LXL04_016680 | RubberDandelionOmics

Gene overview

LXL04_016680

Reference: OH-1004 Chr: Chr03 Coordinates: 130711102-130717002 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2076 bp · LXL04_016680|LXL04_016680|OH1004|cDNA

ATGGGCGGAAAACAGGGTTCGATCATTGTTCATGTCGGCATTGTGTTGTTTACGATTTGGTTACTTTCTTCCTTCGATTACTGCCACCCACTTGCTTACTTCCTTTCTTTCATCTATCTCTACCTGGTTCATGATCGTTATGCAATGAGATTGAGAAGAAAGATACAATTTGAGGAAAGAAAACAGGCAAATCAAAAGAGGGTACTTTCGGATTCTGAATCCGTAAGGTGGTTAAATCATACGATTGAAAGAATTTGGCC...

CDS

Download CDS FASTA

2076 bp · LXL04_016680|LXL04_016680|OH1004|CDS

ATGGGCGGAAAACAGGGTTCGATCATTGTTCATGTCGGCATTGTGTTGTTTACGATTTGGTTACTTTCTTCCTTCGATTACTGCCACCCACTTGCTTACTTCCTTTCTTTCATCTATCTCTACCTGGTTCATGATCGTTATGCAATGAGATTGAGAAGAAAGATACAATTTGAGGAAAGAAAACAGGCAAATCAAAAGAGGGTACTTTCGGATTCTGAATCCGTAAGGTGGTTAAATCATACGATTGAAAGAATTTGGCC...

Protein

Download Protein FASTA

691 aa · LXL04_016680|LXL04_016680|OH1004|PROTEIN

MGGKQGSIIVHVGIVLFTIWLLSSFDYCHPLAYFLSFIYLYLVHDRYAMRLRRKIQFEERKQANQKRVLSDSESVRWLNHTIERIWPICMEEIVSQKILLPIIPWFLQKYKPWTVKEAVVQNIYLGRSPPMFTDMRVCRQSTGDDHLVLELGMNFRTAEDMNAILAVKLTKRLGFGMWAKMHLTGMHVEGKVLVGVKFLPNWPFIGRLRVCFVEPPYFQLTVKPIFAHGLDVTELPGIAGWLDKLLTLAFEETLVEPNML...

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_016680`
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_016680

Location Chr03:130711102-130717002 (-)

Description Similar to NTMC2T6.1: C2 domain-containing protein At1g53590

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g53590`	C2 domain-containing protein At1g53590.	No verified direct reference in this release
`At5g11100`	May be involved in membrane trafficking.	No verified direct reference in this release
`At2g20990`	Plays an important role in maintaining plasma membrane integrity during freezing and osmotic stresses.	Arabidopsis synaptotagmin 1 is required for the maintenance of plasma membrane integrity and cell viability.2008 · DOI: 10.1105/tpc.108.063859 Calcium-dependent freezing tolerance in Arabidopsis involves membrane resealing via synaptotagmin SYT1.2008 · DOI: 10.1105/tpc.108.062679 Arabidopsis synaptotagmin SYTA regulates endocytosis and virus movement protein cell-to-cell transport.2010 · DOI: 10.1073/pnas.0909080107 Arabidopsis synaptotagmin SYT1, a type I signal-anchor protein, requires tandem C2 domains for delivery to the plasma membrane.2010 · DOI: 10.1074/jbc.m109.084046

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016680 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006612 protein targeting to membrane Biological Process

GO:0006869 lipid transport Biological Process

GO:0006897 endocytosis Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0009409 response to cold Biological Process

GO:0009612 response to mechanical stimulus Biological Process

GO:0009615 response to virus Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0046740 transport of virus in host, cell to cell Biological Process

GO:0061817 endoplasmic reticulum-plasma membrane tethering Biological Process

GO:0000325 plant-type vacuole Cellular Component

GO:0005768 endosome Cellular Component

KEGG gene cross-reference

ath:AT1G53590

ath:AT2G20990

ath:AT5G11100

mmu:272636

xtr:496831

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.

Cell membrane0.557

Rank 1 · LXL04_016680 · OH-1004

Cytoplasm0.158

Rank 2 · LXL04_016680 · OH-1004

Endoplasmic reticulum0.139

Rank 3 · LXL04_016680 · OH-1004

Nucleus0.123

Rank 4 · LXL04_016680 · OH-1004

Golgi apparatus0.090

Rank 5 · LXL04_016680 · 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.

PF25669.2SMP_MUG190-like73-146 aa

PF25669.2SMP_MUG190-like187-268 aa

PF00168.37C2289-386 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016680	`PF25669.2`	SMP_MUG190-like	73	146	1.5e-16	61.3
LXL04_016680	`PF25669.2`	SMP_MUG190-like	187	268	1.5e-16	61.3
LXL04_016680	`PF00168.37`	C2	289	386	5.3e-21	75.5

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
`Q93XX4`	Arabidopsis thaliana	C2 domain-containing protein At1g53590	58.476%	Swiss-Prot	strong database homology
`A0JJX5`	Arabidopsis thaliana	Synaptotagmin-4	25.836%	Swiss-Prot	weak database homology
`Q9SKR2`	Arabidopsis thaliana	Synaptotagmin-1	26.087%	Swiss-Prot	weak database homology

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