The dataset studying the DDX53 protein is minimal and limited, largely because the gene model initially associated with DDX53 has been withdrawn and reclassified as a pseudogene, meaning it is not currently recognized as producing a functional protein in humans.
Short answer: The available dataset for the DDX53 protein is largely withdrawn and discontinued, with no current validated protein sequence or functional data, as the original gene model was retracted by NCBI and the gene is considered a pseudogene.
Genomic and Annotation Status of DDX53
According to NCBI’s gene database, the locus formerly identified as LOC100506640, which was thought to encode the DDX53 protein, is now discontinued. The record was withdrawn in August 2011 because subsequent genome annotations no longer predicted a valid gene model at this location on chromosome 9 (NC_000009.11: 35183011..35183530). This means that the sequence initially thought to represent DDX53 does not correspond to a functional gene in the latest human genome builds. As a result, the RefSeq status for this gene is marked as “WITHDRAWN” and the gene type is designated as a pseudogene. This status indicates that DDX53 is not currently recognized as encoding a functional protein product in humans.
Because the gene model is withdrawn, no reliable transcript or protein sequences are available in the primary NCBI databases. While there are downloadable datasets for gene sequences, transcripts, and proteins, these are historical or hypothetical and not validated in current annotations. The withdrawal signifies that any prior functional or experimental claims based on this gene should be approached with caution.
Lack of Protein and Functional Data in Protein Databases
UniProt, a comprehensive protein sequence and annotation database, does not provide any concrete data or entries for DDX53. The site’s fallback message and absence of an active entry suggest that there is no current protein sequence or functional characterization available for this protein. This aligns with the NCBI’s discontinuation of the gene model. Without a validated protein sequence, there is no curated information on DDX53’s structure, function, or interactions.
Similarly, the European Bioinformatics Institute’s InterPro database, which classifies protein families and domains, does not list DDX53 or provide domain architecture information. This lack of classification further implies that DDX53 is not recognized as a functional protein with known conserved domains or motifs.
Expression and Tissue Distribution Data
Since DDX53 is not currently annotated as a protein-coding gene, resources like The Human Protein Atlas do not provide expression or localization data for it. Instead, the Protein Atlas focuses on other genes and proteins with validated evidence. For example, it offers detailed expression profiles for KLHL17 and other genes, but DDX53 is not among them, reflecting the absence of protein-level or RNA-level expression data in normal or pathological human tissues.
Implications for Research and Data Use
The withdrawal of the DDX53 gene model means that researchers should be cautious when interpreting past studies that referenced DDX53 as a functional protein. The current consensus is that the sequence does not encode a protein in humans, and any biological roles or disease associations attributed to DDX53 require re-evaluation or independent validation.
This situation also highlights the dynamic nature of genome annotation, where advances in sequencing, transcriptomics, and bioinformatics can lead to reclassification of genes. It underscores the importance of using up-to-date databases like NCBI’s Gene, UniProt, and InterPro to verify gene and protein status before drawing conclusions.
Takeaway
Despite initial annotation efforts, DDX53 is currently classified as a pseudogene with no validated protein product or functional data. This limits available datasets to withdrawn or hypothetical sequences without experimental confirmation. Researchers interested in DEAD-box helicases or related proteins should seek alternative, well-characterized family members. The case of DDX53 exemplifies how genome annotation updates can affect the availability and reliability of biological datasets, emphasizing the need for continual database cross-checking in molecular biology research.
Likely supporting sources include NCBI Gene database (ncbi.nlm.nih.gov), UniProt (uniprot.org), The Human Protein Atlas (proteinatlas.org), and InterPro (ebi.ac.uk).
