LXL04_010825 | RubberDandelionOmics

Gene overview

LXL04_010825

Reference: OH-1004 Chr: Chr02 Coordinates: 154096549-154099188 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1923 bp · LXL04_010825|LXL04_010825|OH1004|cDNA

ATGGACCGCCAGGGCCATGATTATGCAGCTGCCGCCATGGCATTTGCCCAGCAACAACAAGCCGCCAATATCCAGCAACAACAACAGCCACCACCAggtccaccaccaccaccaccaccatacGGTTTCCACCCACAACATCAGCAATTCCTACCTCCTTTCATACCACCACATCCTTCAATCCCACAATTCCCCCGCCACCCCCtcatgcaacaacaacaaccaccacAAATCCACCCTCACCCCCAATCCCATCCCCA...

CDS

Download CDS FASTA

1923 bp · LXL04_010825|LXL04_010825|OH1004|CDS

ATGGACCGCCAGGGCCATGATTATGCAGCTGCCGCCATGGCATTTGCCCAGCAACAACAAGCCGCCAATATCCAGCAACAACAACAGCCACCACCAGGTCCACCACCACCACCACCACCATACGGTTTCCACCCACAACATCAGCAATTCCTACCTCCTTTCATACCACCACATCCTTCAATCCCACAATTCCCCCGCCACCCCCTCATGCAACAACAACAACCACCACAAATCCACCCTCACCCCCAATCCCATCCCCA...

Protein

Download Protein FASTA

640 aa · LXL04_010825|LXL04_010825|OH1004|PROTEIN

MDRQGHDYAAAAMAFAQQQQAANIQQQQQPPPGPPPPPPPYGFHPQHQQFLPPFIPPHPSIPQFPRHPLMQQQQPPQIHPHPQSHPHLLHLPQQQPPNFPPHIPPHVNPSPFHGPYDAPPPPAPPPSDPEQQKTIDKLVEYAVKNGPEFEAMIREKQKDNPSYSFLFGGEGNSYYRYKLWLASRPPGSMFTPSFPPSSVNLMQMNQSPLNPPHLVPGVQMHQQQHVYPPFYEQQHHQPFVGHGRPEFDQSNRAFKGLSGP...

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_010825`
TK1151 ID	TkA03G550820
OH-1004 ID	LXL04_010825
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.100
Protein coverage (%)	TK1151 100.000 / OH-1004 99.844 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_010825

Location Chr02:154096549-154099188 (+)

Description Similar to CHERP: Calcium homeostasis endoplasmic reticulum protein

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g31200`	As a member of the SWAP1-SFPS-RRC1 splicing factor complex, modulates photomorphogenesis by regulating the gene expression and pre-messenger RNA (mRNA) alternative splicing of a large number of genes, including those involved in plant responses to light signaling.	SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis .2022 · DOI: 10.1073/pnas.2214565119

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_010825 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006396 RNA processing Biological Process

GO:0006397 mRNA processing Biological Process

GO:0006874 intracellular calcium ion homeostasis Biological Process

GO:0008285 negative regulation of cell population proliferation Biological Process

GO:0008380 RNA splicing Biological Process

GO:0010017 red or far-red light signaling pathway Biological Process

GO:0010099 regulation of photomorphogenesis Biological Process

GO:0010114 response to red light Biological Process

GO:0043484 regulation of RNA splicing Biological Process

GO:0051209 release of sequestered calcium ion into cytosol Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT4G31200

hsa:10523

mmu:27967

mmu:67958

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Nucleus0.780

Rank 1 · LXL04_010825 · OH-1004

Cytoplasm0.409

Rank 2 · LXL04_010825 · OH-1004

Cell membrane0.024

Rank 3 · LXL04_010825 · OH-1004

Endoplasmic reticulum0.024

Rank 4 · LXL04_010825 · OH-1004

Mitochondrion0.018

Rank 5 · LXL04_010825 · 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.

PF01805.27Surp126-181 aa

PF04818.20CID268-392 aa

PF25123.1SWAP1_C474-639 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_010825	`PF01805.27`	Surp	126	181	4.3e-16	59.0
LXL04_010825	`PF04818.20`	CID	268	392	1.7e-22	80.6
LXL04_010825	`PF25123.1`	SWAP1_C	474	639	2.3e-90	301.7

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
`O49570`	Arabidopsis thaliana	SUPPRESSOR-OF-WHITE-APRICOT/SURP RNA-binding domain containing protein 1	63.364%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card