Calcium-response element gene transcriptions

# Human genes
Gene ID: 106736470 is LOC106736470 PTH negative calcium response element (nCARE) region on chromosome 11: "This region contains two negative calcium response elements (nCAREs) that regulate expression of the downstream PTH (parathyroid hormone) gene. nCARE motifs are present upstream of multiple calcium-regulated genes and are comprised of a palindromic motif that derives from Alu retroelement sequence. This sequence is bound by a protein complex containing AP endonuclease (Ape1) and Ku antigen (X-ray repair complementing defective repair in Chinese hamster cells). Increased calcium results in acetylation of Ape1 by p300 and recruitment of histone deacetylases to this complex, leading to repression of gene expression."
Gene ID: 627 is BDNF brain derived neurotrophic factor on 11p14.1: "This gene encodes a member of the nerve growth factor family of proteins. Alternative splicing results in multiple transcript variants, at least one of which encodes a preproprotein that is proteolytically processed to generate the mature protein. Binding of this protein to its cognate receptor promotes neuronal survival in the adult brain. Expression of this gene is reduced in Alzheimer's, Parkinson's, and Huntington's disease patients. This gene may play a role in the regulation of the stress response and in the biology of mood disorders."

# Consensus sequences
The calcium-response element (CaRE1) has the consensus sequence: 5'-CTATTTCGAG-3'

# Promoter occurrences
"The Bdnf gene contains nine alternative promoters, each of which is activity inducible in neurons and most of which are regulated by multiple activitydependent transcription factors (West et al. 2014). Bdnf exon IVcontaining transcripts (Bdnf IV) are the most highly expressed and activity regulated of the Bdnf splice variants in developing neurons, and the transcription factors that regulate Bdnf promoter IV have been well described. We first identified calcium response factor (CaRF) as a transcription factor based on its ability to bind the LVGCCresponsive calciumresponse element 1 (CaRE1) in Bdnf promoter IV (Tao et al. 2002). Basal expression of Bdnf IV is reduced in the cortex of adult CaRF knockout mice, consistent with CaRF functioning as an activator of Bdnf promoter IV (McDowell et al. 2010). However, LVGCCinduced transcription of Bdnf IV is unaffected by the loss of CaRF and instead the transcription factor MEF2C mediates the actions of CaRE1 in response to this stimulus (Lyons et al. 2012)."

# Hypotheses
- A1BG has no Calcium-response elements in either promoter.
- A1BG is not transcribed by a Calcium-response element.
- A calcium-response element does not participate in the transcription of A1BG.

# Samplings
Copying a responsive elements consensus sequence 5'-CTATTTCGAG-3' and putting the sequence in "F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence 5'-CTATTTCGAG-3' (starting with SuccessablesCalR.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for 5'-CTATTTCGAG-3', 0.
- negative strand, positive direction, looking for 5'-CTATTTCGAG-3', 0.
- positive strand, negative direction, looking for 5'-CTATTTCGAG-3', 0.
- positive strand, positive direction, looking for 5'-CTATTTCGAG-3', 0.
- complement, negative strand, negative direction, looking for 5'-GATAAAGCTC-3', 0.
- complement, negative strand, positive direction, looking for 5'-GATAAAGCTC-3', 0.
- complement, positive strand, negative direction, looking for 5'-GATAAAGCTC-3', 0.
- complement, positive strand, positive direction, looking for 5'-GATAAAGCTC-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-CTCGAAATAG-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-CTCGAAATAG-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-CTCGAAATAG-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-CTCGAAATAG-3', 0.
- inverse negative strand, negative direction, looking for 5'-GAGCTTTATC-3', 0.
- inverse negative strand, positive direction, looking for 5'-GAGCTTTATC-3', 0.
- inverse positive strand, negative direction, looking for 5'-GAGCTTTATC-3', 0.
- inverse positive strand, positive direction, looking for 5'-GAGCTTTATC-3', 0.

## CalR core promoters

## CalR proximal promoters

## CalR distal promoters

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.