LXL04_001878 | RubberDandelionOmics

Gene overview

LXL04_001878

Reference: OH-1004 Chr: Chr01 Coordinates: 35855379-35856943 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

510 bp · LXL04_001878|LXL04_001878|OH1004|cDNA

ATGCATGCTCAGTCTTCCCCCACTGTTCCTAACGTACTCACCAGTCACCAGATCTCAGTTTTAGAACTTGAAAGAGAGATGAGAGGACCAAAGAGCATTGCCACCATTGCTCAGAAGAAGCTTAATCCTGAGACAACGAAGAAGGTGAAGGCCGATAAGAGTGTGGCAAAGAAGGAGAAAGCGTCAAACAAAAATCCAGGTGCTCCAAAGCGGCCCCCGTCTGCTTTCTTCGTCTTCATGGATGAATTCAGGAAGGACTA...

CDS

Download CDS FASTA

510 bp · LXL04_001878|LXL04_001878|OH1004|CDS

ATGCATGCTCAGTCTTCCCCCACTGTTCCTAACGTACTCACCAGTCACCAGATCTCAGTTTTAGAACTTGAAAGAGAGATGAGAGGACCAAAGAGCATTGCCACCATTGCTCAGAAGAAGCTTAATCCTGAGACAACGAAGAAGGTGAAGGCCGATAAGAGTGTGGCAAAGAAGGAGAAAGCGTCAAACAAAAATCCAGGTGCTCCAAAGCGGCCCCCGTCTGCTTTCTTCGTCTTCATGGATGAATTCAGGAAGGACTA...

Protein

Download Protein FASTA

169 aa · LXL04_001878|LXL04_001878|OH1004|PROTEIN

MHAQSSPTVPNVLTSHQISVLELEREMRGPKSIATIAQKKLNPETTKKVKADKSVAKKEKASNKNPGAPKRPPSAFFVFMDEFRKDYKENFPDNKSVAVVAKEGGVKWKAMSESEKAPYVAKAAEKKAEYGIVLKQFNDDLNENSKEKSASTSKSSSDTHDEVEQEASS

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_001878`
TK1151 ID	TkA01G502320
OH-1004 ID	LXL04_001878
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
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_001878

Location Chr01:35855379-35856943 (+)

Description Similar to HMGB3: High mobility group B protein 3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g20696`	Binds preferentially double-stranded DNA.	No verified direct reference in this release
`At1g20693`	Binds preferentially double-stranded DNA.	No verified direct reference in this release
`At2g17560`	Binds preferentially double-stranded DNA.	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_001878 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0003682 chromatin binding Molecular Function

GO:0003700 DNA-binding transcription factor activity Molecular Function

GO:0030527 structural constituent of chromatin Molecular Function

KEGG gene cross-reference

ath:AT1G20693

ath:AT1G20696

ath:AT2G17560

ini:109177607

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.

Nucleus0.885

Rank 1 · LXL04_001878 · OH-1004

Cytoplasm0.196

Rank 2 · LXL04_001878 · OH-1004

Mitochondrion0.027

Rank 3 · LXL04_001878 · OH-1004

Cell membrane0.025

Rank 4 · LXL04_001878 · OH-1004

Endoplasmic reticulum0.015

Rank 5 · LXL04_001878 · 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.

PF09011.17HMG_box_268-131 aa

PF00505.26HMG_box69-130 aa

PF24815.2HMG_WDHD172-120 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001878	`PF09011.17`	HMG_box_2	68	131	2.6e-11	44.7
LXL04_001878	`PF00505.26`	HMG_box	69	130	2.8e-18	66.8
LXL04_001878	`PF24815.2`	HMG_WDHD1	72	120	7.5e-11	42.5

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
`P93047`	Arabidopsis thaliana	High mobility group B protein 3	52.893%	Swiss-Prot	strong database homology
`O49596`	Arabidopsis thaliana	High mobility group B protein 2	49.587%	Swiss-Prot	moderate database homology
`Q42344`	Arabidopsis thaliana	High mobility group B protein 4	45.794%	Swiss-Prot	moderate database homology

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