TkA04G019820 | RubberDandelionOmics

Gene overview

TkA04G019820

Reference: TK1151 Chr: Chr04 Coordinates: 4962556-4963146 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

513 bp · TkA04G019820|TK1151|cDNA

ATGGATCCTTATACAGAAGTTGAAACCTCCGATTACACCATAAACCCTAATATTTCATCTAGCACGACTTCTCCGTCCGCAGTCACAACTCCCAGCCGCTACGAAAACCAGAAACGCCGCGACTGGAACACCTTCTGTCAGTACCTGAAGAATCACCGGCCACCGCTCGCGCTTTCCCGATGTAGTGGCGGCCACCCTAACCCACCGTGCCCTTGCCCGTGTCCTCTCCGACAGGCGTGGGGAAGCTTGGATGCGTTGAT...

CDS

Download CDS FASTA

513 bp · TkA04G019820|TK1151|CDS

ATGGATCCTTATACAGAAGTTGAAACCTCCGATTACACCATAAACCCTAATATTTCATCTAGCACGACTTCTCCGTCCGCAGTCACAACTCCCAGCCGCTACGAAAACCAGAAACGCCGCGACTGGAACACCTTCTGTCAGTACCTGAAGAATCACCGGCCACCGCTCGCGCTTTCCCGATGTAGTGGCGGCCACCCTAACCCACCGTGCCCTTGCCCGTGTCCTCTCCGACAGGCGTGGGGAAGCTTGGATGCGTTGAT...

Protein

Download Protein FASTA

170 aa · TkA04G019820|TK1151|PROTEIN

MDPYTEVETSDYTINPNISSSTTSPSAVTTPSRYENQKRRDWNTFCQYLKNHRPPLALSRCSGGHPNPPCPCPCPLRQAWGSLDALIGRLRAAYEESGGSPEMNPFGARAVRLYLREVRDLQSKARGISYEKKKRKRPNLQQEHHHHHHQQQFTHMSSFQGFTLPPGDHT

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	`TkA04G019820`
TK1151 ID	TkA04G019820
OH-1004 ID	LXL04_036869
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	85.200
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	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 TkA04G019820

Location Chr04:4962556-4963146 (+)

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

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31160`	Probable transcription regulator that acts as a developmental regulator by promoting cell growth in response to light (By similarity).	Organ boundary1 defines a gene expressed at the junction between the shoot apical meristem and lateral organs.2011 · DOI: 10.1073/pnas.1018542108
`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
`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
`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

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2XAV5`	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_036869 · 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:0010199 organ boundary specification between lateral organs and the meristem Biological Process

GO:0010492 maintenance of shoot apical meristem identity Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0048441 petal development Biological Process

GO:0048834 specification of petal number Biological Process

GO:0080050 regulation of seed development Biological Process

GO:0090698 post-embryonic plant morphogenesis Biological Process

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT1G07090

ath:AT2G31160

ath:AT5G58500

dosa:Os02g0811000

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.

Nucleus0.906

Rank 1 · TkA04G019820 · TK1151

Cytoplasm0.201

Rank 2 · TkA04G019820 · TK1151

Cell membrane0.025

Rank 3 · TkA04G019820 · TK1151

Mitochondrion0.020

Rank 4 · TkA04G019820 · TK1151

Endoplasmic reticulum0.018

Rank 5 · TkA04G019820 · 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_dom23-65 aa

PF17887Jak1_Phl32-48 aa

PF04852ALOG_dom64-120 aa

PF17887Jak1_Phl127-162 aa

PF04852ALOG_dom135-147 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G019820	`PF04852`	ALOG_dom	23	65	3.3e-42	144.3
TkA04G019820	`PF17887`	Jak1_Phl	32	48	0.12	13.0
TkA04G019820	`PF04852`	ALOG_dom	64	120	3.3e-42	144.3
TkA04G019820	`PF17887`	Jak1_Phl	127	162	0.12	13.0
TkA04G019820	`PF04852`	ALOG_dom	135	147	3.3e-42	144.3

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
`O82268`	Arabidopsis thaliana	sp\|O82268\|LSH3_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 3	70.000%	Swiss-Prot	Medium
`Q6NNI3`	Arabidopsis thaliana	sp\|Q6NNI3\|LSH1_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 1	61.600%	Swiss-Prot	High
`Q9M836`	Arabidopsis thaliana	sp\|Q9M836\|LSH2_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 2	58.400%	Swiss-Prot	High
`Q9LW68`	Arabidopsis thaliana	sp\|Q9LW68\|LSH4_ARATH Protein LIGHT-DEPENDENT SHORT HYPOCOTYLS 4	68.800%	Swiss-Prot	Medium
`A2XAV5`	Oryza sativa subsp. indica	sp\|A2XAV5\|G1L6_ORYSI Protein G1-like6	70.100%	Swiss-Prot	Medium

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