LXL04_009176 | RubberDandelionOmics

Gene overview

LXL04_009176

Reference: OH-1004 Chr: Chr02 Coordinates: 119610344-119618862 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4623 bp · LXL04_009176|LXL04_009176|OH1004|cDNA

ATGGCACCAAGGTCGAGCAGAGGAAAAGGAAACAAAACCAAAGCtgataagaagaagaaggaagagaaaGTTGTTCCTAGTGTTCTGGACATAACAATAATCACTCCTTATGAAACTCAAGTTATACTCAAGGGCATCTCCACAGACAAAATCCTCGACGTGAAGAAATTACTAGCTGTTAATGTCGATACTTGCCATCTAACCAACTATTCTCTCTCTCACGAGGTTAAAGGAGCAAAGTTGAATGATAGGTTGGATTT...

CDS

Download CDS FASTA

4623 bp · LXL04_009176|LXL04_009176|OH1004|CDS

ATGGCACCAAGGTCGAGCAGAGGAAAAGGAAACAAAACCAAAGCTGATAAGAAGAAGAAGGAAGAGAAAGTTGTTCCTAGTGTTCTGGACATAACAATAATCACTCCTTATGAAACTCAAGTTATACTCAAGGGCATCTCCACAGACAAAATCCTCGACGTGAAGAAATTACTAGCTGTTAATGTCGATACTTGCCATCTAACCAACTATTCTCTCTCTCACGAGGTTAAAGGAGCAAAGTTGAATGATAGGTTGGATTT...

Protein

Download Protein FASTA

1540 aa · LXL04_009176|LXL04_009176|OH1004|PROTEIN

MAPRSSRGKGNKTKADKKKKEEKVVPSVLDITIITPYETQVILKGISTDKILDVKKLLAVNVDTCHLTNYSLSHEVKGAKLNDRLDLVSLKPCVLKMVEEDYTDEAHAVAHVRRLLDIVASTTRFGKPKTKRVTTGAGGEARSKKGRSQNVQVTAGRPVSPLSDGGETVENGGSSETETTATATSPVSENLDMAAIHPVPKLSDFYEFFSFSNLSPPILQLKRVDPQDAQEKREGDHFEMQIKICNGKLFQVVASTKGFY...

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_009176`
TK1151 ID	TkA03G405530
OH-1004 ID	LXL04_009176
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	99.600
Protein coverage (%)	TK1151 99.820 / OH-1004 71.883 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_009176

Location Chr02:119610344-119618862 (+)

Description Similar to TSS: Protein TSS

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g15290`	May act as the scaffold of a protein complex, which sequesters key factors that are required for the G2 to M transition in meristematic tissues (By similarity).	No verified direct reference in this release
`At4g28080`	Negatively regulates meristematic tissue proliferation by integrating developmental signals with carbon source availability.	No verified direct reference in this release
`At1g01320`	May act as the scaffold of a protein complex, which sequesters key factors that are required for the G2 to M transition in meristematic tissues (By similarity).	REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment.2016 · DOI: 10.1073/pnas.1515741113
`At3g52140`	mRNA-binding protein involved in proper cytoplasmic distribution of mitochondria (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_009176 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000266 mitochondrial fission Biological Process

GO:0000281 mitotic cytokinesis Biological Process

GO:0007005 mitochondrion organization Biological Process

GO:0008053 mitochondrial fusion Biological Process

GO:0010636 positive regulation of mitochondrial fusion Biological Process

GO:0010906 regulation of glucose metabolic process Biological Process

GO:0019750 chloroplast localization Biological Process

GO:0048312 intracellular distribution of mitochondria Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

KEGG gene cross-reference

ath:AT1G01320

ath:AT1G15290

ath:AT3G52140

ath:AT4G28080

ddi:DDB_G0292806

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.

Cytoplasm0.438

Rank 1 · LXL04_009176 · OH-1004

Nucleus0.247

Rank 2 · LXL04_009176 · OH-1004

Cell membrane0.194

Rank 3 · LXL04_009176 · OH-1004

Golgi apparatus0.137

Rank 4 · LXL04_009176 · OH-1004

Endoplasmic reticulum0.108

Rank 5 · LXL04_009176 · 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.

PF15044.12CLU_N48-119 aa

PF12807.13eIF3_p135691-831 aa

PF13424.13TPR_12869-932 aa

PF24885.2TPR_NPHP3872-971 aa

PF13424.13TPR_12901-971 aa

PF13374.13TPR_10901-942 aa

PF13424.13TPR_12985-1059 aa

PF13374.13TPR_10985-1025 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009176	`PF15044.12`	CLU_N	48	119	7.4e-09	36.6
LXL04_009176	`PF12807.13`	eIF3_p135	691	831	1.9e-27	97.2
LXL04_009176	`PF13424.13`	TPR_12	869	932	4.8e-29	101.1
LXL04_009176	`PF24885.2`	TPR_NPHP3	872	971	3.6e-11	43.6
LXL04_009176	`PF13424.13`	TPR_12	901	971	4.8e-29	101.1
LXL04_009176	`PF13374.13`	TPR_10	901	942	9.5e-24	83.3
LXL04_009176	`PF13424.13`	TPR_12	985	1059	4.8e-29	101.1
LXL04_009176	`PF13374.13`	TPR_10	985	1025	9.5e-24	83.3

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.

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Protein	Organism	Description	Identity	Database	Confidence
`F4HZK4`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 3	51.486%	Swiss-Prot	strong database homology
`F4JKH6`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 2	54.726%	Swiss-Prot	strong database homology
`F4HS99`	Arabidopsis thaliana	Protein REDUCED CHLOROPLAST COVERAGE 1	54.072%	Swiss-Prot	strong database homology
`F4J5S1`	Arabidopsis thaliana	Clustered mitochondria protein	36.660%	Swiss-Prot	weak database homology

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