The proliferation associated nuclear element 1 (PANE1) is a novel gene that is involved in immune response besides its primary role in centromere assembly. Different PANE1 transcripts show a distinct expression patterns in resting and activated CD19+ cells. In this study, we cloned and characterized the cDNA sequence of porcine PANE1, which shares high sequence identity with their mammalian counterparts. Chromosome localization by INRA IMpRH panel assigned this gene to SSC 5p14-p15, and it was closely linked to porcine ACO2 and CYP25 genes (61cR, LOD score 4.91). The reverse transcriptase-polymerase chain reaction revealed that porcine PANE1 gene was differently expressed in seven diverse tissues, showed highest expression level in lymph node, but lowest in kidney. A single nucleotide polymorphism (SNP) (C>A) which can be digested by restriction enzyme BssHII was identified in intron 1 of porcine PANE1, allele frequencies determination in different pig breeds and association analysis were performed on this SNP BssHII by PCR-restriction fragment length polymorphism assay. Allele frequencies varied greatly among different pig breeds, and the association results indicated that piglet individuals with the AA genotype had significantly higher levels of lymphocyte percentage (LYMPH%) (17 days) (P = 0.0218), mean corpuscular volume (32 days) (P = 0.0314) and absolute value of lymphocyte (LYMPH#) (32 days) (P = 0.0356), but lower (P < 0.0001) birth weight than those with other two genotypes.