Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal diseases, and the median survival time is very short. Upregulation of hedgehog signaling pathway activity is a vital factor in pathogenesis of PDAC. However, as a negative regulator of hedgehog signaling, it is not very clear what role the suppressor of fused (SUFU) plays in PDAC tissue. In our study for the identification of alternative splicing transcripts of SUFU gene in human PDAC cells, a novel transcript variant of SUFU (SUFUvN) was discovered by 3' rapid amplification of cDNA ends (3'RACE) and cDNA clone. SUFUvN contained an additional new protein-coding exon compared with the transcript variant 1 of SUFU (SUFUv1, NM_016169) published in NCBI website. The sequence of the new protein-coding exon was the same as a fragment of intron between exon 10 and 11 of SUFUv1. Thus, an exon skipping occurred in transcription of SUFUv1. Compared with the expression vector of SUFUvN transfected PDAC cells, the corresponding protein expression encoded by SUFUvN (SUFU isoform N) was detected in PDAC tissue. Furthermore, it was observed that elevated SUFUvN transcription level was related with lymph node metastasis in PDAC tissues, while neither SUFUv1 nor transcript variant 2 of SUFU (SUFUv2, NM_001178133) did. Our data indicate that there exists a novel transcript variant of SUFU which can be transcribed and translated into corresponding protein and its transcription is related with metastasis of lymph nodes in PDAC.