF13832.13`	zf-HC5HC2H_2	676	788	2.4e-27	96.0
LXL04_035172	`PF13771.13`	zf-HC5HC2H	698	789	2.5e-13	50.8
LXL04_035172	`PF00856.34`	SET	924	1029	8e-24	84.8

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

Protein	Organism	Description	Identity	Database	Confidence
`Q9SUE7`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX4	59.553%	Swiss-Prot	strong database homology
`Q8GZ42`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX5	59.372%	Swiss-Prot	strong database homology
`Q9M364`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX3	50.714%	Swiss-Prot	strong database homology
`Q9C5X4`	Arabidopsis thaliana	Histone H3-lysine(4) N-trimethyltransferase ATX1	33.617%	Swiss-Prot	weak database homology
`P0CB22`	Arabidopsis thaliana	Histone-lysine N-methyltransferase ATX2	34.115%	Swiss-Prot	weak database homology

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