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SEP V016 draft

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jakebeal
jakebeal committed Apr 13, 2019
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# SEP V016: Introns and Polypeptide Regions

| SEP | |
| --- | --- |
| **Authors** | Jacob Beal (jakebeal@ieee.org), Marta Vázquez Vilar (marvazvi@ibmcp.upv.es) |
| **Editor** | |
| **Type** | Specification |
| **SBOL Visual Version** | 2.2 |
| **Status** | Draft |
| **Created** | 13-Apr-2019 |
| **Last modified** | |
| **Issue** | TBD |


## Abstract

This SEP proposes new glyphs for introns and polypeptide-regions.

## 1. Rationale <a name="rationale"></a>

Coding sequences are often annotated to note specific regions, tags, or introns. This proposes to adopt new glyphs to supposed such annotation derived from the ones used by the UPV Golden Braid repository.

These glyphs are designed to compose with CDS glyphs, as shown in the examples below.


## 2. Specification <a name="specification"></a>

### Intron

#### Associated SO term(s)
SO:0000188 (intron)

#### Recommended Glyph and Alternates
The intron glyph is a box whose left and right has a number of angles making "torn out" edges, suggesting removal from an enclosing coding sequence:

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/2b4e91f1/Glyphs/intron/intron-specification.png)

#### Prototypical Example

Intron including a gRNA non-coding RNA sequence (blue), embedded in an mKate red fluorescent protein coding sequence:

![example](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/2b4e91f1/Glyphs/intron/intron-example.png)

### Polypeptide Region

#### Associated SO term(s)
SO:0000839 (polypeptide region)

#### Recommended Glyph and Alternates
The polypeptide region glyph is a chevron suggesting a fragment of a coding sequence:

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/2b4e91f1/Glyphs/polypeptide-region/polypeptide-region-specification.png)

For polypeptide regions at the extreme 5' end of a coding sequence, the RECOMMENDED alternative is instead a truncated chevron that can be put flush with the left side of a CDS glyph:

![glyph specification](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/2b4e91f1/Glyphs/polypeptide-region/five-prime-polypeptide-region-specification.png)

#### Prototypical Example

degradation tag on a protein coding sequence
nuclear localization tag on a protein coding sequence

This glyph is intended to be used in composition or superposition with the glyph for the coding sequence of which the polypeptide regions are fragments: Example of a coding sequence with three an N-tag (blue), C-tag (yellow), and internal region (red):

![example of usage](https://raw.githubusercontent.com/SynBioDex/SBOL-visual/2b4e91f1/Glyphs/polypeptide-region/polypeptide-region-example.png)


## 3. Examples <a name='example'></a>

See above.

## 4. Backwards Compatibility <a name='compatibility'></a>

SBOL Visual does not currently have a specific symbol for these elements, so there are no backwards compatibility issues.

## 5. Discussion <a name='discussion'></a>



## Copyright <a name='copyright'></a>

<p xmlns:dct="http://purl.org/dc/terms/" xmlns:vcard="http://www.w3.org/2001/vcard-rdf/3.0#">
<a rel="license"
href="http://creativecommons.org/publicdomain/zero/1.0/">
<img src="http://i.creativecommons.org/p/zero/1.0/88x31.png" style="border-style: none;" alt="CC0" />
</a>
<br />
To the extent possible under law,
<a rel="dct:publisher"
href="sbolstandard.org">
<span property="dct:title">SBOL developers</span></a>
has waived all copyright and related or neighboring rights to
<span property="dct:title">SEP V016</span>.
This work is published from:
<span property="vcard:Country" datatype="dct:ISO3166"
content="US" about="sbolstandard.org">
United States</span>.
</p>

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