The skeletal muscle alpha-actin gene of channel catfish (Ictalurus punctatus) and its association with piscine specific SINE elements

Gene. 2000 Jul 11;252(1-2):173-81. doi: 10.1016/s0378-1119(00)00198-0.


The alpha-actin gene of channel catfish (Ictalurus punctatus) was cloned and sequenced. The gene has a similar organization and exhibited a high level of sequence similarity to those from other vertebrate animals. The upstream region of the alpha-actin gene included a TATA box, a CAAT box, three E-boxes, and a CArG box. Nested deletion segments containing these transcriptional motifs were fused to the reporter gene chloramphenicol acetyl transferase (CAT). Transfection of the clones into C2C12 cells indicated that all these motifs are required for transcriptional activities. The channel catfish alpha-actin gene is associated with two distinct short interspersed repetitive elements (SINEs). The first SINE element showed high levels of sequence similarity to the zebrafish Mermaid element, while the second SINE element is not similar to the Mermaid element except for an 8bp sequence CCCCGTGC suggesting their evolutionary linkage. However, the second SINE element appeared to co-exist with the Mermaid element in most cases and therefore was designated as the Merman element. Approximately 9000 copies and 1200 copies of the Mermaid and Merman elements exist per haploid channel catfish genome, respectively. BLAST searches indicated that both the Mermaid and the Merman elements were frequently associated with gene sequences, mostly those of aquatic animals, suggesting their evolutionary origin in association with aquatic organisms and their function in shaping the evolution of genomes in aquatic animals.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Actins / genetics*
  • Amino Acid Sequence
  • Animals
  • Base Sequence
  • Cell Line
  • Chloramphenicol O-Acetyltransferase / genetics
  • Chloramphenicol O-Acetyltransferase / metabolism
  • DNA / chemistry
  • DNA / genetics
  • DNA / isolation & purification
  • Exons
  • Genes / genetics
  • Ictaluridae / genetics*
  • Introns
  • Molecular Sequence Data
  • Muscle, Skeletal / chemistry
  • Promoter Regions, Genetic / genetics
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Sequence Analysis, DNA
  • Sequence Deletion
  • Sequence Homology, Nucleic Acid
  • Short Interspersed Nucleotide Elements / genetics*


  • Actins
  • Recombinant Fusion Proteins
  • DNA
  • Chloramphenicol O-Acetyltransferase

Associated data

  • GENBANK/AF228714