LXL04_002565 | RubberDandelionOmics

Gene overview

LXL04_002565

Reference: OH-1004 Chr: Chr01 Coordinates: 51730200-51734390 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4191 bp · LXL04_002565|LXL04_002565|OH1004|cDNA

ATGGGgaaacaagaagaagaagaggaggaggtGGAGGACGAGGAGGAAGACGATgacgatgatgatgaagatgatgacgAAGAAGACGATGACAAAAcaatcaaaatcagaaaatcAAAAGAACTGGGAATTTCCTGTATGTTGAATACAGAGGTCGGAGCGGTTCTGGCAGTTATCCGTCGCAGATCCGACCCAACCTCATATATTTACCAAGATGACGCCTTGGATTCCAATATACTAAGTTCGTTAAAATCACTAAG...

CDS

Download CDS FASTA

4191 bp · LXL04_002565|LXL04_002565|OH1004|CDS

ATGGGGAAACAAGAAGAAGAAGAGGAGGAGGTGGAGGACGAGGAGGAAGACGATGACGATGATGATGAAGATGATGACGAAGAAGACGATGACAAAACAATCAAAATCAGAAAATCAAAAGAACTGGGAATTTCCTGTATGTTGAATACAGAGGTCGGAGCGGTTCTGGCAGTTATCCGTCGCAGATCCGACCCAACCTCATATATTTACCAAGATGACGCCTTGGATTCCAATATACTAAGTTCGTTAAAATCACTAAG...

Protein

Download Protein FASTA

1396 aa · LXL04_002565|LXL04_002565|OH1004|PROTEIN

MGKQEEEEEEVEDEEEDDDDDDEDDDEEDDDKTIKIRKSKELGISCMLNTEVGAVLAVIRRRSDPTSYIYQDDALDSNILSSLKSLRSLIFNPRQSWRAIDPSIYLSPFLDVISSEDVPAAATTVALSSILKMLKLDIFDKKTPGAREAVSNVVMAVTGCRLEKTHPVTEAAVMMRILQVLAAVMRHPASVLLNDHAVCTIVNTCFQVVQQSASQGDILQRTARHTMHDLIQIIYSRLLEIEVGDWENSESDTEDATDET...

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_002565`
TK1151 ID	TkA01G440580
OH-1004 ID	LXL04_002565
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.800
Protein coverage (%)	TK1151 97.779 / OH-1004 97.779 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

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_002565

Location Chr01:51730200-51734390 (+)

Description Similar to GNL2: ARF guanine-nucleotide exchange factor GNL2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g19610`	Activates the ARF proteins by exchanging bound GDP for free GTP.	GNOM-LIKE 2, encoding an adenosine diphosphate-ribosylation factor-guanine nucleotide exchange factor protein homologous to GNOM and GNL1, is essential for pollen germination in Arabidopsis.2009 · DOI: 10.1111/j.1744-7909.2009.00858.x
`At1g13980`	Activates the ARF proteins by exchanging bound GDP for free GTP.	Cell wall alterations in the arabidopsis emb30 mutant.2000 · DOI: 10.1105/tpc.12.11.2047 EMB30 is essential for normal cell division, cell expansion, and cell adhesion in Arabidopsis and encodes a protein that has similarity to Sec7.1994 · DOI: 10.1016/0092-8674(94)90444-8
`At5g39500`	Activates the ARF proteins by exchanging bound GDP for free GTP.	Functional diversification of closely related ARF-GEFs in protein secretion and recycling.2007 · DOI: 10.1038/nature05967 An ARF-GEF acting at the Golgi and in selective endocytosis in polarized plant cells.2007 · DOI: 10.1038/nature06023 GNOM-LIKE1/ERMO1 and SEC24a/ERMO2 are required for maintenance of endoplasmic reticulum morphology in Arabidopsis thaliana.2009 · DOI: 10.1105/tpc.109.068270

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002565 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000911 cytokinesis by cell plate formation Biological Process

GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Biological Process

GO:0006897 endocytosis Biological Process

GO:0007005 mitochondrion organization Biological Process

GO:0007029 endoplasmic reticulum organization Biological Process

GO:0007030 Golgi organization Biological Process

GO:0007155 cell adhesion Biological Process

GO:0009793 embryo development ending in seed dormancy Biological Process

GO:0009826 unidimensional cell growth Biological Process

GO:0009846 pollen germination Biological Process

GO:0009880 embryonic pattern specification Biological Process

GO:0009942 longitudinal axis specification Biological Process

KEGG gene cross-reference

ath:AT1G13980

ath:AT5G19610

ath:AT5G39500

cel:CELE_C24H11.7

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.

Cytoplasm0.521

Rank 1 · LXL04_002565 · OH-1004

Golgi apparatus0.284

Rank 2 · LXL04_002565 · OH-1004

Cell membrane0.190

Rank 3 · LXL04_002565 · OH-1004

Nucleus0.149

Rank 4 · LXL04_002565 · OH-1004

Lysosome / Vacuole0.145

Rank 5 · LXL04_002565 · 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.

PF12783.14Sec7-like_HUS264-423 aa

PF01369.26Sec7513-698 aa

PF23325.2TPR_281207-1383 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002565	`PF12783.14`	Sec7-like_HUS	264	423	7.3e-35	120.9
LXL04_002565	`PF01369.26`	Sec7	513	698	3.8e-68	229.4
LXL04_002565	`PF23325.2`	TPR_28	1207	1383	2.7e-40	138.8

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
`F4K2K3`	Arabidopsis thaliana	ARF guanine-nucleotide exchange factor GNL2	61.994%	Swiss-Prot	strong database homology
`Q42510`	Arabidopsis thaliana	ARF guanine-nucleotide exchange factor GNOM	40.098%	Swiss-Prot	moderate database homology
`Q9FLY5`	Arabidopsis thaliana	ARF guanine-nucleotide exchange factor GNL1	37.101%	Swiss-Prot	moderate database homology

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