LXL04_004522 | RubberDandelionOmics

Gene overview

LXL04_004522

Reference: OH-1004 Chr: Chr01 Coordinates: 139137568-139138080 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

513 bp · LXL04_004522|LXL04_004522|OH1004|cDNA

ATGGACCCGGTCCCAGATAAAATCTTCATAGAAAGATTTGACCAAACCCCACAACAaccgccgccgccgccgcctACTTCCTCCACAGACATGCATAAACAACTTGTTCCGTTTCAAATGGGTCCTTCCAATAGTCTGGTTTCAATCCAAACCCCCCAAATCATTCAgtcaaagaagaaaaaggacCGCCATGCGAAGGTGAACGGGAGGGGCCGGAGAGTGAGGGTCCCGGCGCTGTGTGCGGCTCGCATATTCCAGCT...

CDS

Download CDS FASTA

513 bp · LXL04_004522|LXL04_004522|OH1004|CDS

ATGGACCCGGTCCCAGATAAAATCTTCATAGAAAGATTTGACCAAACCCCACAACAACCGCCGCCGCCGCCGCCTACTTCCTCCACAGACATGCATAAACAACTTGTTCCGTTTCAAATGGGTCCTTCCAATAGTCTGGTTTCAATCCAAACCCCCCAAATCATTCAGTCAAAGAAGAAAAAGGACCGCCATGCGAAGGTGAACGGGAGGGGCCGGAGAGTGAGGGTCCCGGCGCTGTGTGCGGCTCGCATATTCCAGCT...

Protein

Download Protein FASTA

170 aa · LXL04_004522|LXL04_004522|OH1004|PROTEIN

MDPVPDKIFIERFDQTPQQPPPPPPTSSTDMHKQLVPFQMGPSNSLVSIQTPQIIQSKKKKDRHAKVNGRGRRVRVPALCAARIFQLTRELGHRTDGQTIDWLLHHVDPSLFPPSSAAGGASQTVVPENRGVVSELDLFPPNMSFTSLLMQVEEDEVKIKNEKNEDARKI

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_004522`
TK1151 ID	TkA01G138870
OH-1004 ID	LXL04_004522
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.400
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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_004522

Location Chr01:139137568-139138080 (-)

Description Similar to TCP6: Transcription factor TCP6

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g41030`	Transcription factor TCP6.	No verified direct reference in this release
`At5g23280`	Transcription factor TCP7.	No verified direct reference in this release
`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
`At1g72010`	Transcription factor TCP22.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0194600`	Transcription activator.	DNA binding and dimerization specificity and potential targets for the TCP protein family.2002 · DOI: 10.1046/j.1365-313x.2002.01294.x PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene.1997 · DOI: 10.1105/tpc.9.9.1607

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_004522 · 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:0009653 anatomical structure morphogenesis Biological Process

GO:0042752 regulation of circadian rhythm Biological Process

GO:0048578 positive regulation of long-day photoperiodism, flowering Biological Process

GO:1900056 negative regulation of leaf senescence Biological Process

GO:0005634 nucleus Cellular Component

GO:0000976 transcription cis-regulatory region binding Molecular Function

GO:0000987 cis-regulatory region sequence-specific DNA binding Molecular Function

GO:0001216 DNA-binding transcription activator activity Molecular Function

GO:0003677 DNA binding Molecular Function

KEGG gene cross-reference

ath:AT1G72010

ath:AT3G27010

ath:AT5G23280

ath:AT5G41030

dosa:Os04g0194600

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.

Nucleus0.950

Rank 1 · LXL04_004522 · OH-1004

Cytoplasm0.191

Rank 2 · LXL04_004522 · OH-1004

Mitochondrion0.021

Rank 3 · LXL04_004522 · OH-1004

Cell membrane0.015

Rank 4 · LXL04_004522 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_004522 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF03634.20TCP59-110 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_004522	`PF03634.20`	TCP	59	110	2.3e-19	71.2

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
`Q9FLM6`	Arabidopsis thaliana	Transcription factor TCP6	52.500%	Swiss-Prot	weak database homology
`Q9FMX2`	Arabidopsis thaliana	Transcription factor TCP7	56.757%	Swiss-Prot	weak database homology
`Q9LSD5`	Arabidopsis thaliana	Transcription factor TCP20	64.407%	Swiss-Prot	weak database homology
`Q9C7G4`	Arabidopsis thaliana	Transcription factor TCP22	59.016%	Swiss-Prot	weak database homology
`O23875`	Oryza sativa subsp. japonica	Transcription factor PCF1	60.870%	Swiss-Prot	weak database homology

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