LXL04_001936 | RubberDandelionOmics

Gene overview

LXL04_001936

Reference: OH-1004 Chr: Chr01 Coordinates: 37399694-37401665 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1668 bp · LXL04_001936|LXL04_001936|OH1004|cDNA

ATGGAAAAAAAGCTGGAACAGGAGGAGGTTGCTCATCGACGTAAGGGTCTGATTCTGGATCCTCAGAggaatcatcatcatcatcatcttcaactTTATCAGCAACTGTTGAATTCAGGACAAGGAGAGAAGGAAGAGGATCAAGAAATTCAGATAGGTTTTCATGGATTCCATCAAAATCATCATCAGCTTCAGCAAAATCGAGAAATCCCACCTCCCGACAACCGTGTTCTCCACGGAGGATTAGGTGGTCCGGCAAA...

CDS

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1668 bp · LXL04_001936|LXL04_001936|OH1004|CDS

ATGGAAAAAAAGCTGGAACAGGAGGAGGTTGCTCATCGACGTAAGGGTCTGATTCTGGATCCTCAGAGGAATCATCATCATCATCATCTTCAACTTTATCAGCAACTGTTGAATTCAGGACAAGGAGAGAAGGAAGAGGATCAAGAAATTCAGATAGGTTTTCATGGATTCCATCAAAATCATCATCAGCTTCAGCAAAATCGAGAAATCCCACCTCCCGACAACCGTGTTCTCCACGGAGGATTAGGTGGTCCGGCAAA...

Protein

Download Protein FASTA

555 aa · LXL04_001936|LXL04_001936|OH1004|PROTEIN

MEKKLEQEEVAHRRKGLILDPQRNHHHHHLQLYQQLLNSGQGEKEEDQEIQIGFHGFHQNHHQLQQNREIPPPDNRVLHGGLGGPAKQPPRPQKKRAYLPSSVDQLTQDGEEYAPRLPEKMGESYQYHNQQLQQQQQASGSSRLGLRGAGGGGGGEIVEVQGGHIVRSTGRKDRHSKVCTAKGPRDRRVRLSAHTAIQFYDVQDRLGYDRPSKAVDWLIKKAKAAIDELAELPAWKPTATTATTTPNSTSIADFEQNPDQ...

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_001936`
TK1151 ID	TkA01G497220
OH-1004 ID	LXL04_001936
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 90.148 / OH-1004 65.946 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_001936

Location Chr01:37399694-37401665 (+)

Description Similar to TCP4: Transcription factor TCP4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g15030`	Transcription factor playing 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).	Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis.2016 · DOI: 10.1105/tpc.16.00360 TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis.2017 · DOI: 10.1371/journal.pgen.1006856 The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana.2018 · DOI: 10.1111/tpj.13772 The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways.2019 · DOI: 10.1371/journal.pgen.1007988 The TCP4 Transcription Factor Directly Activates TRICHOMELESS1 and 2 and Suppresses Trichome Initiation.2019 · DOI: 10.1104/pp.19.00197
`At1g53230`	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).	TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis.2007 · DOI: 10.1105/tpc.106.044792
`At2g31070`	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

Rice

Reference gene ID	Possible function	Papers / DOI
`UniProt: A2WM14`	Transcription activator.	No verified direct reference in this release
`Os01g0213800`	Transcription activator.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_001936 · 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:0009733 response to auxin Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010150 leaf senescence Biological Process

GO:0048366 leaf development Biological Process

GO:0048825 cotyledon development Biological Process

GO:0048826 cotyledon morphogenesis Biological Process

GO:2000032 regulation of secondary shoot formation Biological Process

GO:0005634 nucleus Cellular Component

GO:0001216 DNA-binding transcription activator activity Molecular Function

KEGG gene cross-reference

ath:AT1G53230

ath:AT2G31070

ath:AT3G15030

dosa:Os01g0213800

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.

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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.

Nucleus0.963

Rank 1 · LXL04_001936 · OH-1004

Cytoplasm0.120

Rank 2 · LXL04_001936 · OH-1004

Cell membrane0.019

Rank 3 · LXL04_001936 · OH-1004

Endoplasmic reticulum0.014

Rank 4 · LXL04_001936 · OH-1004

Mitochondrion0.010

Rank 5 · LXL04_001936 · 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.

PF03634.20TCP170-279 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_001936	`PF03634.20`	TCP	170	279	5.8e-34	118.6

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
`Q8LPR5`	Arabidopsis thaliana	Transcription factor TCP4	52.252%	Swiss-Prot	moderate database homology
`Q9MAH8`	Arabidopsis thaliana	Transcription factor TCP3	51.351%	Swiss-Prot	moderate database homology
`O82277`	Arabidopsis thaliana	Transcription factor TCP10	43.233%	Swiss-Prot	weak database homology
`A2WM14`	Oryza sativa subsp. indica	Transcription factor PCF5	50.307%	Swiss-Prot	moderate database homology
`Q8LT07`	Oryza sativa subsp. japonica	Transcription factor PCF5	50.307%	Swiss-Prot	moderate database homology

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