Clue 1: Orient yourself
What are the main parts, stages, or choices in this model?
Use the labels and the picture's left-to-right, near-to-far, or before-and-after order. Name only what you can point to.
The question
Why compare the same working part across people, mice, and fish before trusting an animal study?
Why it matters: Sequence similarity helps researchers decide whether another species can model a human gene before time, animals, and money are committed to an experiment. A strong match supports a shared job, but does not prove identical biology.
On your WebXam
You can compare sequences across species and use the match as evidence for a shared job.
For life
To find the cause, change one thing and watch what changes.
Principle: Same look, different cause
Try the everyday version first
Same look, different cause
Editors compare the same passage across several book editions. Words that stay unchanged across every edition probably carry an important part of the message.
Do not jump to the biology yet. Treat the picture as a small system. Track its parts, follow one change at a time, and keep more than one explanation open until the picture supplies a way to separate them.
Clue 2: Trace one change
What changes while the other parts stay the same?
Follow one object, stage, or path. Point to the first place where the situation changes instead of jumping to the ending.
Clue 3: Keep the cause open
What check would separate two explanations that still fit the picture?
List more than one explanation that still fits. Name the extra observation that would help you separate those possibilities.
Now inspect the illustration
Work from the visible evidence. A useful answer names the part of the picture that supports it and leaves unknown causes open.
- 1What are the main parts, stages, or choices in this model?
- 2What changes while the other parts stay the same?
- 3What check would separate two explanations that still fit the picture?
Tier 1 check
Finish with the everyday model
Explain what a close match across several editions can support and one thing it cannot prove.
Answer in plain words. You can finish this required check without opening either optional section below.
Ready for the real names? Optional tier 2
Craniofacial Research Track
Session 11Reading the Evidence, DecemberLens: Genetics of Disease
BLAST: is IRF6 conserved across species?
Discovery question
Why compare the same working part across people, mice, and fish before trusting an animal study?
Same look, different cause. A shared pattern can support a shared job, but it cannot prove that every species or every case works the same way.
Before this page, you should know
- Every human gene has a public record in NCBI Gene with a stable Gene ID (IRF6 is Gene ID 3664).
- A gene record lists the official symbol, the full name, aliases (other names), and the location.
If not, review
Today's new idea is only
Same look, different cause. A shared pattern can support a shared job, but it cannot prove that every species or every case works the same way.
Goal: Compare one working part across three species and make a careful claim that goes no farther than the amount that matches.
Know by the end
- lines up two sequences position by position and reports , how much of the sequence matches.
- A is the same gene or in another species, descended from a shared ancestor.
- High conservation across distant species is evidence that a does an essential job.
- Because IRF6 is conserved, what the Atit lab learns in zebrafish and mouse can inform human research.
1
Set up the comparison
Model start: I am BLASTing the human IRF6 against other species to see how much of the sequence stays the same.
- Write the human IRF6 accession you are searching with (NP_006138).
- Predict before you run it: will mouse or zebrafish be more similar to human, and why?
2
Read the evidence
Model start: The mouse IRF6 matches the human protein at a high , well above what random sequences would share.
- Find the mouse (Mus musculus) IRF6 hit and write its .
- Find the zebrafish (Danio rerio) IRF6 hit and write its .
- Which is more conserved, and does that match your prediction?
3
Make the claim
- Write a claim: IRF6 is (highly / weakly) conserved across species.
- Back it with evidence: cite the mouse and zebrafish numbers you found.
- Explain why this makes zebrafish and mouse useful model organisms for research.
blast
- Open at https://blast.ncbi.nlm.nih.gov/Blast.cgi and click the blue BLAST (blastp) box.
- In the Enter Query Sequence box, type the human IRF6 accession NP_006138 (you can find this accession in the NCBI Gene 3664 record under the RefSeq protein products, or in UniProt O14896).
- Leave the database set to Non-redundant sequences (nr). Optional: under Organism, you can run it once limited to Mus musculus (taxid:10090) and again limited to Danio rerio (taxid:7955) to isolate each species.
- Click the blue button at the bottom and wait for the results page (it may take up to a minute).
- On the Descriptions tab, find the row whose Scientific Name is Mus musculus and read its Per. Ident () value. Write it down.
- Find the row whose Scientific Name is Danio rerio and read its Per. Ident value. Write it down.
- Note the Query Cover for each so you know how much of the aligned, then compare the two numbers.
Turn in: A short conservation claim with evidence: a one-sentence claim that IRF6 is highly conserved, the mouse and zebrafish numbers as evidence, and one sentence on why this makes them useful model organisms for the Atit lab's work.
BLAST
Open the tool Compares your sequence against everything known, to find matches and measure how similar they are.
When you use this: Use this when you want to know whether another species has the same gene or , so you can tell if a model animal (like the mouse) is a fair stand-in for Mateo's IRF6.
What the screen looks like
Step by step
- 1Open .ncbi.nlm.nih.gov and choose BLAST (blastp).
- 2Paste your IRF6 sequence into the query box and click .
- 3When the results load, look at the very first row (the best match) and read its and E-value.
Capture these fields
- Query (what you searched): Human IRF6 protein (O14896)
- Subject (the best match it returned): Mouse Irf6 protein
- Percent identity (how alike): about 92% identical
- E-value (could this be by chance?): 0.0 (essentially impossible by chance)
- Interpretation: Human and mouse IRF6 are nearly the same protein, so the mouse is a good model for it.
How to read it: High plus a very small E-value means a real match, not a coincidence. The smaller the E-value (closer to 0), the more confident the hit. Strong conservation across species is a clue the gene does an essential job.
Lost? BLAST quick-start guide UniProt
Open the tool The reference record for a : its length, its domains, and what each part does.
When you use this: Use this when you need to know which PART of the a variant hits, so you can predict whether it breaks a working region.
What the screen looks like
Step by step
- 1Open uniprot.org and search IRF6 human, then open entry O14896.
- 2Scroll to the Family and Domains section.
- 3Read the length and which domains exist (for example the ).
Capture these fields
- Accession (the protein's ID): O14896
- Length (amino acids): 467 aa
- Domains / regions: A DNA-binding domain and a protein-partner (SMIR) domain
How to read it: The domains tell you which part of the does which job. A variant that lands inside the is more likely to break IRF6's -factor function than one in a spacer region.
Lost? UniProt help: reading protein domains NCBI Gene
Open the tool The full reference record for a gene: its official symbol, ID, location, and what it does.
When you use this: Use this first, when you have a gene name and need its official ID and address. It is the home base every other database points back to.
What the screen looks like
Step by step
- 1Go to ncbi.nlm.nih.gov/gene and type the gene symbol IRF6 in the search box, then press Search.
- 2Open the top result whose organism is Homo sapiens (human).
- 3At the top of the record, read three things and write them down: the official symbol, the Gene ID number, and the location ( band).
Capture these fields
- Symbol (official gene name): IRF6
- Gene ID (the stable number): 3664
- Location (chromosome band): 1q32.2
- Summary (one line on its job): A transcription factor needed for the skin-surface cells that let the lip and palate fuse.
How to read it: The symbol and Gene ID let you find the exact same gene in every other database. The location should match the band you mapped (1q32). The summary tells you the gene's job in one sentence.
Lost? NCBI Gene help manual (how to use the Gene database)
Level 1, Guided
Use the sentence starters, a word bank from the vocabulary, a labeled diagram, and the exact source link.
Level 2, Collaborative
Complete a partly blank model or table and explain it.
Level 3, Independent
Make a claim from a new example or an unfamiliar entry in .
Team roles
- Manager: keeps the group moving
- Recorder: writes the shared model or table
- Evidence checker: verifies each claim against the source
- Reporter: explains the group's reasoning
Process reflection
- What evidence changed your thinking today?
- What did your group disagree about, and how did you resolve it?
- What question is still unresolved?
By the end of this session, submit ONE of: a labeled diagram with a 2-sentence explanation; a claim, evidence, reasoning paragraph; a completed data table from a real database; or a one-question exit ticket using today's vocabulary.
Recommended here: A short conservation claim with evidence: a one-sentence claim that IRF6 is highly conserved, the mouse and zebrafish percent identity numbers as evidence, and one sentence on why this makes them useful model organisms for the Atit lab's cleft work.
Meets standard if your explanation correctly connects structure, timing, gene or protein function, or evidence source to Mateo's case: Compare one working part across three species and make a careful claim that goes no farther than the amount that matches.
How this is graded (rubric)
For: A short conservation claim with evidence: a one-sentence claim that IRF6 is highly conserved, the mouse and zebrafish percent identity numbers as evidence, and one sentence on why this makes them useful model organisms for the Atit lab's cleft work.
| 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 through the route named under Submit here 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 "A short conservation claim with evidence: a one-sentence claim that IRF6 is highly conserved, the mouse and zebrafish percent identity numbers as evidence, and one sentence on why this makes them useful model organisms for the Atit lab's cleft work.".
- 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 attached to your class form or handed in, and confirmed.
Go deeper Optional tier 3
Everything required is above. Open this section only if you want the research reading and source trail.
Student reading
The idea in plain English
Why compare the same working part across people, mice, and fish before trusting an animal study?
Editors compare the same passage across several book editions. Words that stay unchanged across every edition probably carry an important part of the message.
Same look, different cause. A shared pattern can support a shared job, but it cannot prove that every species or every case works the same way.
- lines up two sequences position by position and reports , how much of the sequence matches.
- A is the same gene or in another species, descended from a shared ancestor.
- High conservation across distant species is evidence that a does an essential job.
- Because IRF6 is conserved, what the Atit lab learns in zebrafish and mouse can inform human research.
This lesson reading is written from the vetted sources in the advanced citation trail below.
Everything you need for today is on this page. These links are optional.
What to read
Read the short plain-language explanation written for this lesson. Plain-language reading for this session
Why this source matters
This explanation gives you the background for today's idea without making you decode a research paper: Same look, different cause. A shared pattern can support a shared job, but it cannot prove that every species or every case works the same way.
Words to unlock first
Reading moves
- Skim the title and abstract first to get the gist.
- Circle the one sentence that states the main claim.
- Box the evidence the authors give for that claim.
- Mark one sentence that confuses you, and move on.
Stop point
Stop after the final 'Use it now' section. The research citations are available separately for advanced readers.
Your output
Write one claim-evidence sentence: state the main idea, then name the example or evidence that supports it.
These records and papers document the science. They are not assigned student reading. Use the plain-language lesson reading above unless your teacher asks you to inspect an original source.