I have found some strange thing in this dataset. Namely, I have exons that correspond to one gene_id, but there is no gene with such gene_id in a dataset.

mm9 = TxDb.Mmusculus.UCSC.mm9.knownGene

exon dataset has a gene with ID 100038977

exon = exons(mm9)
gene_id_exons = select(mm9, keys=as.character(exon$exon_id), columns = c("GENEID"), keytype = "EXONID")
> gene_id_exons[which(gene_id_exons$GENEID == "100038977"),][1:4,]
       EXONID    GENEID
243122 241618 100038977
243123 241619 100038977
243124 241620 100038977
243125 241621 100038977

gene dataset does not have a gene with such ID

gene<-genes(mm9)
> which(gene$gene_id == "100038977")
integer(0)

Why are there exons that belong to the 100038977 gene (Gm1993) but there is no such gene listed in the gene dataset?

The same happens with gene_ids 100039550 (Gm10486),100039890 (Gm15093),100039939 (Gm2506), 100040048 (Ccl27b), 100040631 etc

> select(TxDb.Mmusculus.UCSC.mm9.knownGene, "100038977", c("GENEID","EXONID"), "GENEID")
      GENEID EXONID
1  100038977 241626
2  100038977 241625
3  100038977 241624
4  100038977 241623
5  100038977 241622
6  100038977 241621
7  100038977 241620
8  100038977 241619
9  100038977 241618
10 100038977 245890
11 100038977 245891
12 100038977 245892
13 100038977 245893
14 100038977 245894
15 100038977 245895
16 100038977 245896
17 100038977 245897
18 100038977 245898

> gns <- genes(TxDb.Mmusculus.UCSC.mm9.knownGene)

> gns["100038977",]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
  subscript contains invalid names

> gns <- genes(TxDb.Mmusculus.UCSC.mm9.knownGene, single.strand.genes.only = FALSE)
> gns["100038977",]
GRangesList object of length 1:
$100038977
GRanges object with 2 ranges and 0 metadata columns:
         seqnames               ranges strand
            <Rle>            <IRanges>  <Rle>
  [1]        chrX [24975422, 24997578]      -
  [2] chrX_random [ 1375833,  1397989]      +