Login

Join for Free!
114427 members
table of contents table of contents

The authors established a cartilaginous fish cell line [Squalus acanthias embryo cell …


Biology Articles » Zoology » Ichthyology » RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates » Table 3

Table 3
- RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

Analysis of 3′ UTR regions highly conserved in eight vertebrate genes


Gene Footprint regions (see Fig. 1) Conserved footprint length, nt Percent nucleotide identity Number of species exhibiting the footprint Percent A+T
Azin1 Region 1 29 96 10 75
  Region 2 56 97 8 76
Ctbp1 Region 1 80 89 6 75
Fbxw7 Region 1 20 100 3 55
  Region 2 48 90 6 56
  Region 3 86 91 6 75
Ppp4r2 Region 1 55 93 8 72
  Region 2 203 88 11 69
Pten Region 1 57 90 4 58
  Region 2 37 97 5 50
  Region 3 79 79 7 57
  Region 4 58 91 7 71
Set Region 1 90 93 10 70
Sox4 Region 1 27 94 5 54
  Region 2 49 81 6 55
  Region 3 32 88 6 62
Znf503 Region 1 27 95 6 65
  Region 2 78 93 5 74
  Region 3 74 96 5 73
  • Average nucleotide identity within footprints was 92%. Average A+T composition was 66%. All footprints include S. acanthias and Homo sapiens. Species for ppp4r2 and set are listed in Fig. 2 and SI Fig. 4. Azin Region 1 species are that of ppar4r2 with the exceptions of Tetraodon nigroviridis and Macaca mulatta. Azin Region 2 is as Region 1 but without Xenopus and Danio. Ctbp1 footprints were identified in mouse, chicken, frog, and zebrafish, in addition to human and shark. In fbxw7, the additional species to shark and human were Bos taurus (all Regions) and Mus musculus, D. rerio, and T. nigroviridis in Regions 2 and 3. Neither mouse nor zebrafish footprints were found in fbwx7 Region 1 (see Table 2). Footprints were identified in the regions of sox4 for chicken, mouse, zebrafish, and fugu, with the exception of chicken in Region 1. Footprint regions for znf503 included mouse, rat, and chicken with the addition of zebrafish in Regions 2 and 3. Pten footprints for Regions 3 and 4 were identified in Pleioblastus pygmaeus, M. musculus, B. taurus, Gallus gallus, and D. rerio, as well as shark and human. pten Region 2 included P. pygmaeus and B. taurus. pten Region 1 included D. rerio. Zebrafiish footprints were not found in pten Region 2 (see Table 2). Species not included in any particular region did not contain detectable footprints for that region. Additional supporting detail is given in Table 2.


rating: 1.00 from 1 votes | updated on: 8 Jul 2008 | views: 4879 |

Rate article:







excellent!bad…