About Secondary Structure File Names:

Filenames for the structure diagrams have the following syntax:

  • [version].[molecule].[phylogenetic domain OR organelle].[organism].[intron class].[exon].[intron position (rRNA) OR number (other)].[file type]

Intron-specific fields are shown in green and only appear in intron file names.

File name examples:

  1. b.233.m.P.anserina.ps is version "b" 23S rRNA (3' half) mitochondrial structure from Podospora anserina, in PostScript format.
  2. a.I1.e.T.usneae.C1.SSU.1512.bpseq is a version "a" Group IC1 intron structure from position 1512 of the nuclear 16S rRNA of Trebouxia usneae, in formatted text.
  3. a.I1.y.C.paradoxa.C3.tLEU.pdf is a version "a" Group IC3 intron structure from the Cyanophora paradoxa cyanelle leucine tRNA gene, in PDF format.
  4. a.I1.m.S.cerevisiae.B1.OX1.i4.ps is a version "a" Group IB1 intron structure from the Saccharomyces cerevisiae cytochrome oxidase subunit 1 gene in PostScript format; the intron described is the fourth intron in this cytochrome oxidase subunit 1 gene.

Code Lists:

Version Codes:

Diagram Version:

  1. Older diagram version; needs to be updated.
  2. Newer diagram; mostly up to date.
  3. Internal version; not released.
  4. Most current version.

Molecule Codes:

Molecule:

  • 5: 5S rRNA.
  • 16: 16S rRNA.
  • 235: 23S rRNA, 5' half (23.5 in the RDBMS screen display).
  • 233: 23S rRNA, 3' half (23.3 in the RDBMS screen display).
  • I1: Group I intron.
  • I2: Group II intron.

Phylogenetic Domain OR Organelle Codes

Phylogenetic Domains:

  • (a) Archaea (nuclear)
  • (b) (eu)Bacteria (nuclear)
  • (e) Eucarya (nuclear)
  • (v) Viral

Organelles:

  • (c) Chloroplast
  • (y) Cyanelle
  • (m) Mitochondrion

Organism Names:

For most organisms named as Genus species, the organism name is shortened to G.species. When strain or subspecies information is used to distinguish two diagrams, the names appear as G.species.subspecies. When the species name is unknown, the name appears as Genus.sp.

Intron Class Codes:

When "Molecule" is "I1":

  • UNK = Group I intron, unknown subgroup

  • A1 = Group I intron, A1 subgroup
  • A2 = Group I intron, A2 subgroup
  • A3 = Group I intron, A3 subgroup

  • B1 = Group I intron, B1 subgroup
  • B2 = Group I intron, B2 subgroup
  • B3 = Group I intron, B3 subgroup
  • B4 = Group I intron, B4 subgroup

  • C1 = Group I intron, C1 subgroup
  • C2 = Group I intron, C2 subgroup
  • C3 = Group I intron, C3 subgroup

  • D = Group I intron, D subgroup

  • E = Group I intron, E subgroup

When "Molecule" is "I2":

  • UNK = Group II intron, unknown subgroup
  • A = Group II intron, A subgroup
  • B = Group II intron, B subgroup

Exon Codes (for genes which contain introns):

rRNA Exons:

  • SSU = 16S rRNA.
  • LSU = 23S rRNA.

tRNA Exons:

  • Older Structure Diagrams:
    • tARG = arginine tRNA.
    • tILE = isoleucine tRNA.
    • tLEU = leucine tRNA.
    • tMET = methionine tRNA.
  • Newer Structure Diagrams:
    • trnA = tRNA-Alanine
    • trnG = tRNA-Glycine
    • trnI = tRNA-Isoleucine
    • trnK = tRNA-Lysine
    • trnL = tRNA-Leucine
    • trnS = tRNA-Serine
    • trnV = tRNA-Valine

Protein Exons:

  • A6 = ATPase 6.
  • ATP6 = ATPase 6.
  • CYTB = cytochrome b.
  • DP = DNA Polymerase.
  • ND1 = NADH dehydrogenase subunit 1.
  • ND2 = NADH dehydrogenase subunit 2.
  • ND3 = NADH dehydrogenase subunit 3.
  • ND4 = NADH dehydrogenase subunit 4.
  • ND4L = NADH dehydrogenase subunit 4L.
  • ND5 = NADH dehydrogenase subunit 5.
  • NRDB = ribonucleoside diphosphate reductase B.
  • NRDD = ribonucleoside triphosphate reductase D.
  • OX1 = cytochrome oxidase subunit 1.
  • OX2 = cytochrome oxidase subunit 2.
  • pB = petB (apocytochrome b6).
  • pD = petD.
  • PSBA = chloroplast psbA, photosystem II 32 kD protein.
  • PSBC = chlorophyll a binding protein.
  • S10 = ribosomal protein S10.
  • TD = thymidylate synthetase.

Unknown Exons:

  • TBD = unknown exon.

File Type Codes:

  • ps = PostScript
  • pdf = Adobe Acrobat Portable Document Format
  • bpseq = formatted text information file