TkA06G045240 | RubberDandelionOmics

Gene overview

TkA06G045240

Reference: TK1151 Chr: Chr06 Coordinates: 12259070-12260778 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

960 bp · TkA06G045240|TK1151|cDNA

AAAATTTCCCCTCTTCTTAAACCCTCCCCCCCTCGGATTCTCCATAAGCGACTTCACCATCTTTATTCTTTCCGTCTTTCATTAGTAATCTTCAAGCTATCTTCAATGGCGCCCCCTGATGCTAACTCAAAATCCGTCAACGTAGCACGAGGCAGAAAGAGAGTCGAAGCAGAGACCACTTCTACCACACTCAAACGAGCAAAAAATGGCAGTGCTTTCACCCGATGTGAAGCATGTAACAAGGATGTAGCCGTGGCGTT...

CDS

Download CDS FASTA

765 bp · TkA06G045240|TK1151|CDS

AAAATTTCCCCTCTTCTTAAACCCTCCCCCCCTCGGATTCTCCATAAGCGACTTCACCATCTTTATTCTTTCCGTCTTTCATTAGTAATCTTCAAGCTATCTTCAATGGCGCCCCCTGATGCTAACTCAAAATCCGTCAACGTAGCACGAGGCAGAAAGAGAGTCGAAGCAGAGACCACTTCTACCACACTCAAACGAGCAAAAAATGGCAGTGCTTTCACCCGATGTGAAGCATGTAACAAGGATGTAGCCGTGGCGTT...

Protein

Download Protein FASTA

254 aa · TkA06G045240|TK1151|PROTEIN

KISPLLKPSPPRILHKRLHHLYSFRLSLVIFKLSSMAPPDANSKSVNVARGRKRVEAETTSTTLKRAKNGSAFTRCEACNKDVAVALISMHDCGLDAKIKMHLEAQVVETASDPAVKKPAEKKRTVKAKDPSSKKAKKERDPNKPKRPPTAFFLFMDEFRVTYKESNPDIKKSSMVVKEGGEKWKSMTDEEKKPFTTRAAELKEEYQKALENPIDAVNENENEIDKAEAEPIDVEDDDEEEASPDKEEAVPDDE

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	`TkA06G045240`
TK1151 ID	TkA06G045240
OH-1004 ID	LXL04_036088
Relationship / confidence	Non Reciprocal Best Hit / Complex relationship
Protein identity (%)	59.200
Protein coverage (%)	TK1151 27.953 / OH-1004 24.315 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G045240

Location Chr06:12259070-12260778 (-)

Description Similar to HMGB1: High mobility group B protein 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g23420`	Binds preferentially double-stranded supercoiled DNA.	HMGB6 from Arabidopsis thaliana specifies a novel type of plant chromosomal HMGB protein.2004 · DOI: 10.1021/bi035931c
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036088 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus 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:AT3G51880

ini:109177607

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.

Nucleus0.892

Rank 1 · TkA06G045240 · TK1151

Cytoplasm0.170

Rank 2 · TkA06G045240 · TK1151

Cell membrane0.031

Rank 3 · TkA06G045240 · TK1151

Endoplasmic reticulum0.028

Rank 4 · TkA06G045240 · TK1151

Mitochondrion0.020

Rank 5 · TkA06G045240 · TK1151

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.

PF00505HMG_box121-134 aa

PF09011HMG_box_2142-209 aa

PF00505HMG_box145-211 aa

PF24815HMG_WDHD1148-196 aa

PF02912Phe_tRNA-synt_N184-222 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G045240	`PF00505`	HMG_box	121	134	1.2e-19	71.2
TkA06G045240	`PF09011`	HMG_box_2	142	209	1.7e-14	55.0
TkA06G045240	`PF00505`	HMG_box	145	211	1.2e-19	71.2
TkA06G045240	`PF24815`	HMG_WDHD1	148	196	3.3e-14	53.3
TkA06G045240	`PF02912`	Phe_tRNA-synt_N	184	222	0.12	13.1

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
`Q8LDF9`	Arabidopsis thaliana	sp\|Q8LDF9\|HMGB7_ARATH High mobility group B protein 7	58.400%	Swiss-Prot	High
`P93047`	Arabidopsis thaliana	sp\|P93047\|HMGB3_ARATH High mobility group B protein 3	56.300%	Swiss-Prot	Low
`O49596`	Arabidopsis thaliana	sp\|O49596\|HMGB2_ARATH High mobility group B protein 2	50.700%	Swiss-Prot	Low

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