How to find promoter region of rat gene? - (Nov/08/2007 )

Hi, I have the promoter region sequence for mice delta opioid receptor gene and I need to make a proposal of the promotor region for this gene in rats.
I have no idea how to even start doing this . Please help, thanks!


This the sequence for the mice gene:
GAGCTCCCTGCTGTGACCCTGGCTGTCTTCAGTCTTTTTGACTTGTAGGACCTTTATATATGTTTTTCTTTTTTCTAGAA
GGCTCTTCCTATTTCTTCCCTAAATTAGTTCCCCCACCTCTAAATCCACACAACACCTCAAGTGTCATTTCTTTTAGGAAT
ATTCTCCTGACCCTACCATGCCCCGACATTCCTTGAATAGGACTTCATTGTGTTTTTTTTAGAATCGATGCATCTCTTCTG
GTCTGAGCTGTAAGCTCTTGGGAGCCGGGCCTTGGTCTGATTATGCACACCGATGTACCTGGCTCTTTTGTTAGGCGCCCT
CAGAGTGAATGTGGAGCTAGTGAACTGGGCGCAGGAAAGTGTGGCTGATAACGGATGTTTGTGGTTTTATTTATCGCTCAA
GCAGCCTGCTAGCTCAGAGCATAGAGCCAGACAGGAAAGTTGTGTCTCTAATAACATACACACATCTATCCAGATAGGTGT
GACCTTTTTCAGCTTGATGTAGTGAGATGGTTAGTGACCTTGATTGCGGCTTATGTCTGCCATGTCCGGTGCCAAGCTGTA
CAGACCCAGGTGGGCTTATTTCCAGTGTCTCCCCTTGAGGTTGTAGCTGATCATATTACTAGTCTTCATCCGGAGCCTTTG
GGGGAACTGGACGGTTTTGTTTTTGTTTCTTGGTCAGGAATCATTGGCAGTTCTAGAAGACACGGCAAGGAGCAGAGCGCA
CACAGTACACGGGGGTGGTGGTGGTGGTGGTGGTGGTGGAAATCTGAGTTCTTTACTCCGTTGTCTTCATCTCCCCAAAAC
CCTCTGAAGGCGGCAGGAGATTTTCTTCATCGTGCAGTCACAGAGAATGAACTTGAGAGTGCTTAAGCGGCTCGCTCAAGG
TTACTCCCATCGTCCGTGAAGAGGCGGGAGGCGGGATTCGCATCCAGGTTCTTCTGACTCCGAAGTGGCACGGGGGTGGGG
CGGGAGGCCGGGCCGGGCTGGGGGCACCTGGAGTCAGCGGAGCCCAGGCAGGGAGCGCGCGCGAGGCCTCTCTGGCCCAGC
TCGGAGCCCGGTGGTGCAGCGCCCGCCCCCGATCGCGGGCGCAGACTGCGGCCGCTCCGGACCACGTGGTGCGCGCAGCGG
CTCGGGGCTCCCCGGGCTTGGGCGAGCACTGCGGGCGGTCGACCGGGCGGAGGAGGCGGGACGAGCGCTGCAGCCTGCGCG
TCGGGGCCGTGGCCTCCGTTTTCCGCGCGCCACTCGCTGGGTCCCTGCGCCCAGGGCGCACGAGTGGAGACGGACACGGCG
GCGCCATGG

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Your sequence contains the promoter and the 1st exon. There is a CpG island surrounding the transcription start site indicating it is likely the promoter. Below is the promoter sequence from -500 to -1. There is a CpG island in this sequence (150 -446).

GGAATCACTTGACAGTTCTGGAAGACTCGGCGAGAAGAGCGCACACAGCACGAAGTCACA
GGGGGAAAAATATCTGAGTTCTTTACTCCGTTGTCTTCATCTCTCCCAAACCCTCTGAAG
GAGGCAGCAGATTTTCTTCATCTTGCAGACACAGAGAATGAACTTGAGGGTGCTTAAGCG
GCTCGCTCAAGGTTACTCCCGTCGTCCGTGCAGAGGCGGGAGGCGGGATTCGCATCCAGG
TTCTTCTGACTCCGAAGTGGCACAGGGGGTGGGGCGGGAGGCCCGGCCGGGCTGGGGGCG
CCTAGAGTCAGCAAAGTCCAGGCAGGGAGCGCGCGGGAGGCCTCTCCGGCCCAGCTCGGA
GCCCGTGGTGCAGCGCCCGCCCCCGATAGCGGGCGCAGACTGGCGGCCGCCTCCGGACCA
CGTGGTGCGCGCGGCGGCTCCGGGCTCCCCGGGCTTGGGCGAGCGCTGCGGGCGGCCGAC
CGGGCGGAGGAGGCGGGAGC <-- -1

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Thank you for your help. But I have another question, I tried to look for transcription factors in this sequence after and used TFSEARCH. However, I don't really understand the results that I got. If you could possibly explain this, I will be incredibly grateful. Thank you!

TFMATRIX entries with High-scoring:

1 GGAATCACTT GACAGTTCTG GAAGACTCGG CGAGAAGAGC GCACACAGCA entry score
<------- M00240 Nkx-2. 100.0
<---- M00029 HSF 100.0
----> M00028 HSF 95.3
----> M00029 HSF 93.7
----------> M00147 HSF2 89.1
-----------> M00220 SREBP- 88.7
<---- M00028 HSF 88.5
< M00172 AP-1 88.5
<--------- M00183 c-Myb 87.6
<--------- M00204 GCN4 86.6
<--------- M00046 GCR1 86.4
----> M00029 HSF 86.3
-------> M00253 cap 86.2
--------> M00253 cap 85.3
--------------> M00122 USF 85.3
<-------------- M00122 USF 85.3

51 CGAAGTCACA GGGGGAAAAA TATCTGAGTT CTTTACTCCG TTGTCTTCAT entry score
<----- M00029 HSF 100.0
------> M00048 ADR1 93.8
--------> M00154 STRE 93.4
<----- M00048 ADR1 92.3
-----> M00142 NIT2 91.2
<--------- M00227 v-Myb 89.8
<----- M00028 HSF 88.5
---------- M00172 AP-1 88.5
-----> M00048 ADR1 87.7
---- M00253 cap 87.7
-----------> M00120 dl 87.1
----> M00029 HSF 86.9
----> M00028 HSF 86.5
<------- M00148 SRY 86.4
------------------------> M00207 LAC9 86.3
<---------- M00076 GATA-2 86.2
--------> M00083 MZF1 86.1
< M00087 Ik-2 86.0
----> M00028 HSF 85.9
-------> M00101 CdxA 85.7
<-------- M00253 cap 85.6

101 CTCTCCCAAA CCCTCTGAAG GAGGCAGCAG ATTTTCTTCA TCTTGCAGAC entry score
<---- M00028 HSF 100.0
<-------- M00141 Lyf-1 98.7
<---- M00029 HSF 96.0
------> M00048 ADR1 87.7
---> M00253 cap 87.7
------------ M00087 Ik-2 86.0

151 ACAGAGAATG AACTTGAGGG TGCTTAAGCG GCTCGCTCAA GGTTACTCCC entry score
<-------- M00253 cap 96.2
----> M00029 HSF 95.4
----> M00028 HSF 94.3
<----- M00048 ADR1 87.7
<-------- M00253 cap 86.7
-----> M00029 HSF 86.3
<------ M00240 Nkx-2. 86.0

201 GTCGTCCGTG CAGAGGCGGG AGGCGGGATT CGCATCCAGG TTCTTCTGAC entry score
<----- M00029 HSF 100.0
<---- M00028 HSF 95.3
<---- M00029 HSF 93.7
<- M00048 ADR1 92.3
<----- M00028 HSF 88.5
----------> M00008 Sp1 87.7
------ M00173 AP-1 87.6
----------> M00075 GATA-1 86.9
------ M00172 AP-1 86.7
------> M00048 ADR1 86.2
<----- M00028 HSF 85.4

251 TCCGAAGTGG CACAGGGGGT GGGGCGGGAG GCCCGGCCGG GCTGGGGGCG entry score
-----> M00048 ADR1 98.5
------> M00048 ADR1 95.4
-----> M00048 ADR1 93.8
-----> M00048 ADR1 93.8
-------> M00154 STRE 93.4
---- M00048 ADR1 92.3
--------------> M00255 GC box 92.2
-------------> M00196 Sp1 91.0
-----> M00048 ADR1 89.2
----> M00173 AP-1 87.6
----> M00172 AP-1 86.7
----> M00028 HSF 86.5
------> M00048 ADR1 86.2
-------------> M00001 MyoD 86.0
<------------ M00189 AP-2 86.0

301 CCTAGAGTCA GCAAAGTCCA GGCAGGGAGC GCGCGGGAGG CCTCTCCGGC entry score
-----> M00048 ADR1 86.2
<----- M00048 ADR1 86.2
- M00175 AP-4 85.4

351 CCAGCTCGGA GCCCGTGGTG CAGCGCCCGC CCCCGATAGC GGGCGCAGAC entry score
<------ M00048 ADR1 96.9
----------> M00076 GATA-2 96.8
----------> M00075 GATA-1 96.3
<------ M00048 ADR1 89.2
---------> M00077 GATA-3 88.1
<------------- M00196 Sp1 88.0
------> M00048 ADR1 87.7
<---- M00253 cap 87.6
--------> M00175 AP-4 85.4

401 TGGCGGCCGC CTCCGGACCA CGTGGTGCGC GCGGCGGCTC CGGGCTCCCC entry score
--------> M00217 USF 95.6
<-------- M00217 USF 95.6
--------------> M00121 USF 94.8
<-------------- M00121 USF 94.8
--------------> M00119 Max 92.4
<-------------- M00119 Max 92.4
<---- M00048 ADR1 92.3
--------------> M00118 c-Myc/ 92.3
<-------------- M00118 c-Myc/ 92.3
<------------ M00064 PHO4 91.9
--------------> M00122 USF 91.6
<-------------- M00122 USF 91.6
<------------ M00055 N-Myc 91.2
<------ M00048 ADR1 90.8
------------> M00064 PHO4 90.3
------------> M00055 N-Myc 89.4
<------------ M00123 c-Myc/ 88.2
<------ M00048 ADR1 87.7
--- M00253 cap 87.6
----------> M00187 USF 85.5
<---------- M00187 USF 85.5
------------> M00123 c-Myc/ 85.5
<---------- M00032 c-Ets- 85.3
<------------ M00189 AP-2 85.0

451 GGGCTTGGGC GAGCGCTGCG GGCGGCCGAC CGGGCGGAGG AGGCGGGAGC entry score
- M00048 ADR1 92.3
-----> M00048 ADR1 90.8
------> M00048 ADR1 87.7

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