# Lab #6

## List the 3 nearest genes upstream (towards the centromere) relative to TAZ
1. DNASE1L1
2. RPL10
3. AC245140.2

## Here relative to gene features is the H3K27Ac presence highest?
H3K27Ac is a enhancer mark for histone modification particularly the acetylation of the histone H3 protein that plays a role in epigenetic regulation. We can identify H3K27Ac often near regulatory elements, particularly at proximal and distal regions of transcription start sites of the mRNA of 7 cell lines described in the genome browser: GM1287, H1-hESC, HSMM, HUVEC, K562, NHEK, and NHLF.

## Note the double-lines in the MultiZ alignments of other vertebrate species. What do the double-lines mean? (google, or look in the help pages)
In the gap annotation of MultiZ alignments, double lines means aligning species has one or more unalignable bases in a specific region.

## Create a figure using the genome browser to highlight one potentially important feature around your Project 1 or Project 2 gene that may be relevant to its role in disease.
Figure 1. *Gallus gallus* IFIH1 gene mRNAs alignment using UCSC Genome Browser tool (http://genome.ucsc.edu). The alignment is highlited in light blue color. The dark blue mRNA represent the reference, other mRNAs are represented in black color. Mismatches are represented in red color.

I selected the *Gallus gallus* IFIH1 gene (NM_001193638.1) that codes for the chicken melanoma differentiation-associated 5 protein (MDA5) that is part of a receptor which plays a role in the recognition of double-stranded (ds) RNA, a molecule present in certain pathogens such as certain viruses. It is located in position chr7:21,055,966-21,076,023. I compared it with the seven *Gallus gallus* IFIH1 mRNA available in GenBank and detected some mismatches particularly in the exons 1,3,6, 12 and 16, but in general I observed that the IFIH1 gene is conserved (Figure 1) and one explanation on that might be that commercial chickens have a similar genetic background since the commercial lines are genetically selected according to certain productive parameters. Also, by zooming out I detected 2 neighbor genes, the upstream correspond to the *Gallus gallus* potassium voltage-gated channel subfamily H member 7 (KCNH7), in the position: chr7:20946474-21036251) and the downstream gene correspond to the *Gallus gallus* fibroblast activation protein alpha (FAP), in the position: chr7:21075537-21113889.

## Reference
UCSC Genome Browser: Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D. The human genome browser at UCSC. Genome Res. 2002 Jun;12(6):996-1006.