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→PET-1 Promoter
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note at 1172 in the sequence below (i.e -828 from mRNA start) there appears to be an RAR element: '''gggtga'''gagaggca'''ccctctc'''+
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+Chapter 5 of Wiley’s Current Protocols in Bioinformatics+but it crashed...
=PET-1 Promoter=
=PET-1 Promoter=
−According to TESS (reference below)
+There are the following potential RAR sites in the mouse PET-1 promoter:
+''(Note: substract from 2000 to get upstream position)''
+:RAR-alpha at 1061-1069 (La/Len = 1.53)
+:RAR-beta at 599-604 (1.69)
+:RAR-beta at 1596-1604 (1.71)
+:RAR-beta at 1926-1931 (1.71)
+:RXR-alpha/RXR-beta at 1595-1601 (2.0)
+:RXR-alpha/RXR-beta at 1926-1931 (2.0)
+Hi probability of ER-alpha binding (all La/Len = 1.9 - 2.0) at:
+:599-603
+:1065-1069
+:1597-1601
+:1867-1871
+:1926-1030
+ER/SP-1 binding (all La/Len = 2.0) at:
+:990-994
+:1243-1247
+Found transcription factor binding sites using TESS:
BLAST of mus FEV mRNA ( NM_153111) leads to 100% homology with mus chromosome 1 (AC104542.10) bases 38140 to 40385
BLAST of mus FEV mRNA ( NM_153111) leads to 100% homology with mus chromosome 1 (AC104542.10) bases 38140 to 40385
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Searched using TESS: Combined search query and defaults
Searched using TESS: Combined search query and defaults
−Schug, Jonathan, Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence, Wiley’s Current Protocols in Bioinformatics, ed. Baxevanis, A. D. J. Wiley & sons, 2003. Chapter 5
−TESS: Transcription Element Search Software on the WWW',
+TESS: Transcription Element Search Software on the WWW,
Jonathan Schug and G. Christian Overton,
Jonathan Schug and G. Christian Overton,
Technical Report CBIL-TR-1997-1001-v0.0
Technical Report CBIL-TR-1997-1001-v0.0
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URL: http://www.cbil.upenn.edu/tess
URL: http://www.cbil.upenn.edu/tess
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