I was exploring a microarray dataset from GEO (here is a link to the exact dataset: https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS4136 ) and I was looking at genes that had the largest difference in expression between disease and control individuals. One of the genes that has a significant difference has the identifier "LOC102724870". When I searched NCBI for this gene there was only one result for a withdrawn record ( https://www.ncbi.nlm.nih.gov/gene/102724870 ).
The NCBI record states "This record has been withdrawn by NCBI because the model on which it was based was not predicted in a later annotation." Can someone please explain what this means? Is the listed location in the genome no longer relevant? Is it in fact not a gene at all?
It appears that this particular gene was annotated by the NCBI automated pipeline back in 2014 (Human Annotation Release 106) but was removed due to lack of sufficient evidence during the subsequent annotation run in 2015 (Human Annotation Release 107). You can see the model transcript XR_427749.1 that was annotated for this gene at that time. Note, doing a BLAST search against the human genome using the sequence of this transcript (XR_427749.1) returns pretty good hits to the mitochondrial genome and chromosome 1.
Is the listed location in the genome no longer relevant? Is it in fact not a gene at all?
What it means is that, currently, there is no evidence to warrant annotation of a gene at this location. If, on the other hand, you have clear experimental evidence to support expression from this locus, you can contact RefSeq with said evidence and request annotation.
