TkA05G403970 | RubberDandelionOmics

Gene overview

TkA05G403970

Reference: TK1151 Chr: Chr05 Coordinates: 100527383-100527754 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

372 bp · TkA05G403970|TK1151|cDNA

ATGGATCCAACAAACAACTCATCATCGTCTTCATCTTCTCCAAGTCGATACGAGAGCCAGAAACGTAGAGACTGGGATACATTTGGTCAGTACTTAAGAAACAACAAGCCACCACTTTCTTTCGCTCACTTTAACCCTAGTCATGTTCTTGAGTTTCTTCACTATCTTGATCAATTCGGAAAGACGAAAATCCACATCTTGACATGCCCTTACTTCGGAGTACCAAACCCACCGACAGCTTGCCCTTGTCCTTTCCGGCA...

CDS

Download CDS FASTA

372 bp · TkA05G403970|TK1151|CDS

ATGGATCCAACAAACAACTCATCATCGTCTTCATCTTCTCCAAGTCGATACGAGAGCCAGAAACGTAGAGACTGGGATACATTTGGTCAGTACTTAAGAAACAACAAGCCACCACTTTCTTTCGCTCACTTTAACCCTAGTCATGTTCTTGAGTTTCTTCACTATCTTGATCAATTCGGAAAGACGAAAATCCACATCTTGACATGCCCTTACTTCGGAGTACCAAACCCACCGACAGCTTGCCCTTGTCCTTTCCGGCA...

Protein

Download Protein FASTA

123 aa · TkA05G403970|TK1151|PROTEIN

MDPTNNSSSSSSSPSRYESQKRRDWDTFGQYLRNNKPPLSFAHFNPSHVLEFLHYLDQFGKTKIHILTCPYFGVPNPPTACPCPFRQAWGSLDALVGRLRAAYDEHGGNPEQIRLVRRKSGGF

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	`TkA05G403970`
TK1151 ID	TkA05G403970
OH-1004 ID	LXL04_021542
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	100.000
Protein coverage (%)	TK1151 90.244 / OH-1004 70.701 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 TkA05G403970

Location Chr05:100527383-100527754 (+)

Description Similar to LSH6: Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g58500`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At3g23290`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity).	CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.2011 · DOI: 10.1111/j.1365-313x.2011.04571.x
`At3g04510`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release
`At5g28490`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to continuous red (cR), far-red (cFR) and blue (cB) light in a phytochrome-dependent manner, at least during seedling development.	Overexpression of LSH1, a member of an uncharacterised gene family, causes enhanced light regulation of seedling development.2004 · DOI: 10.1111/j.1365-313x.2003.01993.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os10g0478000`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_021542 · 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:0009299 mRNA transcription Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009637 response to blue light Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0010114 response to red light Biological Process

GO:0010218 response to far red light Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT2G42610

ath:AT3G04510

ath:AT5G28490

ath:AT5G58500

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.

Nucleus0.609

Rank 1 · TkA05G403970 · TK1151

Cytoplasm0.421

Rank 2 · TkA05G403970 · TK1151

Mitochondrion0.069

Rank 3 · TkA05G403970 · TK1151

Endoplasmic reticulum0.041

Rank 4 · TkA05G403970 · TK1151

Cell membrane0.032

Rank 5 · TkA05G403970 · 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.

PF04852ALOG_dom9-112 aa

PF28475DUF841316-39 aa

PF28475DUF841386-105 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA05G403970	`PF04852`	ALOG_dom	9	112	4.8e-51	172.9
TkA05G403970	`PF28475`	DUF8413	16	39	0.19	12.5
TkA05G403970	`PF28475`	DUF8413	86	105	0.19	12.5

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
`Q9FGH2`	Arabidopsis thaliana	sp\|Q9FGH2\|LSH5_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 5	67.500%	Swiss-Prot	High
`Q9LW68`	Arabidopsis thaliana	sp\|Q9LW68\|LSH4_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4	72.200%	Swiss-Prot	High
`Q9M836`	Arabidopsis thaliana	sp\|Q9M836\|LSH2_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 2	69.400%	Swiss-Prot	High
`Q6NNI3`	Arabidopsis thaliana	sp\|Q6NNI3\|LSH1_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1	71.700%	Swiss-Prot	High
`Q7XDD0`	Oryza sativa subsp. japonica	sp\|Q7XDD0\|G1L5_ORYSJ Protein G1-like5	76.800%	Swiss-Prot	High

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