Rough draft.This research track is under review with Dr. Atit's lab. Content and sequence may still change.

Here's an example of what's due today

Is This Gene Important Across Species?

Genetics domain · Lesson 11 of 20 · Medical Interventions (MI), with PBS overlap

Today's goal: Use a multi-species alignment and the logic of conservation to argue which parts of the IRF6 protein are functionally essential, then flag a variant of unknown meaning as likely important or likely tolerated using conservation alone.

Learn first

What a finished product looks like

This is a model of the work you should turn in. Use it to check your own: match the structure and the level of detail, do not copy it. Your wording should be your own.

Two-variant conservation triage note

Completes: A pair of justified recommendations that rank two variants by sequence conservation alone.

Position A (DNA-binding domain, identical in all 17 species):

Recommendation: FLAG, investigate first.
Justification: A position that is identical across 17 species separated by hundreds of millions of years has been held still by purifying selection, which is evidence the region is essential. A change here is likely to matter.

Position B (floppy linker, differs in 9 of 17 species):

Recommendation: likely tolerated.
Justification: A position that drifts freely across many species sits in a region evolution does not protect, so a change there is more likely to be tolerated.

Note: this ranking uses conservation only; a database (ClinVar) check would be the next step before any clinical claim.

Learn first

How this was built, step by step

The finished product above did not appear all at once. Here is the path from the question to the turned-in work, so you can follow the same steps.

1Start from today's question: If we line up the IRF6 from many animals, which parts stay the same, and what does staying the same tell us about importance?
2Work the Model and the Explore questions to reason it out before writing anything.
3Pull the specific evidence the product needs from the reading and any database you used.
4Write it up in the required format: You are handed results for two positions where a variant of unknown meaning was found. Position A is identical in all 17 species and sits in the ; Position B differs in 9 of 17 species and sits in the floppy linker. Write a one-line recommendation for each ("flag, investigate first" or "likely tolerated") and justify each using conservation, not guesswork.
5Check it against the rubric, then submit.

How this is graded (rubric)

For: You are handed BLAST results for two positions where a variant of unknown meaning was found. Position A is identical in all 17 species and sits in the DNA-binding domain; Position B differs in 9 of 17 species and sits in the floppy linker. Write a one-line recommendation for each ("flag, investigate first" or "likely tolerated") and justify each using conservation, not guesswork.

Criterion	Proficient	Developing	Beginning
Complete	Every required part of the artifact is present and filled in.	Most parts are present, but one is missing or left blank.	Several parts are missing.
Accurate	The science and data are correct and match the evidence.	Mostly correct, with a small factual slip.	Key science or data is wrong.
Scientific reasoning (CER)	States a claim, backs it with specific evidence, and explains the reasoning.	Has a claim and evidence, but the reasoning is thin or missing.	Gives an answer with no evidence or reasoning.
Professional communication	Clear, organized, and labeled the way a clinician or scientist would write it.	Readable but disorganized or missing labels.	Hard to follow.
Submitted	Turned in the right way (Schoology for routine work) and confirmed.	Turned in, but in the wrong place or unconfirmed.	Not turned in.

How the model answer scores against this rubric

CompleteProficient: Nothing is left blank: the model fills every part of "You are handed BLAST results for two positions where a variant of unknown meaning was found. Position A is identical in all 17 species and sits in the DNA-binding domain; Position B differs in 9 of 17 species and sits in the floppy linker. Write a one-line recommendation for each ("flag, investigate first" or "likely tolerated") and justify each using conservation, not guesswork.".
AccurateProficient: Every number and claim matches the case evidence.
Scientific reasoning (CER)Proficient: It names a claim, cites the specific evidence, and explains the reasoning, not just the answer.
Professional communicationProficient: It is organized and labeled like a real chart note.
SubmittedProficient: It would be turned in on Schoology and confirmed.

Check yourself

WebXam problem for today's skill

One exam-style question that uses exactly what you practiced today. Try it before you reveal the answer, then read why each choice is right or wrong.

WebXam-style domain: Bio-Molecular TechnologySelf-check skill: Using cross-species conservation as evidence of functional importance

An IRF6 variant of unknown meaning is found at an amino acid that is identical in all 17 species aligned and sits in the DNA-binding domain. A second variant sits in the floppy linker, which differs across 9 of the 17 species. Using conservation alone, which variant should the lab flag to investigate first, and why?

Tap an answer to see the full explanation. Nothing is recorded or graded.

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