LXL04_025678 | RubberDandelionOmics

Gene overview

LXL04_025678

Reference: OH-1004 Chr: Chr05 Coordinates: 115170756-115175569 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2448 bp · LXL04_025678|LXL04_025678|OH1004|cDNA

ATGACCTTCAAGCGATCTGAACCTATAGTTGAAGAACGCAAATCATTCCATTGTCTGGCCTTCCCAGATTTAGCTAAGTATCTTCCTCCTACCCAAACAGAACAGGACGACCCTATGACTGCCTTCATCAAGCTCGATGATTCTCCCATGTTCCAAAAGCAGGTGCGTTACCTTGAACAGACAACAGATGAGCTCAAACTCCGTTGTCAAAAGCTACACAAAGGGAGCAAAAAGTACATGGATGGTCTTGGGGAAGCATG...

CDS

Download CDS FASTA

2448 bp · LXL04_025678|LXL04_025678|OH1004|CDS

ATGACCTTCAAGCGATCTGAACCTATAGTTGAAGAACGCAAATCATTCCATTGTCTGGCCTTCCCAGATTTAGCTAAGTATCTTCCTCCTACCCAAACAGAACAGGACGACCCTATGACTGCCTTCATCAAGCTCGATGATTCTCCCATGTTCCAAAAGCAGGTGCGTTACCTTGAACAGACAACAGATGAGCTCAAACTCCGTTGTCAAAAGCTACACAAAGGGAGCAAAAAGTACATGGATGGTCTTGGGGAAGCATG...

Protein

Download Protein FASTA

815 aa · LXL04_025678|LXL04_025678|OH1004|PROTEIN

MTFKRSEPIVEERKSFHCLAFPDLAKYLPPTQTEQDDPMTAFIKLDDSPMFQKQVRYLEQTTDELKLRCQKLHKGSKKYMDGLGEACNMDLIFADSVEAFGGGQDDPVSVSIGGPIMTKFVSAFREIETFKELLRSQVEHLLVDRLAQFLSEDLQDTKDSRKRLDKASHAYDQALEKVASLKKSTRDEVVVELEEDLQNSKSAFERSRFNLVNSLMNIEAKKKYTFLESLSAIMDAHLRYFKLGYELLSQMEPFIHQVLT...

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_025678`
TK1151 ID	TkA06G045730
OH-1004 ID	LXL04_025678
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	97.800
Protein coverage (%)	TK1151 97.414 / OH-1004 27.730 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_025678

Location Chr05:115170756-115175569 (+)

Description Similar to AGD2: ADP-ribosylation factor GTPase-activating protein AGD2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g60860`	Probable GTPase-activating protein.	No verified direct reference in this release
`At1g10870`	Probable GTPase-activating protein.	No verified direct reference in this release
`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

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025678 · 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.

Cytoplasm0.628

Rank 1 · LXL04_025678 · OH-1004

Cell membrane0.232

Rank 2 · LXL04_025678 · OH-1004

Nucleus0.168

Rank 3 · LXL04_025678 · OH-1004

Golgi apparatus0.149

Rank 4 · LXL04_025678 · OH-1004

Lysosome / Vacuole0.102

Rank 5 · LXL04_025678 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF16746.11BAR_345-272 aa

PF03114.24BAR58-253 aa

PF00169.36PH332-463 aa

PF01412.24ArfGap517-644 aa

PF12796.14Ank_2717-784 aa

PF13857.13Ank_5717-762 aa

PF00023.37Ank722-753 aa

PF13637.13Ank_4727-776 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025678	`PF16746.11`	BAR_3	45	272	1.1e-35	124.1
LXL04_025678	`PF03114.24`	BAR	58	253	1.9e-15	57.9
LXL04_025678	`PF00169.36`	PH	332	463	5.9e-12	46.7
LXL04_025678	`PF01412.24`	ArfGap	517	644	4.2e-33	114.6
LXL04_025678	`PF12796.14`	Ank_2	717	784	1.5e-11	45.4
LXL04_025678	`PF13857.13`	Ank_5	717	762	6.6e-08	33.5
LXL04_025678	`PF00023.37`	Ank	722	753	3.7e-13	49.6
LXL04_025678	`PF13637.13`	Ank_4	727	776	1.4e-07	32.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9C6C3`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD2	59.108%	Swiss-Prot	strong database homology
`Q9SMX5`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD4	58.734%	Swiss-Prot	strong database homology
`Q5W7F2`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD3	47.579%	Swiss-Prot	moderate database homology
`Q9FIT8`	Arabidopsis thaliana	ADP-ribosylation factor GTPase-activating protein AGD1	43.587%	Swiss-Prot	moderate database homology

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