Long noncoding RNAs (lncRNAs) compose a plentiful category of transcripts that gaining a rising importance because of their roles in different biological processes. Although, the action of most lncRNAs stays unclear. LncRNAs are implicated in gene regulation by various epigenetic mechanisms, and growing biological evidence refers to lncRNA roles for muscle development and differentiation. Our aim is to identify the effect of novel lncRNAs (Alternatively spliced) and their target genes on two stages of sheep skeletal muscle growth and development. We used FastQC to examine the Quality control and Trimmomatic software for trimming low-quality reads for twelve samples of the longissimus dorsal muscle tissue involving six young and six adults from Texel sheep had done. Hisat2, Cufflink, Cuffmerge, and Cuffdiff had used for investigating the expression levels. Novel lncRNAs (Alternative spliced) were distinguished using Cuffcompare software and NONCODE databases. We identified the interaction between lncRNAs–mRNAs using RIsearch software. The visualization of lncRNAs – mRNAs regulatory network constructed using Cytoscape software. We revealed 139 novel lncRNA (Alternative spliced) transcripts. Among them, only 65 novel lncRNAs interacted with their target genes may regulate sheep skeletal muscle growth and development. Three novel lncRNA transcripts such as TCONS_00041386, TCONS_00050059, and TCONS_00056428, showed a strong association with mRNAs, and five transcripts such as TCONS_00055761, TCONS_00055762, TCONS_00055763, TCONS_00055764, and TCONS_00055770 had made complex network correlations with mRNAs. Our research provides more knowledge of the mechanisms of association with novel lncRNAs, which play a vital role in the regulation of sheep skeletal muscle tissue development and growth.

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