IRESite_Id:588 promoter-less plasmid pGem-LamB1-F used to evaluate potential promoter activity in LamB1_-335

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `588`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-04-14 17:19:58`
Reviewed by: Martin Mokrejš

IRESite record type:

promoter-less_plasmid_with_putative_IRES

The name of the plasmid:
pGem-LamB1-F

Description of the plasmid (facultative for promoter-less plasmid records):
pGem-LamB1-F plasmid contains LamB1 5'-UTR followed by firefly luciferase ORF under the T7 promoter. The plasmids lacks T7 promoter transcription termination signal Tphi and eukaryotic transcription termination signals as well.

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa (ATCC CCL-2)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
LamB1

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

TAATACGACT CACTATAGGG CGAATTCGAT TCTAGCTAGC GGGACCTGGA AGCGCCCCAG CCCCGCAGCG ATCGCAGATT CGGCTTTCAA ACAAAAGAGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCCCCGGGG GGTGGGACCG GGACCTCACC CGGTCCTCGC AGAGTTGCGG CCGCCCGCCC CTTCAGCCCC GGCTCTCCGT ATGCGCATGA GCAGAGGCGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTCCCTCTGT TCCTCCCAAG GCTAAACTTT CTAATTCCCT TCTTTGGGCT CGGGGGCTCC CGGAGCAGGG CGAGAGCTCG CGTCGCCGGA AAGGAAGACG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGAAGAAAGG GCAGGCGGCT CGGCGGGCGT CTTCTCCACT CCTCTGCCGC GTCCCCGTGG CTGCAGGGAG CCGGCCTCGA GATCTGCGAT CTAAGTAAGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTGGCATTCC GGTACTGTTG GTAAAGCCAC CATGGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCGC TGGAAGATGG AACCGCTGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GAGCAACTGC ATAAGGCTAT GAAGAGATAC GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGGA CATCACTTAC GCTGAGTACT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCGAAATGTC CGTTCGGTTG GCAGAAGCTA TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC AATTCTTTAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCCGGTGTTG GGCGCGTTAT TTATCGGAGT TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGGGCAT TTCGCAGCCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACCGTGGTGT TCGTTTCCAA AAAGGGGTTG CAAAAAATTT TGAACGTGCA AAAAAAGCTC CCAATCATCC AAAAAATTAT TATCATGGAT TCTAAAACGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTACCAGGG ATTTCAGTCG ATGTACACGT TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTGCCA GAGTCCTTCG ATAGGGACAA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GACAATTGCA CTGATCATGA ACTCCTCTGG ATCTACTGGT CTGCCTAAAG GTGTCGCTCT GCCTCATAGA ACTGCCTGCG TGAGATTCTC GCATGCCAGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GATCCTATTT TTGGCAATCA AATCATTCCG GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC GGATATTTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TATGTGGATT TCGAGTCGTC TTAATGTATA GATTTGAAGA AGAGCTGTTT CTGAGGAGCC TTCAGGATTA CAAGATTCAA AGTGCGCTGC TGGTGCCAAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCTATTCTCC TTCTTCGCCA AAAGCACTCT GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGTGGCG CTCCCCTCTC TAAGGAAGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGGGAAGCGG TTGCCAAGAG GTTCCATCTG CCAGGTATCA GGCAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC GAGGGGGATG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATAAACCGGG CGCGGTCGGT AAAGTTGTTC CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAAA GAGGCGAACT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GTGTGTGAGA GGTCCTATGA TTATGTCCGG TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC TGGAGACATA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCTTACTGGG ACGAAGACGA ACACTTCTTC ATCGTTGACC GCCTGAAGTC TCTGATTAAG TACAAAGGCT ATCAGGTGGC TCCCGCTGAA TTGGAATCCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCTTGCTCCA ACACCCCAAC ATCTTCGACG CAGGTGTCGC AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT TGGAGCACGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AAAGACGATG ACGGAAAAAG AGATCGTGGA TTACGTCGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA CGAAGTACCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAAGGTCTTA CCGGAAAACT CGACGCAAGA AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGATCGCCGT GTAATTCTAG AGTCGACCTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CAGGCATGCA AGCTTGAGTA TTCTATAGTG TCACCTAAAT AGCTTGGCGT AATCATGGTC ATAGCTGTTT CCTGTGTGAA ATTGTTATCC GCTCACAATT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCACACAACA TACGAGCCGG AAGCATAAAG TGTAAAGCCT GGGGTGCCTA ATGAGTGAGC TAACTCACAT TAATTGCGTT GCGCTCACTG CCCGCTTTCC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGTCGGGAAA CCTGTCGTGC CAGCTGCATT AATGAATCGG CCAACGCGCG GGGAGAGGCG GTTTGCGTAT TGGGCGCTCT TCCGCTTCCT CGCTCACTGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTCGCTGCGC TCGGTCGTTC GGCTGCGGCG AGCGGTATCA GCTCACTCAA AGGCGGTAAT ACGGTTATCC ACAGAATCAG GGGATAACGC AGGAAAGAAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATGTGAGCAA AAGGCCAGCA AAAGGCCAGG AACCGTAAAA AGGCCGCGTT GCTGGCGTTT TTCCATAGGC TCCGCCCCCC TGACGAGCAT CACAAAAATC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GACGCTCAAG TCAGAGGTGG CGAAACCCGA CAGGACTATA AAGATACCAG GCGTTTCCCC CTGGAAGCTC CCTCGTGCGC TCTCCTGTTC CGACCCTGCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCTTACCGGA TACCTGTCCG CCTTTCTCCC TTCGGGAAGC GTGGCGCTTT CTCATAGCTC ACGCTGTAGG TATCTCAGTT CGGTGTAGGT CGTTCGCTCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AAGCTGGGCT GTGTGCACGA ACCCCCCGTT CAGCCCGACC GCTGCGCCTT ATCCGGTAAC TATCGTCTTG AGTCCAACCC GGTAAGACAC GACTTATCGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CACTGGCAGC AGCCACTGGT AACAGGATTA GCAGAGCGAG GTATGTAGGC GGTGCTACAG AGTTCTTGAA GTGGTGGCCT AACTACGGCT ACACTAGAAG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AACAGTATTT GGTATCTGCG CTCTGCTGAA GCCAGTTACC TTCGGAAAAA GAGTTGGTAG CTCTTGATCC GGCAAACAAA CCACCGCTGG TAGCGGTGGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTTTTTGTTT GCAAGCAGCA GATTACGCGC AGAAAAAAAG GATCTCAAGA AGATCCTTTG ATCTTTTCTA CGGGGTCTGA CGCTCAGTGG AACGAAAACT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CACGTTAAGG GATTTTGGTC ATGAGATTAT CAAAAAGGAT CTTCACCTAG ATCCTTTTAA ATTAAAAATG AAGTTTTAAA TCAATCTAAA GTATATATGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GTAAACTTGG TCTGACAGTT ACCAATGCTT AATCAGTGAG GCACCTATCT CAGCGATCTG TCTATTTCGT TCATCCATAG TTGCCTGACT CCCCGTCGTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TAGATAACTA CGATACGGGA GGGCTTACCA TCTGGCCCCA GTGCTGCAAT GATACCGCGA GACCCACGCT CACCGGCTCC AGATTTATCA GCAATAAACC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCCAGCCGG AAGGGCCGAG CGCAGAAGTG GTCCTGCAAC TTTATCCGCC TCCATCCAGT CTATTAATTG TTGCCGGGAA GCTAGAGTAA GTAGTTCGCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGTTAATAGT TTGCGCAACG TTGTTGCCAT TGCTACAGGC ATCGTGGTGT CACGCTCGTC GTTTGGTATG GCTTCATTCA GCTCCGGTTC CCAACGATCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGGCGAGTTA CATGATCCCC CATGTTGTGC AAAAAAGCGG TTAGCTCCTT CGGTCCTCCG ATCGTTGTCA GAAGTAAGTT GGCCGCAGTG TTATCACTCA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGGTTATGGC AGCACTGCAT AATTCTCTTA CTGTCATGCC ATCCGTAAGA TGCTTTTCTG TGACTGGTGA GTACTCAACC AAGTCATTCT GAGAATAGTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TATGCGGCGA CCGAGTTGCT CTTGCCCGGC GTCAATACGG GATAATACCG CGCCACATAG CAGAACTTTA AAAGTGCTCA TCATTGGAAA ACGTTCTTCG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GGGCGAAAAC TCTCAAGGAT CTTACCGCTG TTGAGATCCA GTTCGATGTA ACCCACTCGT GCACCCAACT GATCTTCAGC ATCTTTTACT TTCACCAGCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TTTCTGGGTG AGCAAAAACA GGAAGGCAAA ATGCCGCAAA AAAGGGAATA AGGGCGACAC GGAAATGTTG AATACTCATA CTCTTCCTTT TTCAATATTA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTGAAGCATT TATCAGGGTT ATTGTCTCAT GAGCGGATAC ATATTTGAAT GTATTTAGAA AAATAAACAA ATAGGGGTTC CGCGCACATT TCCCCGAAAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GTGCCACCTG ACGTCTAAGA AACCATTATT ATCATGACAT TAACCTATAA AAATAGGCGT ATCACGAGGC CCTTTCGTCT CGCGCGTTTC GGTGATGACG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GTGAAAACCT CTGACACATG CAGCTCCCGG AGACGGTCAC AGCTTGTCTG TAAGCGGATG CCGGGAGCAG ACAAGCCCGT CAGGGCGCGT CAGCGGGTGT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TGGCGGGTGT CGGGGCTGGC TTAACTATGC GGCATCAGAG CAGATTGTAC TGAGAGTGCA CCATATGCGG TGTGAAATAC CGCACAGATG CGTAAGGAGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AAATACCGCA TCAGGACGCG CCCTGTAGCG GCGCATTAAG CGCGGCGGGT GTGGTGGTTA CGCGCAGCGT GACCGCTACA CTTGCCAGCG CCCTAGCGCC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGCTCCTTTC GCTTTCTTCC CTTCCTTTCT CGCCACGTTC GCCGGCTTTC CCCGTCAAGC TCTAAATCGG GGGCTCCCTT TAGGGTTCCG ATTTAGTGCT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TTACGGCACC TCGACCCCAA AAAACTTGAT TAGGGTGATG GTTCACGTAG TGGGCCATCG CCCTGATAGA CGGTTTTTCG CCCTTTGACG TTGGAGTCCA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CGTTCTTTAA TAGTGGACTC TTGTTCCAAA CTGGAACAAC ACTCAACCCT ATCTCGGTCT ATTCTTTTGA TTTATAAGGG ATTTTGCCGA TTTCGGCCTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTGGTTAAAA AATGAGCTGA TTTAACAAAA ATTTAACGCG AATTTTAACA AAATATTAAC GCTTACAATT TCCATTCGCC ATTCAGGCTG CGCAACTGTT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGGAAGGGCG ATCGGTGCGG GCCTCTTCGC TATTACGCCA GCTGGCGAAA GGGGGATGTG CTGCAAGGCG ATTAAGTTGG GTAACGCCAG GGTTTTCCCA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GTCACGACGT TGTAAAACGA CGGCCAGTGA ATTG
^5201      ^5211      ^5221      ^5231

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc

The description of the protein encoded in this ORF:
Firefly luciferase

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

432-2084

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `LamB1_-335_-1`	The functional status of IRES: `functional`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

41-375

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

GGGACCTGGA AGCGCCCCAG CCCCGCAGCG ATCGCAGATT CGGCTTTCAA ACAAAAGAGG CGCCCCGGGG GGTGGGACCG GGACCTCACC CGGTCCTCGC 
^41        ^51        ^61        ^71        ^81        ^91        ^101       ^111       ^121       ^131       

AGAGTTGCGG CCGCCCGCCC CTTCAGCCCC GGCTCTCCGT ATGCGCATGA GCAGAGGCGC CTCCCTCTGT TCCTCCCAAG GCTAAACTTT CTAATTCCCT 
^141       ^151       ^161       ^171       ^181       ^191       ^201       ^211       ^221       ^231       

TCTTTGGGCT CGGGGGCTCC CGGAGCAGGG CGAGAGCTCG CGTCGCCGGA AAGGAAGACG GGAAGAAAGG GCAGGCGGCT CGGCGGGCGT CTTCTCCACT 
^241       ^251       ^261       ^271       ^281       ^291       ^301       ^311       ^321       ^331       

CCTCTGCCGC GTCCCCGTGG CTGCAGGGAG CCGGC
^341       ^351       ^361       ^371

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

Last change to the database: 2019-03-18 09:32:49 GMT+1