LXL04_036268 | RubberDandelionOmics

Gene overview

LXL04_036268

Reference: OH-1004 Chr: Chr08 Coordinates: 39075208-39077427 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

522 bp · LXL04_036268|LXL04_036268|OH1004|cDNA

ATGTATGCACCTTCTTCCCCGTTGATGCTGACTCACCATTACATTGAGAGGTTGGCTGTGAAGAAAACTGCAGCTAAGGGGAAAGCTGCTAAGGATCCGAATAAACCTAAAAGACCTGCTAGCGCCTTCTTCGTTTTCATGGAGGAGTTTAGGAAGCAGTATAAAGAAGAAAACCCCGAGAACAAATCTGTTGCTGCTGTTGGTAACGCTGGTGGGGCCAAATGGAAGTCACTGACAGAATCTGAAAAAGCACCTTTTCA...

CDS

Download CDS FASTA

522 bp · LXL04_036268|LXL04_036268|OH1004|CDS

ATGTATGCACCTTCTTCCCCGTTGATGCTGACTCACCATTACATTGAGAGGTTGGCTGTGAAGAAAACTGCAGCTAAGGGGAAAGCTGCTAAGGATCCGAATAAACCTAAAAGACCTGCTAGCGCCTTCTTCGTTTTCATGGAGGAGTTTAGGAAGCAGTATAAAGAAGAAAACCCCGAGAACAAATCTGTTGCTGCTGTTGGTAACGCTGGTGGGGCCAAATGGAAGTCACTGACAGAATCTGAAAAAGCACCTTTTCA...

Protein

Download Protein FASTA

173 aa · LXL04_036268|LXL04_036268|OH1004|PROTEIN

MYAPSSPLMLTHHYIERLAVKKTAAKGKAAKDPNKPKRPASAFFVFMEEFRKQYKEENPENKSVAAVGNAGGAKWKSLTESEKAPFQAKADKRKKQYEKDMDTYNNKPAASANDEADDDSDKSKSEVNDEADSDSGDILKHLACLELEDNKNVKPDFSIISVSLRRKYKNLKI

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_036268`
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_036268

Location Chr08:39075208-39077427 (-)

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

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Functional annotation source: OH1004 · LXL04_036268 · 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

gmx:547975

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.

Nucleus0.752

Rank 1 · LXL04_036268 · OH-1004

Cytoplasm0.283

Rank 2 · LXL04_036268 · OH-1004

Cell membrane0.050

Rank 3 · LXL04_036268 · OH-1004

Extracellular0.047

Rank 4 · LXL04_036268 · OH-1004

Mitochondrion0.045

Rank 5 · LXL04_036268 · 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_233-105 aa

PF00505.26HMG_box36-105 aa

PF24815.2HMG_WDHD139-89 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036268	`PF09011.17`	HMG_box_2	33	105	2.5e-13	51.2
LXL04_036268	`PF00505.26`	HMG_box	36	105	5.7e-22	78.7
LXL04_036268	`PF24815.2`	HMG_WDHD1	39	89	1.3e-10	41.8

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.

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Protein	Organism	Description	Identity	Database	Confidence
`P93047`	Arabidopsis thaliana	High mobility group B protein 3	66.667%	Swiss-Prot	moderate database homology
`O49596`	Arabidopsis thaliana	High mobility group B protein 2	59.350%	Swiss-Prot	moderate database homology
`Q42344`	Arabidopsis thaliana	High mobility group B protein 4	56.303%	Swiss-Prot	moderate database homology

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