LXL04_024178 | RubberDandelionOmics

Gene overview

LXL04_024178

Reference: OH-1004 Chr: Chr05 Coordinates: 83360914-83361939 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

966 bp · LXL04_024178|LXL04_024178|OH1004|cDNA

ATGAACATCTCAAATAATTTAAGAGAATCAGACCACGAATCAAAGCAAGAAGGTAGTGCTAACGATGGTAGTAGCAAAATTACCCCTAGACCAAACTTCACCACATCATCATGGTCCCGATTGAAAGACCCAAGAATTGTTCGAGTTTCTAGAGCTTTTGGTGGAAAAGATCGACATAGTAAAGTGTGTACGGTTAGGGGCTTAAGAGACCGGCGAGTTAGGCTTTCAGTTCCCACCGCTATCCAATTATATGATCTTCA...

CDS

Download CDS FASTA

966 bp · LXL04_024178|LXL04_024178|OH1004|CDS

ATGAACATCTCAAATAATTTAAGAGAATCAGACCACGAATCAAAGCAAGAAGGTAGTGCTAACGATGGTAGTAGCAAAATTACCCCTAGACCAAACTTCACCACATCATCATGGTCCCGATTGAAAGACCCAAGAATTGTTCGAGTTTCTAGAGCTTTTGGTGGAAAAGATCGACATAGTAAAGTGTGTACGGTTAGGGGCTTAAGAGACCGGCGAGTTAGGCTTTCAGTTCCCACCGCTATCCAATTATATGATCTTCA...

Protein

Download Protein FASTA

321 aa · LXL04_024178|LXL04_024178|OH1004|PROTEIN

MNISNNLRESDHESKQEGSANDGSSKITPRPNFTTSSWSRLKDPRIVRVSRAFGGKDRHSKVCTVRGLRDRRVRLSVPTAIQLYDLQDRLGLNQPSKVVDWLLDAAKHEIDELPPLQIPPGSFGQNLQAMFNNCSQSEDVKSNVGGINWEDYWIPDKSKATAQDTSEDGEKYDQEDPRNKHDHHHHGLLHNVVVPNSSFLKWDPSNLSLSQFHHQHDDTVHNFNMNVSALPSMPSGSHQVLLYPPQPPPPAQTQSYFPSH...

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_024178`
TK1151 ID	TkA06G169210
OH-1004 ID	LXL04_024178
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	94.100
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_024178

Location Chr05:83360914-83361939 (+)

Description Similar to TCP13: Transcription factor TCP13

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g02150`	Plays a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164).	Involvement of a nuclear-encoded basic helix-loop-helix protein in transcription of the light-responsive promoter of psbD.2001 · DOI: 10.1104/pp.125.2.595
`At5g60970`	Plays a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164).	No verified direct reference in this release
`At5g08070`	Plays a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164).	No verified direct reference in this release
`At4g18390`	Plays a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164).	TCP2 positively regulates HY5/HYH and photomorphogenesis in Arabidopsis.2016 · DOI: 10.1093/jxb/erv495
`At1g30210`	Plays a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164).	ABAP1 is a novel plant Armadillo BTB protein involved in DNA replication and transcription.2008 · DOI: 10.1038/emboj.2008.191

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_024178 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0009408 response to heat Biological Process

GO:0009637 response to blue light Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010150 leaf senescence Biological Process

GO:0031347 regulation of defense response Biological Process

GO:0045944 positive regulation of transcription by RNA polymerase II Biological Process

GO:0048366 leaf development Biological Process

GO:2000032 regulation of secondary shoot formation Biological Process

GO:2000306 positive regulation of photomorphogenesis Biological Process

KEGG gene cross-reference

ath:AT1G30210

ath:AT3G02150

ath:AT4G18390

ath:AT5G08070

ath:AT5G60970

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.

Nucleus0.966

Rank 1 · LXL04_024178 · OH-1004

Cytoplasm0.105

Rank 2 · LXL04_024178 · OH-1004

Cell membrane0.029

Rank 3 · LXL04_024178 · OH-1004

Endoplasmic reticulum0.021

Rank 4 · LXL04_024178 · OH-1004

Plastid0.012

Rank 5 · LXL04_024178 · 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.

PF03634.20TCP55-178 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_024178	`PF03634.20`	TCP	55	178	2.2e-29	103.7

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
`Q9S7W5`	Arabidopsis thaliana	Transcription factor TCP13	70.175%	Swiss-Prot	weak database homology
`Q9FME3`	Arabidopsis thaliana	Transcription factor TCP5	36.000%	Swiss-Prot	moderate database homology
`Q9LEZ9`	Arabidopsis thaliana	Transcription factor TCP17	80.488%	Swiss-Prot	weak database homology
`Q93V43`	Arabidopsis thaliana	Transcription factor TCP2	45.033%	Swiss-Prot	weak database homology
`Q9C758`	Arabidopsis thaliana	Transcription factor TCP24	61.111%	Swiss-Prot	weak database homology

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