LXL04_037713 | RubberDandelionOmics

Gene overview

LXL04_037713

Reference: OH-1004 Chr: Chr09 Coordinates: 19160948-19163561 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2034 bp · LXL04_037713|LXL04_037713|OH1004|cDNA

ATGCTTTGTTTACCTCTCCGTTCTATTTCCCCTCACCCCAAAATCCAATTTCGATCGCAAACCCAAGTGTCGAGATTCTTGTCAACAACCCATTTTGTTCATCTCCATCGTCAAAATAAATATTTGAACAGAATTATCCACAGGAGTTACGGATATACTCCTGGTCCATGTCCTTGTTTGAAATCCGAAACAGAAATCTTCACTTCCAGCGAAGAAGAGTTCGATATGGAATTAGGCCGCCTGTTGAGGCTGTTGCCGGA...

CDS

Download CDS FASTA

2034 bp · LXL04_037713|LXL04_037713|OH1004|CDS

ATGCTTTGTTTACCTCTCCGTTCTATTTCCCCTCACCCCAAAATCCAATTTCGATCGCAAACCCAAGTGTCGAGATTCTTGTCAACAACCCATTTTGTTCATCTCCATCGTCAAAATAAATATTTGAACAGAATTATCCACAGGAGTTACGGATATACTCCTGGTCCATGTCCTTGTTTGAAATCCGAAACAGAAATCTTCACTTCCAGCGAAGAAGAGTTCGATATGGAATTAGGCCGCCTGTTGAGGCTGTTGCCGGA...

Protein

Download Protein FASTA

677 aa · LXL04_037713|LXL04_037713|OH1004|PROTEIN

MLCLPLRSISPHPKIQFRSQTQVSRFLSTTHFVHLHRQNKYLNRIIHRSYGYTPGPCPCLKSETEIFTSSEEEFDMELGRLLRLLPEEMRRRANEHQELHQLIEVVMDLGRKPLARFPSGDFVLSDHLITVDDLEHATSLVGDFAIDNRAGISRTLHRISAIRNRKGAIIGLTCRVGRAISGSAKLLQDLVKDGASLLLIGPPGVGKTTIIRDIARMLANEYKKRVMIVDTSNEIGGDGDIPHAGIGNARRMQVPDTDMQ...

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_037713`
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_037713

Location Chr09:19160948-19163561 (+)

Description Similar to SPD1: Protein SEEDLING PLASTID DEVELOPMENT 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g10420`	Required during eoplast (a highly reduced plastid type present during the degreening and dehydration stages of seed maturation) development in embryos and early stages of eoplast redifferentiation during seedling growth.	A mutation in Arabidopsis seedling plastid development1 affects plastid differentiation in embryo-derived tissues during seedling growth.2011 · DOI: 10.1104/pp.110.161414

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_037713 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009657 plastid organization Biological Process

GO:0010431 seed maturation Biological Process

GO:0030435 sporulation resulting in formation of a cellular spore Biological Process

GO:0090677 reversible differentiation Biological Process

GO:0009507 chloroplast Cellular Component

GO:0009941 chloroplast envelope Cellular Component

GO:0031969 chloroplast membrane Cellular Component

GO:0031972 chloroplast intermembrane space Cellular Component

GO:0003676 nucleic acid binding Molecular Function

GO:0005524 ATP binding Molecular Function

KEGG gene cross-reference

ath:AT3G10420

bsu:BSU24430

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.

Plastid0.772

Rank 1 · LXL04_037713 · OH-1004

Mitochondrion0.122

Rank 2 · LXL04_037713 · OH-1004

Cytoplasm0.086

Rank 3 · LXL04_037713 · OH-1004

Nucleus0.076

Rank 4 · LXL04_037713 · OH-1004

Peroxisome0.038

Rank 5 · LXL04_037713 · 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.

PF19568.6Spore_III_AA171-323 aa

PF13401.13AAA_22195-281 aa

PF00004.36AAA197-284 aa

PF07728.21AAA_5197-282 aa

PF13238.13AAA_18198-290 aa

PF25516.2PTPase459-538 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_037713	`PF19568.6`	Spore_III_AA	171	323	1e-14	55.2
LXL04_037713	`PF13401.13`	AAA_22	195	281	4.6e-06	27.7
LXL04_037713	`PF00004.36`	AAA	197	284	4.1e-08	34.4
LXL04_037713	`PF07728.21`	AAA_5	197	282	5.4e-06	27.2
LXL04_037713	`PF13238.13`	AAA_18	198	290	1.5e-06	29.4
LXL04_037713	`PF25516.2`	PTPase	459	538	4.6e-25	88.0

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
`F4J3R7`	Arabidopsis thaliana	Protein SEEDLING PLASTID DEVELOPMENT 1	49.565%	Swiss-Prot	moderate database homology

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