LXL04_014562 | RubberDandelionOmics

Gene overview

LXL04_014562

Reference: OH-1004 Chr: Chr03 Coordinates: 52552023-52554377 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1584 bp · LXL04_014562|LXL04_014562|OH1004|cDNA

ATGACGACATCTTCTTCTACAGAAAACAAATTCTCAGTTCCAATTAAAGAGAAAACTATTCAGTATTATCTTTACCCGCCTCCCATTGGCCAATTTGAAGATGTTATGGCCAGTTATAAACTCTTCATGGATACACTTGGAAAATTCCATGCTGCTATGGGGACCAAATTCAAGATTCCGATTGTTGGCGGCAAGGATCTGGACTTGCATCGCCTATTTATGGAAGTCACTTCTCGTGGTGGCATTAAAAGGGTTCTTGA...

CDS

Download CDS FASTA

1584 bp · LXL04_014562|LXL04_014562|OH1004|CDS

ATGACGACATCTTCTTCTACAGAAAACAAATTCTCAGTTCCAATTAAAGAGAAAACTATTCAGTATTATCTTTACCCGCCTCCCATTGGCCAATTTGAAGATGTTATGGCCAGTTATAAACTCTTCATGGATACACTTGGAAAATTCCATGCTGCTATGGGGACCAAATTCAAGATTCCGATTGTTGGCGGCAAGGATCTGGACTTGCATCGCCTATTTATGGAAGTCACTTCTCGTGGTGGCATTAAAAGGGTTCTTGA...

Protein

Download Protein FASTA

527 aa · LXL04_014562|LXL04_014562|OH1004|PROTEIN

MTTSSSTENKFSVPIKEKTIQYYLYPPPIGQFEDVMASYKLFMDTLGKFHAAMGTKFKIPIVGGKDLDLHRLFMEVTSRGGIKRVLEDKKWREVTNVFNFPPSATNASFILRKYYMSLLHHFEQVYYFKAKAWTPVPTDTWQSTKSTLTSMTEMNKVVLPLTENQLTSGKRQRTETEEASPESSIGFPVTGTIDGKFESGYLCTVGIGGEQLQGVLYQTLCTPLREVTQDANATMVRQRRRRRKKSEMKKRDPAHPKPNR...

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_014562`
TK1151 ID	TkA02G412790
OH-1004 ID	LXL04_014562
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.500
Protein coverage (%)	TK1151 94.297 / OH-1004 87.856 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_014562

Location Chr03:52552023-52554377 (+)

Description Similar to HMGB15: High mobility group B protein 15

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g04880`	Binds preferentially DNA with A/T-rich content.	No verified direct reference in this release
`At3g13350`	Binds preferentially DNA with A/T-rich content.	No verified direct reference in this release
`At1g76110`	Binds preferentially DNA with A/T-rich content.	NUCLEAR FUSION DEFECTIVE1 encodes the Arabidopsis RPL21M protein and is required for karyogamy during female gametophyte development and fertilization.2006 · DOI: 10.1104/pp.106.079319 A novel family of plant DNA-binding proteins containing both HMG-box and AT-rich interaction domains.2008 · DOI: 10.1021/bi801772k
`At1g55650`	Binds preferentially DNA with A/T-rich content.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014562 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000741 karyogamy Biological Process

GO:0006337 nucleosome disassembly 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:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009846 pollen germination Biological Process

GO:0009860 pollen tube growth Biological Process

GO:0010197 polar nucleus fusion Biological Process

GO:0019760 glucosinolate metabolic process Biological Process

GO:0030071 regulation of mitotic metaphase/anaphase transition Biological Process

KEGG gene cross-reference

ath:AT1G04880

ath:AT1G55650

ath:AT1G76110

ath:AT3G13350

mmu:77044

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.977

Rank 1 · LXL04_014562 · OH-1004

Cytoplasm0.081

Rank 2 · LXL04_014562 · OH-1004

Cell membrane0.019

Rank 3 · LXL04_014562 · OH-1004

Endoplasmic reticulum0.010

Rank 4 · LXL04_014562 · OH-1004

Plastid0.008

Rank 5 · LXL04_014562 · 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.

PF01388.28ARID39-123 aa

PF27637.1MNM1_beta189-218 aa

PF09011.17HMG_box_2253-322 aa

PF00505.26HMG_box256-323 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014562	`PF01388.28`	ARID	39	123	4e-23	82.4
LXL04_014562	`PF27637.1`	MNM1_beta	189	218	2.3e-08	34.2
LXL04_014562	`PF09011.17`	HMG_box_2	253	322	4e-11	44.1
LXL04_014562	`PF00505.26`	HMG_box	256	323	1.6e-15	58.0

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9MAT6`	Arabidopsis thaliana	High mobility group B protein 15	50.820%	Swiss-Prot	moderate database homology
`Q9LTT3`	Arabidopsis thaliana	High mobility group B protein 10	43.377%	Swiss-Prot	moderate database homology
`Q9SGS2`	Arabidopsis thaliana	High mobility group B protein 9	43.087%	Swiss-Prot	moderate database homology
`Q9LG02`	Arabidopsis thaliana	Putative high mobility group B protein 11	38.908%	Swiss-Prot	moderate database homology

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