LXL04_012301 | RubberDandelionOmics

Gene overview

LXL04_012301

Reference: OH-1004 Chr: Chr03 Coordinates: 9955544-9964667 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3363 bp · LXL04_012301|LXL04_012301|OH1004|cDNA

ATGAAGATGGCAGTGGGAAAGTTCAAGAAAAAGTCTGAAGATAAACAGACGACAGAAAAAGAAAACAAGTTTAACATGTTTATCTCTTTTCCGGATGACGTTTATATACACATTTTTAAAACGCTTCCTGATGGTTTCCTACGTTATAATGCTAAGTATGTCTGTAGACAATGGTTTGATATAATCACCAACAAGATCTTGCTAGACCAAGTTTCTTTAATCCTCCAAAATCCAACCGGAATCTACACATCACGATATGT...

CDS

Download CDS FASTA

3363 bp · LXL04_012301|LXL04_012301|OH1004|CDS

ATGAAGATGGCAGTGGGAAAGTTCAAGAAAAAGTCTGAAGATAAACAGACGACAGAAAAAGAAAACAAGTTTAACATGTTTATCTCTTTTCCGGATGACGTTTATATACACATTTTTAAAACGCTTCCTGATGGTTTCCTACGTTATAATGCTAAGTATGTCTGTAGACAATGGTTTGATATAATCACCAACAAGATCTTGCTAGACCAAGTTTCTTTAATCCTCCAAAATCCAACCGGAATCTACACATCACGATATGT...

Protein

Download Protein FASTA

1120 aa · LXL04_012301|LXL04_012301|OH1004|PROTEIN

MKMAVGKFKKKSEDKQTTEKENKFNMFISFPDDVYIHIFKTLPDGFLRYNAKYVCRQWFDIITNKILLDQVSLILQNPTGIYTSRYVNLRKEGQELEVKEQYLDIPHIGTIRSWCNEFLVITDIYRKGCMYVYNLVTKVATYLPRCTSCVGCYSCQCGVALSFDNLKGVYKVLRVYMGPPMQCHILILKSEILSSCVTLKWKNIKVPDFMSQDMQNWCHPISVQGRYFYWDVHCSNYLISMDMVKEKIFPFLLPRSCGDH...

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_012301`
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_012301

Location Chr03:9955544-9964667 (-)

Description Similar to TOC34: Translocase of chloroplast 34

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g07870`	F-box protein At3g07870.	No verified direct reference in this release
`At5g05000`	GTPase involved in protein precursor import into chloroplasts.	Two Toc34 homologues with different properties.2003 · DOI: 10.1021/bi034001q The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins.2003 · DOI: 10.1105/tpc.012955 An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02024.x Deletion of core components of the plastid protein import machinery causes differential arrest of embryo development in Arabidopsis thaliana.2006 · DOI: 10.1055/s-2005-873044
`At5g42970`	Component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes such as photomorphogenesis and auxin and jasmonate responses.	Arabidopsis cop8 and fus4 mutations define the same gene that encodes subunit 4 of the COP9 signalosome.1999 · DOI: 10.1105/tpc.11.10.1967
`At1g02280`	GTPase involved in protein precursor import into chloroplasts.	Chloroplast protein translocon components atToc159 and atToc33 are not essential for chloroplast biogenesis in guard cells and root cells.2001 · DOI: 10.1104/pp.127.1.90 Two Toc34 homologues with different properties.2003 · DOI: 10.1021/bi034001q Unusual nucleotide-binding properties of the chloroplast protein import receptor, atToc33.2003 · DOI: 10.1016/s0014-5793(03)00478-2 Dimerization of Toc-GTPases at the chloroplast protein import machinery.2003 · DOI: 10.1074/jbc.m305946200 The Arabidopsis ppi1 mutant is specifically defective in the expression, chloroplast import, and accumulation of photosynthetic proteins.2003 · DOI: 10.1105/tpc.012955 The roles of toc34 and toc75 in targeting the toc159 preprotein receptor to chloroplasts.2003 · DOI: 10.1074/jbc.m307873200 An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis.2004 · DOI: 10.1111/j.1365-313x.2004.02024.x In vivo assessment of the significance of phosphorylation of the Arabidopsis chloroplast protein import receptor, atToc33.2006 · DOI: 10.1016/j.febslet.2005.12.055 Phospho-mimicry mutant of atToc33 affects early development of Arabidopsis thaliana.2007 · DOI: 10.1016/j.febslet.2007.11.071

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012301 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000338 protein deneddylation Biological Process

GO:0006886 intracellular protein transport Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009585 red, far-red light phototransduction Biological Process

GO:0009640 photomorphogenesis Biological Process

GO:0010100 negative regulation of photomorphogenesis Biological Process

GO:0010971 positive regulation of G2/M transition of mitotic cell cycle Biological Process

GO:0019750 chloroplast localization Biological Process

GO:0045036 protein targeting to chloroplast Biological Process

GO:0005576 extracellular region Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT1G02280

ath:AT3G07870

ath:AT5G05000

ath:AT5G42970

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.

Cytoplasm0.613

Rank 1 · LXL04_012301 · OH-1004

Nucleus0.316

Rank 2 · LXL04_012301 · OH-1004

Cell membrane0.126

Rank 3 · LXL04_012301 · OH-1004

Endoplasmic reticulum0.072

Rank 4 · LXL04_012301 · OH-1004

Extracellular0.064

Rank 5 · LXL04_012301 · 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.

PF08268.18FBA_3126-319 aa

PF12937.13F-box-like391-429 aa

PF08268.18FBA_3462-728 aa

PF08268.18FBA_3897-1097 aa

PF03478.25Beta-prop_KIB1-4914-1102 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_012301	`PF08268.18`	FBA_3	126	319	6.7e-30	104.9
LXL04_012301	`PF12937.13`	F-box-like	391	429	1.3e-16	60.8
LXL04_012301	`PF08268.18`	FBA_3	462	728	6.7e-30	104.9
LXL04_012301	`PF08268.18`	FBA_3	897	1097	6.7e-30	104.9
LXL04_012301	`PF03478.25`	Beta-prop_KIB1-4	914	1102	2.2e-14	54.3

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
`Q9SFC7`	Arabidopsis thaliana	F-box protein At3g07870	26.032%	Swiss-Prot	weak database homology
`Q38906`	Arabidopsis thaliana	Translocase of chloroplast 34, chloroplastic	56.250%	Swiss-Prot	weak database homology
`Q8L5U0`	Arabidopsis thaliana	COP9 signalosome complex subunit 4	61.017%	Swiss-Prot	weak database homology
`O23680`	Arabidopsis thaliana	Translocase of chloroplast 33, chloroplastic	58.537%	Swiss-Prot	weak database homology

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