How to find the promoter sequence of this gene - (May/23/2006 )

HI,How to find the promoter sequence and design the MSP primer of this gene?
The gene's name is IGSF4 OR TSLC1 ,I find the sequence of this gene from NCBI
1 gacatggcga gtgtagtgct gccgagcgga tcccagtgtg cggcggcagc ggcggcggcg
61 gcgcctcccg ggctccggct ccggcttctg ctgttgctct tctccgccgc ggcactgatc
121 cccacaggtg atgggcagaa tctgtttacg aaagacgtga cagtgatcga gggagaggtt
181 gcgaccatca gttgccaagt caataagagt gacgactctg tgattcagct actgaatccc
241 aacaggcaga ccatttattt cagggacttc aggcctttga aggacagcag gtttcagttg
301 ctgaattttt ctagcagtga actcaaagta tcattgacaa acgtctcaat ttctgatgaa
361 ggaagatact tttgccagct ctataccgat cccccacagg aaagttacac caccatcaca
421 gtcctggtcc caccacgtaa tctgatgatc gatatccaga gagacactgc ggtggaaggt
481 gaggagattg aagtcaactg cactgctatg gccagcaagc cagccacgac tatcaggtgg
541 ttcaaaggga acacagagct aaaaggcaaa tcggaggtgg aagagtggtc agacatgtac
601 actgtgacca gtcagctgat gctgaaggtg cacaaggagg acgatggggt cccagtgatc
661 tgccaggtgg agcaccctgc ggtcactgga aacctgcaga cccagcggta tctagaagta
721 cagtataagc cacaagtgca cattcagatg acttatcctc tacaaggctt aacccgggaa
781 ggggacgcgc ttgagttaac atgtgaagcc atcgggaagc cccagcctgt gatggtaact
841 tgggtgagag tcgatgatga aatgcctcaa cacgccgtac tgtctgggcc caacctgttc
901 atcaataacc taaacaaaac agataatggt acataccgct gtgaagcttc aaacatagtg
961 gggaaagctc actcggatta tatgctgtat gtatacgatc cccccacaac tatccctcct
1021 cccacaacaa ccaccaccac caccaccacc accaccacca ccatccttac catcatcaca
1081 gattcccgag caggtgaaga aggctcgatc agggcagtgg atcatgccgt gatcggtggc
1141 gtcgtggcgg tggtggtgtt cgccatgctg tgcttgctca tcattctggg gcgctatttt
1201 gccagacata aaggtacata cttcactcat gaagccaaag gagccgatga cgcagcagac
1261 gcagacacag ctataatcaa tgcagaagga ggacagaaca actccgaaga aaagaaagag
1321 tacttcatct agatcagcct ttttgtttca atgaggtgtc caactggccc tatttagatg
1381 ataaagagac agtgatattg gaacttgcga gaaattcgtg tgttttttta tgaatgggtg
1441 gaaaggtgtg agactgggaa ggcttgggat ttgctgtgta aaaaaaaaaa aaaatgttct
1501 ttggaaagta cactctgctg tttgacacct cttttttcgt ttgtttgttt gtttaatttt
1561 tatttcttcc taccaagtca aacttggata cttggattta gtttcagtag attgcagaaa
1621 attctgtgcc ttgttttttg tttgtttgtt gcgttccttt cttttccccc tttgtgcaca
1681 tttatttcct ccctctaccc caatttcgga ttttttccaa aatctcccat tttggaattt
1741 gcctgctggg attccttaga ctcttttcct tcccttttct gttctagttt tttacttttg
1801 tttattttta tggtaactgc tttctgttcc aaattcagtt tcataaaagg agaaccagca
1861 cagcttagga tttcatagtt cagaatttag tgtatccata atgcattctt ctctgttgtc
1921 gtaaagattt gggtgaacaa acaatgaaaa ctctttgctg ctgcccatgt ttcaaatact
1981 tagagcagtg aagactagaa aattagactg tgattcagaa aatgttctgt ttgctgtgga
2041 actacattac tgtacagggt tatctgcaag tgaggtgtgt cacaatgaga ttgaatttca
2101 ctgtctttaa ttctgtatct gtagacggct cagtatagat accctacgct gtccagaaag
2161 gtttggggca gaaaggactc ctcctttttc catgccctaa acagacctga caggtgaggt
2221 ctgttccttt tatataagtg gacaaatttt gagttgccac aggaggggaa gtagggaggg
2281 gggaaataca gttctgctct ggttgtttct gttccaaatg attccatcca cctttcccaa
2341 tcggccttac ttctcactaa tttgtaggaa aaagcaagtt cgtctgttgt gcgaatgact
2401 gaatgggaca gagttgattt tttttttttt tttcctttgt gcttagttag gaaggcagta
2461 ggatgtggcc tgcatgtact gtatattaca gatatttgtc atgctgggat ttccaactcg
2521 aatctgtgtg aaactttcat tccttcagat ttggcttgac aaaggcagga ggtacaaaag
2581 aagggctggt attgttctca cactggtctg ctgtcgctct cagttctcga taggtcagag
2641 cagaggtgga aaaacagcat gtacggattt tcagttactt aatcaaaact caaatgtgag
2701 tgtttttatc tttttacctt tcatacacta gccttggcct ctttcctcag ccttaagaac
2761 catctgccaa aaattactga tcctcgcatg atggcagcca tagtgcatag ctactaaaat
2821 cagtgacctt gaacatatct tagatgggga gcctcgggaa aaggtagagg agtcacgtta
2881 ccatttacat gttttaaaga aagaagtgtg gggattttca ctgaaacgtc taggaaatct
2941 agaagtagtc ctgaaggaca gaaactaaac tcttaccata tgtttggtaa gactccagac
3001 tccagctaac agtccctatg gaaagatggc atcaaaaaag atagatctat atatatatat
3061 aaatatatat tctattacat tttcagtgag taattttgga ttttgcaagg tgcattttta
3121 ctattgttac attatgtgga aaacttatgc tgatttattt aagggggaaa aagtgtcaac
3181 tctttgttat ttgaaaacat gtttattttt cttgtcttta ttttaacctt tgatagaacc
3241 attgcaatat gggggccttt tgggaacgga ctggtatgta aaagaaaatc cattatcgag
3301 cagcatttta tttacccctc ccctatccct aggcacttaa ccaagacaaa aagccacaat
3361 gaacatccct ttttcaatga attttataat ctgcagctct attccgagcc cttagcaccc
3421 attccgacca tagtataatc atatcaaagg gtgagaatca tttagcatgt tgttgaaagg
3481 ttttttttca gttgttcttt ttagaaaaaa ag

THANKS

had a quick look at your gene in genome browser and (see attached) there is a CpG island at the 5' end of this gene which could be a part of the promoter. Just click on the green CpG island and it will pull up the sequenc from which you can design assays for

Good luck!

Nick

Here is the actual promoter sequence (1kb upstream). Sequence highlighted is the first exon.

GAAGGGCTGGGGGCGCAGAGGAGGAGTGAGAGGGTTTGAGCCCCGAAGGAGGAACACGGC
AGACCCTGCCTTCACCACACTCCCTCTCCCCAACTCCCACCACCCCCGCTCTTCACCTGA
AGCCTTGACTAATTTTTTCCGTTGTTGTGTAATCTTAAATATCTAATATTACAAATATTT
CACACATATATTCAACACACACCTATATATTAAAACCAGGGAGGAGACCCTCGACAAGCG
GAGGAGCCTGAGCATACCCTCCTCGATCTACCTTTCCCGAGATTCTGCCGCAAAAAGACC
GACTGGAAAATCTCAGAACCCGACTCTACGGCTGCCTTCTCCAACTATCCCCGAGTCTAC
CGCTAGGCTGTTGAGCGGGCTCTCCCGCTCCGCCGGACGTGCAAAGCACGCATGCACTTC
TCCCAGATTGTTTTGTCAATCCGGGGACCTGCCTTCTTACTCTCCACTCCCGCACAGCCC
CCGTTCCCAAAGATCTATTCCTTCGGTGCAAGGTGAGTGACGGAAATTTGCAACGTCTGG
TTCGCTAGGCCAGATGCACTCGGTGTGCGGGACAGAGGACCCTCTTAAGGGAGATTCTCC
AGTCGTCGGTCTGATACAGCGATTGCTATAAACATTCCTAATAAAGGTGTACAAGAAGCT
AGACCCGCCCCCTGGAGCCCGAGTCCTTGCACGCCAGGCGCCCGGGAGAACACTTTTTCC
TTGATCCGGGGAAAGCAAAACCCGAATTTTAACATAAACATATTTGCATACGCCCCTCCC
CTTGGCCCCGCCCCTAGGTGGCGCGGGCGCGCCGCCGAACGCCAGCGCCAGGGGGCGGGG
TGGGGGAGGGAGCGAGGCCCTCCGAGAGCCGGGTTGGGCTCGCGGCGCTGTGATTGGTCT
GCCCGGACTCCGCCTCCAGCGCATGTCATTAGCATCTCATTAGCTGTCCGCTCGGGCTCC
GGAGGCAGCCAACGCCGCCAGTCTGAGGCAGGTGCCCGACATGGCGAGTGTAGTGCTGCC
GAGCGGATCCCAGTGTGCGGCGGCAGCGGCGGCGGCGGCGCCTCCCGGGCTCCGGCTCCG
GCTTCTGCTGTTGCTCTTCTCCGCCGCGGCACTGATCCCCACAGGTAGGTGTGGGCACCG

Usually, you find out the ATG of the first exon and then consider the 1kb or even 2kb upstream region would contain promoter of that gene. I know once study on GPCRs where they considered 5kb region

Thank you very much!

Hi PCRMAN
I Have the same question,my gene name is stathmin. Waiting for your reply,THANKS
1 atcaccgggc gtccgctccg gggtgccgtc gaggagacaa tagggggcgt gggccctcgt
61 ttacctccct ccctccctcc cttccctgcg ggccccgccg ggttccccat tgtctgaagg
121 gacggggcgg tgccccaggg accagcggct ttaggaccaa actgcgggca gccagggccg
181 cgaccctccc tgcgaccgtc ccctggcgac cgcagctggt gattgagggg cggcgctccc
241 gggccccacg agggttcttc tgtcttcgcg gccggacgcg cggacagcgt gggtggcggc
301 aggactttcc ttatcccagt tgattgtgca gaatacactg cctgtcgctt gtcttctatt
361 caccatggct tcttctgata tccaggtgaa agaactggag aagcgtgcct caggccaggc
421 ttttgagctg attctcagcc ctcggtcaaa agaatctgtt ccagaattcc ccctttcccc
481 tccaaagaag aaggatcttt ccctggagga aattcagaag aaattagaag ctgcagaaga
541 aagacgcaag tcccatgaag ctgaggtctt gaagcagctg gctgagaaac gagagcacga
601 gaaagaagtg cttcagaagg caatagaaga gaacaacaac ttcagtaaaa tggcagaaga
661 gaaactgacc cacaaaatgg aagctaataa agagaaccga gaggcacaaa tggctgccaa
721 actggaacgt ttgcgagaga aggataagca cattgaagaa gtgcggaaga acaaagaatc
781 caaagaccct gctgacgaga ctgaagctga ctaatttgtt ctgagaactg actttctccc
841 catccccttc ctaaatatcc aaagactgta ctggccagtg tcattttatt ttttccctcc
901 tgacaaatat tttagaagct aatgtaggac tgtataggta gatccagatc cagactgtaa
961 gatgttgttt taggggctaa aggggagaaa ctgaaagtgt tttactcttt ttctaaagtg
1021 ttggtctttc taatgtagct atttttcttg ttgcatcttt tctacttcag tacacttggt
1081 gtactgggtt aatggctagt actgtattgg ctctgtgaaa acatatttgt gaaaagagta
1141 tgtagtggct tcttttgaac tgttagatgc tgaatatctg ttcacttttc aatcccaatt
1201 ctgtcccaat cttaccagat gctactggac ttgaatggtt aataaaactg cacagtgctg
1261 ttggtggcag tgacttcttt tgagttaggt taataaatca agccatagag cccctcctgg
1321 ttgatacttg ttccagatgg ggcctttggg gctggtagaa atacccaacg cacaaatgac
1381 cgcacgttct ctgccccgtt tcttgcccca gtgtggtttg cattgtctcc ttccacaatg
1441 actgctttgt ttggatgcct cagcccaggt cagctgttac tttctttcag atgtttattt
1501 gcaaacaacc attttttgtt ctgtgtccct tttaaaaggc agattaaaag cacaagcgtg
1561 tttctagaga acagttgaga gagaatctca agattctact tggtggtttg cttgctctac
1621 gttacaggtg gggcatgtcc tcatcctttc ctgccataaa agctatgaca cgagaatcag
1681 aatattaata aaactttatg tactgctgta gcaaaaaaaa aaaaaaaaaa

pcrman: what if there more than one ATG ...
how could you know the first promotor?


Jiang M: how to determine the size of your promotor?

STMN1 5'-flanking region (the first 1kb).

can we estimate/guess the position of a promoter theoretically?
i mean without using databases, softwares....