LXL04_025876 | RubberDandelionOmics

Gene overview

LXL04_025876

Reference: OH-1004 Chr: Chr05 Coordinates: 118022850-118027596 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1767 bp · LXL04_025876|LXL04_025876|OH1004|cDNA

ATGGAGGCTATTAAAAAACAAGCAAGCAAACTCAGGGAACAAGTAGCCAAACAGCAGCAGGCTGTATTAAGTCGACTGGGTAAAGATGCTGAAATATACGACGCAGAGGAACTTAATTGCCACCAAAAACTTCAAGACCTCTATAAGTCTACAACGGCAACCAAGCATTTTCAAAAGGAAATTGTTCGTGGTGTTGAAGGTTTTATTTCAATAAGCagaaaacaaaaacaaatagCAAAAAGATTAGCTGAAGATTGTCA...

CDS

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1767 bp · LXL04_025876|LXL04_025876|OH1004|CDS

ATGGAGGCTATTAAAAAACAAGCAAGCAAACTCAGGGAACAAGTAGCCAAACAGCAGCAGGCTGTATTAAGTCGACTGGGTAAAGATGCTGAAATATACGACGCAGAGGAACTTAATTGCCACCAAAAACTTCAAGACCTCTATAAGTCTACAACGGCAACCAAGCATTTTCAAAAGGAAATTGTTCGTGGTGTTGAAGGTTTTATTTCAATAAGCAGAAAACAAAAACAAATAGCAAAAAGATTAGCTGAAGATTGTCA...

Protein

Download Protein FASTA

588 aa · LXL04_025876|LXL04_025876|OH1004|PROTEIN

MEAIKKQASKLREQVAKQQQAVLSRLGKDAEIYDAEELNCHQKLQDLYKSTTATKHFQKEIVRGVEGFISISRKQKQIAKRLAEDCHKFGTDNTTARFPLAKVALELGGSQISIEEKSDNMLEIFHNQVCEPLRGSIRGAPLEDARHLARSCEKLRQEVETQAVEVLRRQTKYRDPTTESVLKLKNMEKKLSEVRASMVTLEKEAISAMLSVEEHQQQITLQKLVMMVDAERDYHRHVVGILEELHAEMILALHMQESTK...

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_025876`
TK1151 ID	TkA06G033260
OH-1004 ID	LXL04_025876
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	99.700
Protein coverage (%)	TK1151 91.270 / OH-1004 58.673 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

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Basic Information and Functional Annotation

Gene ID LXL04_025876

Location Chr05:118022850-118027596 (+)

Description Similar to SH3P2: SH3 domain-containing protein 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g34660`	May regulate autophagosome formation or maturation.	A BAR-domain protein SH3P2, which binds to phosphatidylinositol 3-phosphate and ATG8, regulates autophagosome formation in Arabidopsis.2013 · DOI: 10.1105/tpc.113.118307 SH3 Domain-Containing Protein 2 Plays a Crucial Role at the Step of Membrane Tubulation during Cell Plate Formation.2017 · DOI: 10.1105/tpc.17.00108
`At4g18060`	May be involved in the recruitment of DRP2A to the accessory protein complex and in the negative regulation of its GTPase activity.	No verified direct reference in this release
`At1g31440`	Lipid binding protein bound strongly to phosphatidic acid, phosphatidylinositol-4-phosphate and phosphatidylinositol-4,5- bisphosphate.	Role of SH3 domain-containing proteins in clathrin-mediated vesicle trafficking in Arabidopsis.2001 · DOI: 10.1105/tpc.010279
`At2g38250`	Probable transcription factor that may play a role in the induction of CAM4 in response to pathogen and salt.	Pathogen- and NaCl-induced expression of the SCaM-4 promoter is mediated in part by a GT-1 box that interacts with a GT-1-like transcription factor.2004 · DOI: 10.1104/pp.104.041442
`At5g01380`	Probable transcription factor that binds specifically to the core DNA sequence 5'-GTTAC-3'.	Analysis of GT-3a identifies a distinct subgroup of trihelix DNA-binding transcription factors in Arabidopsis.2004 · DOI: 10.1016/s0014-5793(04)00222-4

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_025876 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009920 cell plate formation involved in plant-type cell wall biogenesis Biological Process

GO:0072583 clathrin-dependent endocytosis Biological Process

GO:1903527 positive regulation of membrane tubulation Biological Process

GO:0000421 autophagosome membrane Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005768 endosome Cellular Component

GO:0005770 late endosome Cellular Component

GO:0005776 autophagosome Cellular Component

KEGG gene cross-reference

ath:AT1G31440

ath:AT2G38250

ath:AT4G18060

ath:AT4G34660

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.

Cytoplasm0.583

Rank 1 · LXL04_025876 · OH-1004

Nucleus0.353

Rank 2 · LXL04_025876 · OH-1004

Cell membrane0.150

Rank 3 · LXL04_025876 · OH-1004

Golgi apparatus0.047

Rank 4 · LXL04_025876 · OH-1004

Lysosome / Vacuole0.040

Rank 5 · LXL04_025876 · 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.

PF07653.24SH3_2288-338 aa

PF00018.35SH3_1289-334 aa

PF14604.13SH3_9290-338 aa

PF13837.13Myb_DNA-bind_4352-435 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_025876	`PF07653.24`	SH3_2	288	338	2.3e-06	27.9
LXL04_025876	`PF00018.35`	SH3_1	289	334	4e-10	39.8
LXL04_025876	`PF14604.13`	SH3_9	290	338	7.9e-12	45.6
LXL04_025876	`PF13837.13`	Myb_DNA-bind_4	352	435	1.3e-19	71.1

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
`Q8VWF1`	Arabidopsis thaliana	SH3 domain-containing protein 2	44.658%	Swiss-Prot	moderate database homology
`Q8L7W0`	Arabidopsis thaliana	SH3 domain-containing protein 3	38.592%	Swiss-Prot	moderate database homology
`Q9C865`	Arabidopsis thaliana	SH3 domain-containing protein 1	50.725%	Swiss-Prot	weak database homology
`O80450`	Arabidopsis thaliana	Trihelix transcription factor GT-3b	35.023%	Swiss-Prot	weak database homology
`Q9SDW0`	Arabidopsis thaliana	Trihelix transcription factor GT-3a	32.889%	Swiss-Prot	weak database homology

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