|In this study the cis and trans regulatory effect of long non-coding genes (lncRNA) on the expression of genes in fish infected by Viral hemorrhagic septicemia virus (VHS) was investigated using RNA-seq technology. At the end of experimental period (the thirty fifth day), total RNA was extracted from spleen tissue (group treated with virus) and physiological serum (control group) was used to prepare the library for RNA-seq. After library preparation, sequencing was carried out by Illumina High Seq 2500 platform. The results of RNA-seq analysis showed that 63 lncRNA genes had differential expression that were associated with 92 cis coding genes in the range of 20k up and downstream sites of the target genes. Among the pairs of coding and non-coding genes, those with both more than 90% and less than 90% expression correlations were considered as positive and negative co-expression genes, respectively. The coding genes such as Interlukin10, BHLHE41, RBP47, gastrotropin, synaptopodin, OX2, and SMC2 were associated with cis and trans with 8 and 13 lncRNA genes, respectively. Interlukin10, gastrotropin, synaptopodin, OX2, and SMC2 genes had higher expression in the virus-treated group. The two genes RBP47 and BHLHE41 were more expressed in the control group. Gene ontology analysis showed the activity of cytokine genes, including interleukin 10 gene, which plays an important role in inflammatory responses in the immune system.