InBase, The Old Intein Database and Registry

hosted by Hideo Iwai lab

- This is the InBase from NEB as it was in 2010 and no update since 2010. All links to NEB are not functional.

InBase is a curated database devoted to inteins.

When referencing InBase, please use the following InBase Reference: Perler, F. B. (2002). InBase, the Intein Database. Nucleic Acids Res. 30, 383-384.

Newer data InBase 2.0 beta

What is Protein Splicing?

Protein splicing is defined as the excision of an intervening protein sequence (the INTEIN) from a protein precursor and the concomitant ligation of the flanking protein fragments (the EXTEINS) to form a mature extein host protein and the free intein (Perler 1994). Protein splicing results in a native peptide bond between the ligated exteins (Cooper 1993). Extein ligation differentiates protein splicing from other forms of autoproteolysis. Conserved intein motifs differentiate inteins from other types of in-frame sequences present in one homolog and absent in another homolog or from other types of protein rearrangements.

Please Note: The term 'Protein Splicing' has been associated with inteins since 1994 (Perler 1994). Recent papers have described protein rearrangements that are not intein-mediated. The mechanism of these rearrangements is currently unknown, but preliminary evidence suggests that they are mediated by various cellular enzymes. For clarity, we suggest calling these non-intein mediated events either protein rearrangements or Protein Editing.

For more information, click on the following subjects:
  1. The Intein Registry:
    A. Inteins Listed in Order of Phylogenetic Domain of Life, Genus and Species
    B. Inteins Alleles = Inteins Grouped by Extein Insertion Site
    C. Selected Intein Properties
    Please note: Finding DOD homing endonuclease motifs is not sufficient evidence that the gene contains an intein since DOD homing endonucleases are also present in introns and as free standing genes.
  2. On-line Submission of Intein Data
    Don't forget to submit intein sequences!!
    This section contains an explanation of each field within an intein record.
  3. How to Identify an Intein:
    A. Conserved Intein Features - Do you Have an Intein?
    B. To download a fasta format file containing amino acid sequences of all inteins in this InBase (2010), here
    (Please acknowledge New England Labs for the use of this file and cite "Perler, FB (2002). Nucleic Acids Res. 30, 383-384.")
  4. Intein Motifs
    A. Splicing Motifs (Blocks A, B, F, G)
    B. DOD Homing Endonuclease Motifs
  5. The Mechanism of Protein Splicing
    A. The Standard Intein-mediated Splicing Pathway
    B. Animation of The Protein Splicing Pathway.
    C. An Alternative Protein Splicing Pathway for Inteins Lacking an N-terminal Nucleophile
    D. Similarity to the Hedgehog Protein Family Autoprocessing Domains
    E. Intein Structure
    F. Selected Mechanism References
  6. An Introduction to Protein Splicing
    A. Protein Splicing Basics
    B. Teacher's Packet - download intein slides -(This section is still under construction).
  7. The Intein Bibliography
  8. Intein Links

The Intein Registry Curator adds new information to intein records as submitted and attempts to fill in all fields if not provided by the contributor. The 'Initially Contributed by' field only indicates the person who made the initial submission or the name of the scientist associated with the intein if the submission is made by the curator. The 'Independently Found by' field indicates that another person has independently identified and submitted information about an intein prior to publication or release in the database. Updates are acknowledged in the 'Reference' and 'Comments' fields. Researchers should be aware that once an intein sequence is available in a public database, it may be identified and submitted by anyone searching databases for inteins. We therefore urge the initial discoverer to submit his or her entry as soon as possible to avoid seeing their intein submitted by another party. Entries may be submitted confidentially.


- Homing Endonucleases and Inteins

- Chemical Ligation: Tools for Biomolecule Synthesis and Modification

- Split Inteins: Methods and Protocols