LXL04_014678 | RubberDandelionOmics

Gene overview

LXL04_014678

Reference: OH-1004 Chr: Chr03 Coordinates: 54738642-54743038 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1587 bp · LXL04_014678|LXL04_014678|OH1004|cDNA

ATGACATTGGCAGCTGGGATCGGGTATGTGCTGCTAGCACTTGGACCTTCTCTCACCCTCTTCGTTTCCGTCATCTCCCCTAAACCCTTCTTGATCCTCACCCTTCTCTCCAGTACACTGGTGTGGCTGATTAGTTTGATTGTGCTTTCTGGAATTTGGAGGGTGTTCCTTCCATTTAAAACAACAGCATGGTGGCCTTATGCAATTCTTATATTGACTTCCATTGCTTTCCAAGAAGGCCTTCGCCTTGTATTGTGGAA...

CDS

Download CDS FASTA

1587 bp · LXL04_014678|LXL04_014678|OH1004|CDS

ATGACATTGGCAGCTGGGATCGGGTATGTGCTGCTAGCACTTGGACCTTCTCTCACCCTCTTCGTTTCCGTCATCTCCCCTAAACCCTTCTTGATCCTCACCCTTCTCTCCAGTACACTGGTGTGGCTGATTAGTTTGATTGTGCTTTCTGGAATTTGGAGGGTGTTCCTTCCATTTAAAACAACAGCATGGTGGCCTTATGCAATTCTTATATTGACTTCCATTGCTTTCCAAGAAGGCCTTCGCCTTGTATTGTGGAA...

Protein

Download Protein FASTA

528 aa · LXL04_014678|LXL04_014678|OH1004|PROTEIN

MTLAAGIGYVLLALGPSLTLFVSVISPKPFLILTLLSSTLVWLISLIVLSGIWRVFLPFKTTAWWPYAILILTSIAFQEGLRLVLWKGYKKLEDMLDAFADRVAKPRLYLTDKMQIALAGGLGHGLAHAVFFCLSLLTPSFGPATVYVDKCSYAPFFLISAIISLAFVTIHTFSMVIAFNGYAEGNKTDQLIVPIFHLIAGTLTLVNLVSGGCIVGIPLLYVVAFSTLAYCGKMFHIRFTVLLAFFGQLILKTGLNGSLG...

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_014678`
TK1151 ID	TkA02G405160
OH-1004 ID	LXL04_014678
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	59.300
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 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_014678

Location Chr03:54738642-54743038 (-)

Description Similar to At2g31440: Gamma-secretase subunit APH1-like

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g31440`	Probable subunit of the gamma-secretase complex, an endoprotease complex that catalyzes the intramembrane cleavage of integral proteins such as Notch receptors.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os03g0733400`	Transposase-like protein that is essential for plant growth and development.	No verified direct reference in this release
`Os05g0239150`	Transposase-like protein that is essential for plant growth and development.	No verified direct reference in this release
`Os01g0518400`	Transposase-like protein that is essential for plant growth and development.	No verified direct reference in this release
`Os05g0583200`	Transposase-like protein that is essential for plant growth and development.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_014678 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006351 DNA-templated transcription Biological Process

GO:0007219 Notch signaling pathway Biological Process

GO:0009791 post-embryonic development Biological Process

GO:0016485 protein processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0070765 gamma-secretase complex Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0030674 protein-macromolecule adaptor activity Molecular Function

GO:0046983 protein dimerization activity Molecular Function

KEGG gene cross-reference

ath:AT2G31440

dosa:Os01g0518400

dosa:Os03g0733400

dosa:Os05g0239150

dosa:Os05g0583200

osa:4339741

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.

Endoplasmic reticulum0.590

Rank 1 · LXL04_014678 · OH-1004

Lysosome / Vacuole0.117

Rank 2 · LXL04_014678 · OH-1004

Cytoplasm0.116

Rank 3 · LXL04_014678 · OH-1004

Golgi apparatus0.100

Rank 4 · LXL04_014678 · OH-1004

Nucleus0.094

Rank 5 · LXL04_014678 · 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.

PF06105.18Aph-15-236 aa

PF27039.1ZBED1_RNase-like_helical299-358 aa

PF14372.13hAT-like_RNase-H402-451 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_014678	`PF06105.18`	Aph-1	5	236	3e-69	233.5
LXL04_014678	`PF27039.1`	ZBED1_RNase-like_helical	299	358	5.5e-15	56.1
LXL04_014678	`PF14372.13`	hAT-like_RNase-H	402	451	1e-09	39.2

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
`Q8L9G7`	Arabidopsis thaliana	Gamma-secretase subunit APH1-like	73.950%	Swiss-Prot	weak database homology
`Q6AVI0`	Oryza sativa subsp. japonica	Zinc finger BED domain-containing protein RICESLEEPER 2	28.063%	Swiss-Prot	weak database homology
`B9FJG3`	Oryza sativa subsp. japonica	Zinc finger BED domain-containing protein RICESLEEPER 1	27.962%	Swiss-Prot	weak database homology
`Q0JMB2`	Oryza sativa subsp. japonica	Zinc finger BED domain-containing protein RICESLEEPER 4	25.869%	Swiss-Prot	weak database homology
`Q75HY5`	Oryza sativa subsp. japonica	Zinc finger BED domain-containing protein RICESLEEPER 3	25.106%	Swiss-Prot	weak database homology

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