biology

Uncharacterized LOC644249 gene

Uncharacterized LOC644249 gene is a biology topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Uncharacterized LOC644249 gene rather than just read about it. In short: Uncharacterized LOC644249 gene., also known as RP11-195B21.3, is about 1058 base pairs long and is found in Homo sapiens on chromosome 9q12. More specifically, the sequence is located on Chromosome: 9; NC_000009.11(67977457..67987991 bp).

Key takeaways

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Reference excerpt

Uncharacterized LOC644249 gene., also known as RP11-195B21.3, is about 1058 base pairs long and is found in Homo sapiens on chromosome 9q12. More specifically, the sequence is located on Chromosome: 9; NC_000009.11(67977457..67987991 bp). This gene’s protein product is the “coiled-coil domain-containing protein 29” which is 291 amino acids long and may contain a conserved domain in the superfamily, pfam 12001. In particular, this conserved domain contains the domain of unknown function DUF3496 which is about 110 amino acids long, functionally uncharacterized, and found in eukaryotes. Other possible motifs for the protein product exist but the DUF3496 remains the most likely. This protein may play a role as a transmembrane protein.

Gene

Genomic Location For humans, this gene is located on chromosome 9q12 (67977457..67987991) bp.

Promoter The promoter is predicted to be about 601 bp in length and is about 100 bp upstream from the transcription start site of the primary transcript .

Transcript

This gene is predicted to have 4 exons, with a very small 3'UTR which is capped with a poly A tail very shortly after the 4th exon.

Protein The protein product is the coiled-coil domain-containing protein 29, abbreviated CCDC29, is about 291 amino acids in length and contains the DUF3496 motif. Also, this protein is also predicted to have a possible transmembrane site at about 284 - 291 aa.

Isoelectric Point:6.043 Molecular Weight 33.6 kdal

Charge Distribution Analysis 1 0000000000 0--0-000-0 +0-00+0-00 0++0+0+0-- 000-+-0000 +00000+-00 61 0000-0000+ +00000-+0- --++00+--0 000+000-00 +0-00+00-0 +0-0--+000 121 00-+0--000 0-0000-+00 -000+-0000 00++-000+- 0-0+00-0+0 00–000-0- 181 -0+-000000 +000000++0 0+00++0000 00+000-+-0 0+00000000 ++-0-0000- 241 00000000++ 0000000+00 0000000000 +000000000 0000000000 0

Motif The DUF3496 motif is about 110 aa long and is conserved within eukaryotes. As the name implies, it is currently unknown in function but can be found across different species. On CCDC 29, its relative location is about 153 - 259 aa.

Expression

This GEO profile of LOC644249 was included in a gene expression profile which was conducted in a study that analyzed adipose tissues of subjects at risk of metabolic syndrome. This GEO profile may suggest that LOC644249 is ubiquitously expressed in adipose tissue but no direct correlation of the effects of the expression levels of LOC644249 with adipose tissue can be made.

Transcript Variant Only two transcript variants were predicted to might occur. One transcript variant predicted the loss of exon 4. The loss of exon 4 would lead to the loss of roughly half of the DUF3496 and the entire loss of the transmembrane domain. The other transcript variant predicted the loss of exon 2, which would not lead to the loss of DUF3496 and leaves the reading frame relatively intact.

Homology Orthologs of CCDC29 seem to be only limited to primates as shown by the table below. A paralog of CCDC29 which is not only limited to primates, Ankyrin repeat domain-containing protein 26, showed that this paralog is reserved within vertebrate animals only. The most distant ortholog of Ankyrin repeat domain-containing protein 26 was found to be the gallus gallus species.

Protein Post-Modification

N glycosylation

One possible N-glycosylation site was predicted, but a signal peptide was not detected. Thus, it is possible that CCDC29 does not undergo this particular modification even though it has the possible site.

Phosphorylation

A total of 13 likely phosphorylation sites were predicted: Ser: 5 Thr: 6 Tyr: 2 The main concentration of the phosphorylation sites seem to be localized within the DUF3496 motif and the 3' end of the protein.

Protein structure The CCDC29, as the name implies, is thought to have the coiled coil motif. Protein structure prediction software confirms this motif 97.6% confidence.

Transmembrane

CCDC29 is predicted to have one transmembrane helix located at the N terminal 270.

Function Currently unknown as of 5/9/2013.

References

Illustrations

The GEO profile of LOC644249 on adipose tissue.

Worked examples

Example 1 — a first encounter with Uncharacterized LOC644249 gene

Start with the simplest possible case. Write down what Uncharacterized LOC644249 gene claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Uncharacterized LOC644249 gene before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Uncharacterized LOC644249 gene ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Uncharacterized LOC644249 gene

In research: Uncharacterized LOC644249 gene appears in biology research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Uncharacterized LOC644249 gene in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Uncharacterized LOC644249 gene is common in secondary-school and first-year university syllabi. It links to neighbouring topics Human proteins, Uncharacterized proteins, so understanding it makes those chapters shorter.
In everyday life: Look for Uncharacterized LOC644249 gene outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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Frequently asked questions

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Why does Uncharacterized LOC644249 gene matter?

Because it connects several biology ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

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Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

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