LXL04_029204 | RubberDandelionOmics

Gene overview

LXL04_029204

Reference: OH-1004 Chr: Chr06 Coordinates: 83707973-83721843 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5928 bp · LXL04_029204|LXL04_029204|OH1004|cDNA

ATGTCATCCTTAAGTCGGGAACTAGTTTTCCTAATCCTGCAATTCCTGGATGAGGAAAAGTTCAAAGAAACTGTCCACAAGTTGGAACAAGAATCGGCTTTTTTCTTCAACATGAAATATTTTGAGGAACAAGTTCAAGCTGGTGAATGGGATGAGGTTGAAAAGTATCTATGTGGGTTCACTAAGGTTGAAGACAATCGTTACTCAATGAAGATATTCTTTGAAATAAGGAAACAGAAGAATGACAGAGCAAAAGCTGT...

CDS

Download CDS FASTA

5928 bp · LXL04_029204|LXL04_029204|OH1004|CDS

ATGTCATCCTTAAGTCGGGAACTAGTTTTCCTAATCCTGCAATTCCTGGATGAGGAAAAGTTCAAAGAAACTGTCCACAAGTTGGAACAAGAATCGGCTTTTTTCTTCAACATGAAATATTTTGAGGAACAAGTTCAAGCTGGTGAATGGGATGAGGTTGAAAAGTATCTATGTGGGTTCACTAAGGTTGAAGACAATCGTTACTCAATGAAGATATTCTTTGAAATAAGGAAACAGAAGAATGACAGAGCAAAAGCTGT...

Protein

Download Protein FASTA

1975 aa · LXL04_029204|LXL04_029204|OH1004|PROTEIN

MSSLSRELVFLILQFLDEEKFKETVHKLEQESAFFFNMKYFEEQVQAGEWDEVEKYLCGFTKVEDNRYSMKIFFEIRKQKNDRAKAVEILVKDLKVFSTFNEELFKEITQLLTLDNFRQNEQLSKYGDTKSARSIMLVELKKLIEANPLFREKLTLPVFKASRLRTLINQSLNWQHQLCKNPRPNPDIKTLFIDHTCASNNGGRAPPPINSPLSGPVPKAGVFPPIGAHGPFQPVVSPSAGWMATANLSMPHAGVAAGPP...

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_029204`
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_029204

Location Chr06:83707973-83721843 (+)

Description Similar to TPR2: Protein TOPLESS-RELATED PROTEIN 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g15750`	Transcriptional corepressor.	No verified direct reference in this release
`At1g80490`	Transcriptional corepressor.	Arabidopsis resistance protein SNC1 activates immune responses through association with a transcriptional corepressor.2010 · DOI: 10.1073/pnas.1002828107
`At3g15880`	Transcription corepressor of Zinc finger transcription factors GAF1/IDD2 and ENY/IDD1 in regulation of gibberellin homeostasis and signaling.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os08g0162100`	Transcriptional corepressor involved in branch formation regulation, presumably by suppressing primary branch formation and promoting secondary branch formation.	OsLIS-L1 encoding a lissencephaly type-1-like protein with WD40 repeats is required for plant height and male gametophyte formation in rice.2012 · DOI: 10.1007/s00425-011-1532-7
`Os03g0254700`	Probable downstream regulator of strigolactones signaling (By similarity).	MODD Mediates Deactivation and Degradation of OsbZIP46 to Negatively Regulate ABA Signaling and Drought Resistance in Rice.2016 · DOI: 10.1105/tpc.16.00171

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029204 · 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:0009867 jasmonic acid mediated signaling pathway Biological Process

GO:0010051 xylem and phloem pattern formation Biological Process

GO:0010072 primary shoot apical meristem specification Biological Process

GO:0010229 inflorescence development Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0042802 identical protein binding Molecular Function

GO:0042803 protein homodimerization activity Molecular Function

KEGG gene cross-reference

ath:AT1G15750

dosa:Os08g0162100

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.

Cytoplasm0.585

Rank 1 · LXL04_029204 · OH-1004

Nucleus0.394

Rank 2 · LXL04_029204 · OH-1004

Cell membrane0.100

Rank 3 · LXL04_029204 · OH-1004

Mitochondrion0.055

Rank 4 · LXL04_029204 · OH-1004

Golgi apparatus0.051

Rank 5 · LXL04_029204 · 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.

PF17814.8LisH_TPL5-33 aa

PF21889.2TPR1-like_2nd37-154 aa

PF21359.3zf_topless157-197 aa

PF24807.2WD40_CDC20-Fz328-490 aa

PF25174.2Beta-prop_THOC3332-501 aa

PF25168.2Beta-prop_WDR36-Utp21_2nd376-496 aa

PF25173.2Beta-prop_WDR3_1st377-496 aa

PF24814.2WD40_Prp19389-472 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029204	`PF17814.8`	LisH_TPL	5	33	5.6e-13	49.0
LXL04_029204	`PF21889.2`	TPR1-like_2nd	37	154	9.5e-105	346.5
LXL04_029204	`PF21359.3`	zf_topless	157	197	3.7e-25	88.0
LXL04_029204	`PF24807.2`	WD40_CDC20-Fz	328	490	4.1e-35	122.2
LXL04_029204	`PF25174.2`	Beta-prop_THOC3	332	501	4.5e-48	164.3
LXL04_029204	`PF25168.2`	Beta-prop_WDR36-Utp21_2nd	376	496	2e-29	103.6
LXL04_029204	`PF25173.2`	Beta-prop_WDR3_1st	377	496	2.4e-50	171.5
LXL04_029204	`PF24814.2`	WD40_Prp19	389	472	3.6e-48	164.7
LXL04_029204	`PF25391.2`	WD40_Gbeta	399	495	1.8e-19	70.7
LXL04_029204	`PF25175.2`	Beta-prop_WDR5	400	651	2.4e-47	162.3
LXL04_029204	`PF23381.2`	Beta-prop_IFT122_1st	400	495	1.4e-44	153.2
LXL04_029204	`PF24796.2`	WDR55	406	494	9.3e-33	114.3
LXL04_029204	`PF24817.2`	WD40_WDHD1_1st	414	506	3.4e-42	145.3
LXL04_029204	`PF25172.2`	Beta-prop_WDR3_2nd	434	494	1.9e-26	93.7
LXL04_029204	`PF00400.39`	WD40	437	472	1.2e-34	117.9
LXL04_029204	`PF24796.2`	WDR55	490	651	9.3e-33	114.3

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
`Q94AI7`	Arabidopsis thaliana	Protein TOPLESS	63.850%	Swiss-Prot	moderate database homology
`Q0WV90`	Arabidopsis thaliana	Topless-related protein 1	63.328%	Swiss-Prot	moderate database homology
`Q27GK7`	Arabidopsis thaliana	Topless-related protein 4	61.063%	Swiss-Prot	moderate database homology
`Q0J7U6`	Oryza sativa subsp. japonica	Protein TOPLESS-RELATED PROTEIN 2	72.671%	Swiss-Prot	moderate database homology
`Q10NY2`	Oryza sativa subsp. japonica	Protein TPR3	63.453%	Swiss-Prot	moderate database homology

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