Transcripts of uncertain coding potential (TUCP) are part of long noncoding RNAs, which include short open reading frames and could be translated into small peptides. In recent years, a growing number of TUCPs has been implicated in multiple biological activities, such as embryogenesis and transcriptional regulation. However, the abundance of TUCPs and their roles in goat endometrium during pregnancy recognition (day 16) remain undocumented. In this study, bioinformatics analyses were conducted to identify the differentially expressed (DE) TUCPs between pregnant animals and corresponding nonpregnant controls. A total of 5551 TUCPs were identified; 114 TUCPs were DE in goat endometrium, of which 74 TUCPs were upregulated in pregnant endometrium, whereas 40 TUCPs were downregulated. The related genes of TUCP were predicted by using coexpression and colocalization methods. In summary, 419 genes were predicted by colocalization, and 9464 genes were predicted by coexpression. The kyoto encyclopedia of genes and genomes (KEGG) and gene ontology (GO) analysis showed that TUCPs, which are highly expressed in pregnant endometrium, were mainly associated with endometrial remodeling, nutrient synthesis, and transportation. However, TUCPs that were lowly expressed in pregnant endometrium were mainly associated with immune tolerance, which is necessary for the protection and development of the embryo in the uterus. These findings may be used for the comparative analysis of TUCP transcripts in endometrium and assist in the selection of applicable candidate genes associated with embryo implantation for further functional analyses.
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