LXL04_009291 | RubberDandelionOmics

Gene overview

LXL04_009291

Reference: OH-1004 Chr: Chr02 Coordinates: 122092166-122096993 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2664 bp · LXL04_009291|LXL04_009291|OH1004|cDNA

ATGTGGGTTATCAAACCCTTATGCATCACGCCTGCCGTAAGATTCGAACTCGTGACCTCCCAAACGATCATTGCAACACAACTTTTAAAGAGTAAGAGCAATATAGGAAACATCGGGGACTTCAATGGCAGCCACGAAAAATCGCTACCTCTGTTTTCCCTCCTCCCTATTTCCCCGCATCTTTCATTCAAAGATGATCCCAAACccactctttctctctctacGTTGTCCTTTCCTGTTATTGTTCCTACATCCTTCCT...

CDS

Download CDS FASTA

2664 bp · LXL04_009291|LXL04_009291|OH1004|CDS

ATGTGGGTTATCAAACCCTTATGCATCACGCCTGCCGTAAGATTCGAACTCGTGACCTCCCAAACGATCATTGCAACACAACTTTTAAAGAGTAAGAGCAATATAGGAAACATCGGGGACTTCAATGGCAGCCACGAAAAATCGCTACCTCTGTTTTCCCTCCTCCCTATTTCCCCGCATCTTTCATTCAAAGATGATCCCAAACCCACTCTTTCTCTCTCTACGTTGTCCTTTCCTGTTATTGTTCCTACATCCTTCCT...

Protein

Download Protein FASTA

887 aa · LXL04_009291|LXL04_009291|OH1004|PROTEIN

MWVIKPLCITPAVRFELVTSQTIIATQLLKSKSNIGNIGDFNGSHEKSLPLFSLLPISPHLSFKDDPKPTLSLSTLSFPVIVPTSFLSVIDSERHDHKIQEAMMYFSKLDDSPMFRQQIQCLEEIAETLRERGSKFYKGCRKYTDGLNEANERDAAFASSLENFGGGPDPISVAVGGPDMIKFAVVLREVGTYKESLRTKVEHTLSDRLLRFTNIELQDIKEARKRFDKADAVYSQIRDKFLSLRKSTRTEIASAMEEEL...

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_009291`
TK1151 ID	TkA03G416110
OH-1004 ID	LXL04_009291
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.700
Protein coverage (%)	TK1151 99.747 / OH-1004 88.839 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

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_009291

Location Chr02:122092166-122096993 (+)

Description Similar to AGD3: ADP-ribosylation factor GTPase-activating protein AGD3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g13300`	GTPase-activating protein (GAP) for ADP ribosylation factor (ARF).	A series of novel mutants of Arabidopsis thaliana that are defective in the formation of continuous vascular network: calling the auxin signal flow canalization hypothesis into question.2000 · DOI: 10.1242/dev.127.15.3197 VAN3 ARF-GAP-mediated vesicle transport is involved in leaf vascular network formation.2005 · DOI: 10.1242/dev.01716
`At5g61980`	Probable GTPase-activating protein (By similarity).	A class I ADP-ribosylation factor GTPase-activating protein is critical for maintaining directional root hair growth in Arabidopsis.2008 · DOI: 10.1104/pp.108.119529
`At1g10870`	Probable GTPase-activating protein.	No verified direct reference in this release
`At1g60860`	Probable GTPase-activating protein.	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_009291 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006897 endocytosis Biological Process

GO:0007010 cytoskeleton organization Biological Process

GO:0009733 response to auxin Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010051 xylem and phloem pattern formation Biological Process

GO:0010087 phloem or xylem histogenesis Biological Process

GO:0030029 actin filament-based process Biological Process

GO:0032456 endocytic recycling Biological Process

GO:0048768 root hair cell tip growth Biological Process

GO:1990090 cellular response to nerve growth factor stimulus Biological Process

GO:0001726 ruffle Cellular Component

GO:0005634 nucleus Cellular Component

KEGG gene cross-reference

ath:AT1G10870

ath:AT1G60860

ath:AT5G13300

ath:AT5G61980

rno:619382

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.

Cytoplasm0.604

Rank 1 · LXL04_009291 · OH-1004

Cell membrane0.209

Rank 2 · LXL04_009291 · OH-1004

Nucleus0.186

Rank 3 · LXL04_009291 · OH-1004

Golgi apparatus0.164

Rank 4 · LXL04_009291 · OH-1004

Lysosome / Vacuole0.107

Rank 5 · LXL04_009291 · 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.

PF16746.11BAR_3109-338 aa

PF03114.24BAR123-319 aa

PF00169.36PH394-521 aa

PF01412.24ArfGap590-710 aa

PF12796.14Ank_2790-857 aa

PF13857.13Ank_5791-834 aa

PF00023.37Ank794-825 aa

PF13606.13Ank_3794-823 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009291	`PF16746.11`	BAR_3	109	338	6.1e-36	124.9
LXL04_009291	`PF03114.24`	BAR	123	319	2.6e-10	41.1
LXL04_009291	`PF00169.36`	PH	394	521	5.6e-14	53.3
LXL04_009291	`PF01412.24`	ArfGap	590	710	4.4e-35	121.0
LXL04_009291	`PF12796.14`	Ank_2	790	857	2.2e-13	51.3
LXL04_009291	`PF13857.13`	Ank_5	791	834	4.7e-16	59.4
LXL04_009291	`PF00023.37`	Ank	794	825	7.5e-15	54.9
LXL04_009291	`PF13606.13`	Ank_3	794	823	6e-11	42.2
LXL04_009291	`PF13637.13`	Ank_4	799	848	1.1e-09	39.0
LXL04_009291	`PF13857.13`	Ank_5	814	867	4.7e-16	59.4
LXL04_009291	`PF00023.37`	Ank	828	858	7.5e-15	54.9

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
`Q5W7F2`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD3	57.683%	Swiss-Prot	strong database homology
`Q9FIT8`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD1	54.077%	Swiss-Prot	strong database homology
`Q9SMX5`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD4	41.502%	Swiss-Prot	moderate database homology
`Q9C6C3`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD2	41.636%	Swiss-Prot	moderate database homology

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