LXL04_013072 | RubberDandelionOmics

Gene overview

LXL04_013072

Reference: OH-1004 Chr: Chr03 Coordinates: 23572857-23573246 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

390 bp · LXL04_013072|LXL04_013072|OH1004|cDNA

ATGGAGCATCTCCAACCatccaacaacaacaacaaaccTCTTCAACTGGGTCCCCCTGATCCAACTCCGGCAACCTCCACGGCGGCAAAGAAGAAAAGCCGCCACACCAAGGTCAACGGAAGAGGTCTGAGAGTCAGAGTTCCCGCGCTCTGCGCCGCTCGCATCTTCCAACTCACCCGGGAACTCGGCCACCGCTCCGACGGCCAAACCATCGAATGGCTCCTCCACCATGTCGACCCCGCTCTCTTTCCCACATCCTT...

CDS

Download CDS FASTA

390 bp · LXL04_013072|LXL04_013072|OH1004|CDS

ATGGAGCATCTCCAACCATCCAACAACAACAACAAACCTCTTCAACTGGGTCCCCCTGATCCAACTCCGGCAACCTCCACGGCGGCAAAGAAGAAAAGCCGCCACACCAAGGTCAACGGAAGAGGTCTGAGAGTCAGAGTTCCCGCGCTCTGCGCCGCTCGCATCTTCCAACTCACCCGGGAACTCGGCCACCGCTCCGACGGCCAAACCATCGAATGGCTCCTCCACCATGTCGACCCCGCTCTCTTTCCCACATCCTT...

Protein

Download Protein FASTA

129 aa · LXL04_013072|LXL04_013072|OH1004|PROTEIN

MEHLQPSNNNNKPLQLGPPDPTPATSTAAKKKSRHTKVNGRGLRVRVPALCAARIFQLTRELGHRSDGQTIEWLLHHVDPALFPTSFRDATAVPDNQRMSELDLFPNLSFTSLLMQVEEEEIKTTKRMI

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_013072`
TK1151 ID	TkA02G518690
OH-1004 ID	LXL04_013072
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.100
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_013072

Location Chr03:23572857-23573246 (-)

Description Similar to TCP9: Transcription factor TCP9

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g45680`	Transcription factor TCP9.	No verified direct reference in this release
`At1g72010`	Transcription factor TCP22.	No verified direct reference in this release
`At1g58100`	Can specifically bind site II elements in the promoter region of PP438/PNM1.	An Arabidopsis dual-localized pentatricopeptide repeat protein interacts with nuclear proteins involved in gene expression regulation.2011 · DOI: 10.1105/tpc.110.081638
`At3g47620`	Transcription factor involved the regulation of plant development.	Transcription factor AtTCP14 regulates embryonic growth potential during seed germination in Arabidopsis thaliana.2008 · DOI: 10.1111/j.1365-313x.2007.03308.x TCP14 and TCP15 affect internode length and leaf shape in Arabidopsis.2011 · DOI: 10.1111/j.1365-313x.2011.04674.x Arabidopsis thaliana DOF6 negatively affects germination in non-after-ripened seeds and interacts with TCP14.2012 · DOI: 10.1093/jxb/err388 The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers.2012 · DOI: 10.1105/tpc.111.093518 The Arabidopsis immune adaptor SRFR1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity.2014 · DOI: 10.1111/tpj.12527 The ubiquitin receptors DA1, DAR1, and DAR2 redundantly regulate endoreduplication by modulating the stability of TCP14/15 in Arabidopsis.2015 · DOI: 10.1105/tpc.114.132274 Pseudomonas syringae Type III Effector HopBB1 Promotes Host Transcriptional Repressor Degradation to Regulate Phytohormone Responses and Virulence.2017 · DOI: 10.1016/j.chom.2017.01.003 ORANGE Represses Chloroplast Biogenesis in Etiolated Arabidopsis Cotyledons via Interaction with TCP14.2019 · DOI: 10.1105/tpc.18.00290
`At3g27010`	Transcription factor that binds to the site II motif (3'- TGGGCC/T-5') in the promoter of PCNA-2 and to 3'-GCCCG/A-5' elements in the promoters of cyclin CYCB1-1 and ribosomal protein genes.	Internal telomeric repeats and 'TCP domain' protein-binding sites co-operate to regulate gene expression in Arabidopsis thaliana cycling cells.2003 · DOI: 10.1046/j.1365-313x.2003.01682.x Arabidopsis TCP20 links regulation of growth and cell division control pathways.2005 · DOI: 10.1073/pnas.0504039102

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013072 · 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:0008361 regulation of cell size Biological Process

GO:0009624 response to nematode Biological Process

GO:0009653 anatomical structure morphogenesis Biological Process

GO:0009735 response to cytokinin Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009739 response to gibberellin Biological Process

GO:0010029 regulation of seed germination Biological Process

GO:0010229 inflorescence development Biological Process

GO:0031347 regulation of defense response Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

KEGG gene cross-reference

ath:AT1G58100

ath:AT1G72010

ath:AT2G45680

ath:AT3G27010

ath:AT3G47620

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.

Nucleus0.840

Rank 1 · LXL04_013072 · OH-1004

Cytoplasm0.226

Rank 2 · LXL04_013072 · OH-1004

Cell membrane0.034

Rank 3 · LXL04_013072 · OH-1004

Endoplasmic reticulum0.029

Rank 4 · LXL04_013072 · OH-1004

Mitochondrion0.025

Rank 5 · LXL04_013072 · 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.

PF03634.20TCP30-118 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_013072	`PF03634.20`	TCP	30	118	2.6e-18	67.8

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O64647`	Arabidopsis thaliana	Transcription factor TCP9	60.000%	Swiss-Prot	moderate database homology
`Q9C7G4`	Arabidopsis thaliana	Transcription factor TCP22	64.516%	Swiss-Prot	weak database homology
`Q9C518`	Arabidopsis thaliana	Transcription factor TCP8	74.510%	Swiss-Prot	weak database homology
`Q93Z00`	Arabidopsis thaliana	Transcription factor TCP14	69.091%	Swiss-Prot	weak database homology
`Q9LSD5`	Arabidopsis thaliana	Transcription factor TCP20	53.165%	Swiss-Prot	moderate database homology

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