LXL04_015296 | RubberDandelionOmics

Gene overview

LXL04_015296

Reference: OH-1004 Chr: Chr03 Coordinates: 67710315-67717205 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5109 bp · LXL04_015296|LXL04_015296|OH1004|cDNA

ATGATTCTTCACctctccaccaccacctccacctccacctccacctccacctccaccgctAGACTGCACCGCAGCCTCCTCCCCTCCAAATCACACAATTTCTCCCGCGATCATCAATTCACTCGCTACCGAGCAGCATGGCAAGAGCTTGCTGGAGTATTAGTTTTCTCAGCCATTCCTTTCACCGCCGTTAAAGCAATAGCCAACAGTCCCCTTGGCGAGACTCTGCAGAGACGAATGGAGGAGAAAAAGAAAGCTGC...

CDS

Download CDS FASTA

5109 bp · LXL04_015296|LXL04_015296|OH1004|CDS

ATGATTCTTCACCTCTCCACCACCACCTCCACCTCCACCTCCACCTCCACCTCCACCGCTAGACTGCACCGCAGCCTCCTCCCCTCCAAATCACACAATTTCTCCCGCGATCATCAATTCACTCGCTACCGAGCAGCATGGCAAGAGCTTGCTGGAGTATTAGTTTTCTCAGCCATTCCTTTCACCGCCGTTAAAGCAATAGCCAACAGTCCCCTTGGCGAGACTCTGCAGAGACGAATGGAGGAGAAAAAGAAAGCTGC...

Protein

Download Protein FASTA

1702 aa · LXL04_015296|LXL04_015296|OH1004|PROTEIN

MILHLSTTTSTSTSTSTSTARLHRSLLPSKSHNFSRDHQFTRYRAAWQELAGVLVFSAIPFTAVKAIANSPLGETLQRRMEEKKKAAVQNASVYKSLAENAKKYSFWYGKQRPRWLGPLPFQYPTYLDGDLPGDYGFDIAGLGQDPAAFKKYYNFEILHARWAMLGALGALIPEVLDLVGAFHFVEPVWWRVGYSKLQGETIDYLGIPGLHFAGSQGVIVIAICQALLMVGPEYARYCGIEALEPLGIYLPGDVNYPGGV...

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_015296`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_015296

Location Chr03:67710315-67717205 (+)

Description Similar to Retrovirus-related Pol polyprotein from transposon TNT 1-94

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g76570`	The light-harvesting complex (LHC) functions as a light receptor, it captures and delivers excitation energy to photosystems with which it is closely associated (Probable).	Light-harvesting complex B7 shifts the irradiance response of photosynthetic light-harvesting regulation in leaves of Arabidopsis thaliana.2014 · DOI: 10.1016/j.jplph.2013.09.007
`UniProt: Q94HW2`	Retrovirus-related Pol polyprotein from transposon RE1.	No verified direct reference in this release
`At4g02960`	Retrovirus-related Pol polyprotein from transposon RE2.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_015296 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006310 DNA recombination Biological Process

GO:0006508 proteolysis Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009768 photosynthesis, light harvesting in photosystem I Biological Process

GO:0015074 DNA integration Biological Process

GO:0009507 chloroplast Cellular Component

GO:0009522 photosystem I Cellular Component

GO:0009523 photosystem II Cellular Component

GO:0009535 chloroplast thylakoid membrane Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0003964 RNA-directed DNA polymerase activity Molecular Function

GO:0004190 aspartic-type endopeptidase activity Molecular Function

KEGG gene cross-reference

ath:AT1G76570

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.

Plastid0.366

Rank 1 · LXL04_015296 · OH-1004

Mitochondrion0.343

Rank 2 · LXL04_015296 · OH-1004

Cytoplasm0.109

Rank 3 · LXL04_015296 · OH-1004

Peroxisome0.105

Rank 4 · LXL04_015296 · OH-1004

Nucleus0.044

Rank 5 · LXL04_015296 · 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.

PF00504.29Chloroa_b-bind124-299 aa

PF13961.13DUF4219365-390 aa

PF14223.15Retrotran_gag_2377-541 aa

PF22936.2Pol_BBD698-778 aa

PF13976.12gag_pre-integrs806-873 aa

PF00665.33rve887-988 aa

PF29688.1TnsB_C954-1007 aa

PF25597.2SH3_retrovirus1061-1123 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_015296	`PF00504.29`	Chloroa_b-bind	124	299	6.7e-41	141.2
LXL04_015296	`PF13961.13`	DUF4219	365	390	8.7e-07	29.2
LXL04_015296	`PF14223.15`	Retrotran_gag_2	377	541	3.6e-12	47.1
LXL04_015296	`PF22936.2`	Pol_BBD	698	778	1.2e-24	87.1
LXL04_015296	`PF13976.12`	gag_pre-integrs	806	873	3.8e-18	65.7
LXL04_015296	`PF00665.33`	rve	887	988	1e-11	45.7
LXL04_015296	`PF29688.1`	TnsB_C	954	1007	5.7e-06	26.9
LXL04_015296	`PF25597.2`	SH3_retrovirus	1061	1123	7.9e-18	64.7
LXL04_015296	`PF07727.20`	RVT_2	1248	1397	1.2e-72	245.1
LXL04_015296	`PF07727.20`	RVT_2	1400	1459	1.2e-72	245.1

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
`Q9C9K1`	Arabidopsis thaliana	Chlorophyll a-b binding protein 7, chloroplastic	80.565%	Swiss-Prot	weak database homology
`Q94HW2`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE1	36.445%	Swiss-Prot	weak database homology
`Q9ZT94`	Arabidopsis thaliana	Retrovirus-related Pol polyprotein from transposon RE2	36.719%	Swiss-Prot	weak database homology

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