IRESite_Id:264 characteristics of NDST4S IRES studied in pCAT-NDST4S-eGFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `264`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-02-21 00:00:00`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
hopefully_full-length_mRNA

The mRNA/+RNA description:

Putative in vivo transcript from CMV promoter of pCAT-NDST4S-eGFP including the SV40 early poly(A) signal.

The mRNA/+RNA sequence represented in the +DNA notation:

TCAGATCCGC TAGCGCTACC GGACTCAGAT CTAGCTTCGA CGAGATTTTC AGGAGCTAAG GAAGCTAAAA TGGAGAAAAA AATCACTGGA TATACCACCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTGATATATC CCAATCGCAT CGTAAAGAAC ATTTTGAGGC ATTTCAGTCA GTTGCTCAAT GTACCTATAA CCAGACCGTT CAGCTGGATA TTACGGCCTT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTTAAAGACC GTAAAGAAAA ATAAGCACAA GTTTTATCCG GCCTTTATTC ACATTCTTGC CCGCCTGATG AATGCTCATC CGGAATTCCG TATGGCAATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AAAGACGGTG AGCTGGTGAT ATGGGATAGT GTTCACCCTT GTTACACCGT TTTCCATGAG CAAACTGAAA CGTTTTCATC GCTCTGGAGT GAATACCACG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACGATTTCCG GCAGTTTCTA CACATATATT CGCAAGATGT GGCGTGTTAC GGTGAAAACC TGGCCTATTT CCCTAAAGGG TTTATTGAGA ATATGTTTTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTCTCAGCC AATCCCTGGG TGAGTTTCAC CAGTTTTGAT TTAAACGTGG CCAATATGGA CAACTTCTTC GCCCCCGTTT TCACCATGGG CAAATATTAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACGCAAGGCG ACAAGGTGCT GATGCCGCTG GCGATTCAGG TTCATCATGC CGTCTGTGAT GGCTTCCATG TCGGCAGAAT GCTTAATGAA TTACAACAGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACTGCGATGA GTGGCAGGGC GGGGCGTAAT TTTTTTAAGG CAGTTATTGG TGCCCTTAAA CGCCTGGTGC TACGCCTGAA GAGCTCAAGC TTGGTCCAGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CACCGGCACC GGAGCTGAGG AGTGCTCTCA GAATCCTGTT GAGGCAGATG GCACGAACTG AAAGCTCCGC TAATTAACGT GGAGCCAAGT AAACCTGAAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCTGGATATC TCATTTTCTA ACTTCGGATA AATTCAAGTT AGCAAAAGAA AAAAAAATTG AAATGCTTCT CTAGATAATG CTTAAAGGAC CCTGCAGCAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTCTTGGTAT TGGACATAGC ATCTCAGCTG TTGCCTCCTG GTCCGTTGAC TACCAGATTT GACTCATTTG TGATTCCTTC GAGAATCTCC CATGATTTGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AATGGTTACA TGAATGTTTG GGAAGGAAAA CTGGCAACAT CTTAGTATAT GTTCTCCATG GCACATTAGG GAAAGAAGCC AGAAAAGGCT CCCAACGCAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGATTTTTAA AATGGATCCA CCGGTCGCCA CCATGGTGAG CAAGGGCGAG GAGCTGTTCA CCGGGGTGGT GCCCATCCTG GTCGAGCTGG ACGGCGACGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAACGGCCAC AAGTTCAGCG TGTCCGGCGA GGGCGAGGGC GATGCCACCT ACGGCAAGCT GACCCTGAAG TTCATCTGCA CCACCGGCAA GCTGCCCGTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCCTGGCCCA CCCTCGTGAC CACCCTGACC TACGGCGTGC AGTGCTTCAG CCGCTACCCC GACCACATGA AGCAGCACGA CTTCTTCAAG TCCGCCATGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCGAAGGCTA CGTCCAGGAG CGCACCATCT TCTTCAAGGA CGACGGCAAC TACAAGACCC GCGCCGAGGT GAAGTTCGAG GGCGACACCC TGGTGAACCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CATCGAGCTG AAGGGCATCG ACTTCAAGGA GGACGGCAAC ATCCTGGGGC ACAAGCTGGA GTACAACTAC AACAGCCACA ACGTCTATAT CATGGCCGAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAGCAGAAGA ACGGCATCAA GGTGAACTTC AAGATCCGCC ACAACATCGA GGACGGCAGC GTGCAGCTCG CCGACCACTA CCAGCAGAAC ACCCCCATCG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCGACGGCCC CGTGCTGCTG CCCGACAACC ACTACCTGAG CACCCAGTCC GCCCTGAGCA AAGACCCCAA CGAGAAGCGC GATCACATGG TCCTGCTGGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTTCGTGACC GCCGCCGGGA TCACTCTCGG CATGGACGAG CTGTACAAGT AAAGCGGCCG CGACTCTAGA TCATAATCAG CCATACCACA TTTGTAGAGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTTTACTTGC TTTAAAAAAC CTCCCACACC TCCCCCTGAA CCTGAAACAT AAAATGAATG CAATTGTTGT TGTTAACTTG TTTATTGCAG CTTATAATGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTACAaataa agcaatagca tcacaaattt cacaaataaa gca
^2101      ^2111      ^2121      ^2131      ^2141

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pCAT-NDST4S-eGFP The name of the promoter used to express this mRNA:
CMV

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

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Mus musculus

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

TAGTTATTAA TAGTAATCAA TTACGGGGTC ATTAGTTCAT AGCCCATATA TGGAGTTCCG CGTTACATAA CTTACGGTAA ATGGCCCGCC TGGCTGACCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCAACGACC CCCGCCCATT GACGTCAATA ATGACGTATG TTCCCATAGT AACGCCAATA GGGACTTTCC ATTGACGTCA ATGGGTGGAG TATTTACGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAACTGCCCA CTTGGCAGTA CATCAAGTGT ATCATATGCC AAGTACGCCC CCTATTGACG TCAATGACGG TAAATGGCCC GCCTGGCATT ATGCCCAGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CATGACCTTA TGGGACTTTC CTACTTGGCA GTACATCTAC GTATTAGTCA TCGCTATTAC CATGGTGATG CGGTTTTGGC AGTACATCAA TGGGCGTGGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAGCGGTTTG ACTCACGGGG ATTTCCAAGT CTCCACCCCA TTGACGTCAA TGGGAGTTTG TTTTGGCACC AAAATCAACG GGACTTTCCA AAATGTCGTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACAACTCCGC CCCATTGACG CAAATGGGCG GTAGGCGTGT ACGGTGGGAG GTCTATATAA GCAGAGCTGG TTTAGTGAAC CGTCAGATCC GCTAGCGCTA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCGGACTCAG ATCTAGCTTC GACGAGATTT TCAGGAGCTA AGGAAGCTAA AATGGAGAAA AAAATCACTG GATATACCAC CGTTGATATA TCCCAATCGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATCGTAAAGA ACATTTTGAG GCATTTCAGT CAGTTGCTCA ATGTACCTAT AACCAGACCG TTCAGCTGGA TATTACGGCC TTTTTAAAGA CCGTAAAGAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAATAAGCAC AAGTTTTATC CGGCCTTTAT TCACATTCTT GCCCGCCTGA TGAATGCTCA TCCGGAATTC CGTATGGCAA TGAAAGACGG TGAGCTGGTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATATGGGATA GTGTTCACCC TTGTTACACC GTTTTCCATG AGCAAACTGA AACGTTTTCA TCGCTCTGGA GTGAATACCA CGACGATTTC CGGCAGTTTC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TACACATATA TTCGCAAGAT GTGGCGTGTT ACGGTGAAAA CCTGGCCTAT TTCCCTAAAG GGTTTATTGA GAATATGTTT TTCGTCTCAG CCAATCCCTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGTGAGTTTC ACCAGTTTTG ATTTAAACGT GGCCAATATG GACAACTTCT TCGCCCCCGT TTTCACCATG GGCAAATATT ATACGCAAGG CGACAAGGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTGATGCCGC TGGCGATTCA GGTTCATCAT GCCGTCTGTG ATGGCTTCCA TGTCGGCAGA ATGCTTAATG AATTACAACA GTACTGCGAT GAGTGGCAGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCGGGGCGTA ATTTTTTTAA GGCAGTTATT GGTGCCCTTA AACGCCTGGT GCTACGCCTG AAGAGCTCAA GCTTGGTCCA GACACCGGCA CCGGAGCTGA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGAGTGCTCT CAGAATCCTG TTGAGGCAGA TGGCACGAAC TGAAAGCTCC GCTAATTAAC GTGGAGCCAA GTAAACCTGA ATTCTGGATA TCTCATTTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TAACTTCGGA TAAATTCAAG TTAGCAAAAG AAAAAAAAAT TGAAATGCTT CTCTAGATAA TGCTTAAAGG ACCCTGCAGC AGTTCTTGGT ATTGGACATA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCATCTCAGC TGTTGCCTCC TGGTCCGTTG ACTACCAGAT TTGACTCATT TGTGATTCCT TCGAGAATCT CCCATGATTT GCAATGGTTA CATGAATGTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGGGAAGGAA AACTGGCAAC ATCTTAGTAT ATGTTCTCCA TGGCACATTA GGGAAAGAAG CCAGAAAAGG CTCCCAACGC ATTGATTTTT AAAATGGATC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CACCGGTCGC CACCATGGTG AGCAAGGGCG AGGAGCTGTT CACCGGGGTG GTGCCCATCC TGGTCGAGCT GGACGGCGAC GTAAACGGCC ACAAGTTCAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGTGTCCGGC GAGGGCGAGG GCGATGCCAC CTACGGCAAG CTGACCCTGA AGTTCATCTG CACCACCGGC AAGCTGCCCG TGCCCTGGCC CACCCTCGTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACCACCCTGA CCTACGGCGT GCAGTGCTTC AGCCGCTACC CCGACCACAT GAAGCAGCAC GACTTCTTCA AGTCCGCCAT GCCCGAAGGC TACGTCCAGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGCGCACCAT CTTCTTCAAG GACGACGGCA ACTACAAGAC CCGCGCCGAG GTGAAGTTCG AGGGCGACAC CCTGGTGAAC CGCATCGAGC TGAAGGGCAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGACTTCAAG GAGGACGGCA ACATCCTGGG GCACAAGCTG GAGTACAACT ACAACAGCCA CAACGTCTAT ATCATGGCCG ACAAGCAGAA GAACGGCATC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAGGTGAACT TCAAGATCCG CCACAACATC GAGGACGGCA GCGTGCAGCT CGCCGACCAC TACCAGCAGA ACACCCCCAT CGGCGACGGC CCCGTGCTGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGCCCGACAA CCACTACCTG AGCACCCAGT CCGCCCTGAG CAAAGACCCC AACGAGAAGC GCGATCACAT GGTCCTGCTG GAGTTCGTGA CCGCCGCCGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GATCACTCTC GGCATGGACG AGCTGTACAA GTAAAGCGGC CGCGACTCTA GATCATAATC AGCCATACCA CATTTGTAGA GGTTTTACTT GCTTTAAAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACCTCCCACA CCTCCCCCTG AACCTGAAAC ATAAAATGAA TGCAATTGTT GTTGTTAACT TGTTTATTGC AGCTTATAAT GGTTACAaat aaagcaatag 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

catcacaaat ttcacaaata aagcattttt ttcactgcat tctagttgtg gtttgtccaa actcatcaat gtatcttaag gcgtaaattg taagcgttaa 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

tattttgtta aaattcgcgt taaatttttg ttaaatcagc tcatttttta accaataggc cgaaatcggc aaaatccctt ataaatcaaa agaatagacc 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

gagatagggt tgagtgttgt tccagtttgg aacaagagtc cactattaaa gaacgtggac tccaacgtca aagggcgaaa aaccgtctat cagggcgatg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gcccactacg tgaaccatca ccctaatcaa gttttttggg gtcgaggtgc cgtaaagcac taaatcggaa ccctaaaggg agcccccgat ttagagcttg 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

acggggaaag ccggcgaacg tggcgagaaa ggaagggaag aaagcgaaag gagcgggcgc tagggcgctg gcaagtgtag cggtcacgct gcgcgtaacc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

accacacccg ccgcgcttaa tgcgccgcta cagggcgcgt caggtggcac ttttcgggga aatgtgcgcg gaacccctat ttgtttattt ttctaaatac 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

attcaaatat gtatccgctc atgagacaat aaccctgata aatgcttcaa taatattgaa aaaggaagag tcctgaggcg gaaagaacca gctgtggaat 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

gtgtgtcagt tagggtgtgg aaagtcccca ggctccccag caggcagaag tatgcaaagc atgcatctca attagtcagc aaccaggtgt ggaaagtccc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

caggctcccc agcaggcaga agtatgcaaa gcatgcatct caattagtca gcaaccatag tcccgcccct aactccgccc atcccgcccc taactccgcc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

cagttccgcc cattctccgc cccatggctg actaattttt tttatttatg cagaggccga ggccgcctcg gcctctgagc tattccagaa gtagtgagga 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ggcttttttg gaggcctagg cttttgcaaa gatcgatcaa gagacaggat gaggatcgtt tcgcatgatt gaacaagatg gattgcacgc aggttctccg 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

gccgcttggg tggagaggct attcggctat gactgggcac aacagacaat cggctgctct gatgccgccg tgttccggct gtcagcgcag gggcgcccgg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ttctttttgt caagaccgac ctgtccggtg ccctgaatga actgcaagac gaggcagcgc ggctatcgtg gctggccacg acgggcgttc cttgcgcagc 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

tgtgctcgac gttgtcactg aagcgggaag ggactggctg ctattgggcg aagtgccggg gcaggatctc ctgtcatctc accttgctcc tgccgagaaa 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

gtatccatca tggctgatgc aatgcggcgg ctgcatacgc ttgatccggc tacctgccca ttcgaccacc aagcgaaaca tcgcatcgag cgagcacgta 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ctcggatgga agccggtctt gtcgatcagg atgatctgga cgaagagcat caggggctcg cgccagccga actgttcgcc aggctcaagg cgagcatgcc 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

cgacggcgag gatctcgtcg tgacccatgg cgatgcctgc ttgccgaata tcatggtgga aaatggccgc ttttctggat tcatcgactg tggccggctg 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ggtgtggcgg accgctatca ggacatagcg ttggctaccc gtgatattgc tgaagagctt ggcggcgaat gggctgaccg cttcctcgtg ctttacggta 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

tcgccgctcc cgattcgcag cgcatcgcct tctatcgcct tcttgacgag ttcttctgag cgggactctg gggttcgaaa tgaccgacca agcgacgccc 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aacctgccat cacgagattt cgattccacc gccgccttct atgaaaggtt gggcttcgga atcgttttcc gggacgccgg ctggatgatc ctccagcgcg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

gggatctcat gctggagttc ttcgcccacc ctagggggag gctaactgaa acacggaagg agacaatacc ggaaggaacc cgcgctatga cggcaataaa 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

aagacagaat aaaacgcacg gtgttgggtc gtttgttcat aaacgcgggg ttcggtccca gggctggcac tctgtcgata ccccaccgag accccattgg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ggccaatacg cccgcgtttc ttccttttcc ccaccccacc ccccaagttc gggtgaaggc ccagggctcg cagccaacgt cggggcggca ggccctgcca 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

tagcctcagg ttactcatat atactttaga ttgatttaaa acttcatttt taatttaaaa ggatctaggt gaagatcctt tttgataatc tcatgaccaa 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

aatcccttaa cgtgagtttt cgttccactg agcgtcagac cccgtagaaa agatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ttgcaaacaa aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc cgaaggtaac tggcttcagc agagcgcaga 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

taccaaatac tgtccttcta gtgtagccgt agttaggcca ccacttcaag aactctgtag caccgcctac atacctcgct ctgctaatcc tgttaccagt 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ggctgctgcc agtggcgata agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg cagcggtcgg gctgaacggg gggttcgtgc 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

acacagccca gcttggagcg aacgacctac accgaactga gatacctaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga aaggcggaca 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ctgacttgag cgtcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcaacgcg gcctttttac ggttcctggc cttttgctgg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ccttttgctc acatgttctt tcctgcgtta tcccctgatt ctgtggataa ccgtattacc gccatgcat
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861

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

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

2

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:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase

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):

70-729

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
eGFP

The description of the protein encoded in this ORF:
enhanced green fluorescent protein

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):

1233-1952

Remarks:

NDST4 is transcribed from two different promoters. The longer NDST4L and shorter NDST4S share only partially
the first exon (432bp vs. 140bp), and completely share the second exon. The upstream promoter is TATA-less.
The downstream promoter includes CAAT/TATA box 77/68 bases upstream the transcription start site and is
located in the first cistron. Total lengths of 5'-UTRs are 669 and 377bp. See Fig. 1 in Grobe and Esko (2002).

The splice sites in all NDST variants are A(G/G)TAAGT...intron...CA(G/N).

A region of the first exon shared by both NDST4L and NDST4S is similar to htrp3 mRNA 5'-UTR region:

>gi|2295902|gb|U47050.1|HSU47050 Homo sapiens calcium influx channel (htrp3) mRNA, complete cds
Length=3417

 Score =  119 bits (60),  Expect = 3e-24
 Identities = 109/124 (87%), Gaps = 1/124 (0%)
 Strand=Plus/Plus

Query  28   GAGTGCTCTCAGAATCCTGTTGAGGCAGATGGCACGAACTGAAAGCTCCG-CTAATTAAC  86
Sbjct  4    .........TG....AT.............T...T..............TT.........  63

Query  87   GTGGAGCCAAGTAAACCTGAATTCTGGATATCTCATTTTCTAACTTCGGATAAATTCAAG  146
Sbjct  64   C...........G.........A.............G.......ACG.............  123

Query  147  TTAG  150
Sbjct  124  ....  127

Citations:

Grobe K., Esko J. D. (2002) Regulated translation of heparan sulfate N-acetylglucosamine N-deacetylase/n-sulfotransferase isozymes by structured 5'-untranslated regions and internal ribosome entry sites. J. Biol. Chem. 277(34):30699-30706

IRESs:

IRES:

Version: `1`	Last change: `2007-04-16 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NDST4S`	The functional status of IRES: `functional`

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

793-1214

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `64`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `485`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-440`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-19`

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

GGTCCAGACA CCGGCACCGG AGCTGAGGAG TGCTCTCAGA ATCCTGTTGA GGCAGATGGC ACGAACTGAA AGCTCCGCTA ATTAACGTGG AGCCAAGTAA 
^793       ^803       ^813       ^823       ^833       ^843       ^853       ^863       ^873       ^883       

ACCTGAATTC TGGATATCTC ATTTTCTAAC TTCGGATAAA TTCAAGTTAG CAAAAGAAAA AAAAATTGAA ATGCTTCTCT AGATAATGCT TAAAGGACCC 
^893       ^903       ^913       ^923       ^933       ^943       ^953       ^963       ^973       ^983       

TGCAGCAGTT CTTGGTATTG GACATAGCAT CTCAGCTGTT GCCTCCTGGT CCGTTGACTA CCAGATTTGA CTCATTTGTG ATTCCTTCGA GAATCTCCCA 
^993       ^1003      ^1013      ^1023      ^1033      ^1043      ^1053      ^1063      ^1073      ^1083      

TGATTTGCAA TGGTTACATG AATGTTTGGG AAGGAAAACT GGCAACATCT TAGTATATGT TCTCCATGGC ACATTAGGGA AAGAAGCCAG AAAAGGCTCC 
^1093      ^1103      ^1113      ^1123      ^1133      ^1143      ^1153      ^1163      ^1173      ^1183      

CAACGCATTG ATTTTTAAAA TG
^1193      ^1203      ^1213

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 334

Version: `1`	Last change: `2007-02-20 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cricetulus griseus CHO-K1 (ATCC CCL-61)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

39.000

Name of IRES used as the positive control:

EMCV

Name of the plasmid used as the positive control. `pCAT-EMCV-eGFP`
`IRESite Id` of the plasmid used as positive control. `263`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `713`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Fig. 6

Citations:

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