IRESite_Id:266 characteristics of NDST4L-delta100 IRES studied in pCAT-NDST4L-delta100-eGFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `266`	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-NDST4L-delta100-eGFP including the SV40 early poly(A)
signal. 112 bp were deleted on the 3'-end of the putative NDST4L IRES.

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 TTGAAAAGAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CGACTCCAGC TAAGCAAGAG GCACAGCAGC AGTGGCAGAA GCAGACAGGA GCAGCTGGTA TTCCGGTGAT TAAATAGTTC TCATAGCCTT TTTGCTGTAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCGGTCTGCT CCCTGGGGTA AGGcTCGTGT CCGAGAAGGA AGCTGCATTT TAACGGTGTG CTGAACAGAG GTCTGAATCA TTCCAGCTGG CTGCTTGTTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGAAAAGGAC AATGTGTGTA TAAATAAAAA GACTGCTGGA AGGGTCCAGA CACCGGCACC GGAGCTGAGG AGTGCTCTCA GAATCCTGTT GAGGCAGATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCACGAACTG AAAGCTCCGC TAATTAACGT GGAGCCAAGT AAACCTGAAT TCTGGATATC TCATTTTCTA ACTTCGGATA AATTCAAGTT AGCAAAAGAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AAAAAAATTG AAATGCTTCT CTAGATAATG CTTAAAGGAC CCTGCAGCAG TTCTTGGTAT TGGACATAGC ATCTCAGCTG TTGCCTCCTG GTCCGTTGAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TACCAGATTT GACTCATTTG TGATTCCTTC GAGAATCTCC CATGATTTGC AAATGGATCC ACCGGTCGCC ACCATGGTGA GCAAGGGCGA GGAGCTGTTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACCGGGGTGG TGCCCATCCT GGTCGAGCTG GACGGCGACG TAAACGGCCA CAAGTTCAGC GTGTCCGGCG AGGGCGAGGG CGATGCCACC TACGGCAAGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGACCCTGAA GTTCATCTGC ACCACCGGCA AGCTGCCCGT GCCCTGGCCC ACCCTCGTGA CCACCCTGAC CTACGGCGTG CAGTGCTTCA GCCGCTACCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGACCACATG AAGCAGCACG ACTTCTTCAA GTCCGCCATG CCCGAAGGCT ACGTCCAGGA GCGCACCATC TTCTTCAAGG ACGACGGCAA CTACAAGACC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGCGCCGAGG TGAAGTTCGA GGGCGACACC CTGGTGAACC GCATCGAGCT GAAGGGCATC GACTTCAAGG AGGACGGCAA CATCCTGGGG CACAAGCTGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGTACAACTA CAACAGCCAC AACGTCTATA TCATGGCCGA CAAGCAGAAG AACGGCATCA AGGTGAACTT CAAGATCCGC CACAACATCG AGGACGGCAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGTGCAGCTC GCCGACCACT ACCAGCAGAA CACCCCCATC GGCGACGGCC CCGTGCTGCT GCCCGACAAC CACTACCTGA GCACCCAGTC CGCCCTGAGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAAGACCCCA ACGAGAAGCG CGATCACATG GTCCTGCTGG AGTTCGTGAC CGCCGCCGGG ATCACTCTCG GCATGGACGA GCTGTACAAG TAAAGCGGCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCGACTCTAG ATCATAATCA GCCATACCAC ATTTGTAGAG GTTTTACTTG CTTTAAAAAA CCTCCCACAC CTCCCCCTGA ACCTGAAACA TAAAATGAAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCAATTGTTG TTGTTAACTT GTTTATTGCA GCTTATAATG GTTACAaata aagcaatagc atcacaaatt tcacaaataa agca
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pCAT-NDST4L-delta100-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 GCTTGAAAAG ACCGACTCCA GCTAAGCAAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGGCACAGCA GCAGTGGCAG AAGCAGACAG GAGCAGCTGG TATTCCGGTG ATTAAATAGT TCTCATAGCC TTTTTGCTGT ACCCGGTCTG CTCCCTGGGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TAAGGcTCGT GTCCGAGAAG GAAGCTGCAT TTTAACGGTG TGCTGAACAG AGGTCTGAAT CATTCCAGCT GGCTGCTTGT TTTGAAAAGG ACAATGTGTG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TATAAATAAA AAGACTGCTG GAAGGGTCCA GACACCGGCA CCGGAGCTGA GGAGTGCTCT CAGAATCCTG TTGAGGCAGA TGGCACGAAC TGAAAGCTCC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCTAATTAAC GTGGAGCCAA GTAAACCTGA ATTCTGGATA TCTCATTTTC TAACTTCGGA TAAATTCAAG TTAGCAAAAG AAAAAAAAAT TGAAATGCTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCTAGATAA TGCTTAAAGG ACCCTGCAGC AGTTCTTGGT ATTGGACATA GCATCTCAGC TGTTGCCTCC TGGTCCGTTG ACTACCAGAT TTGACTCATT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGTGATTCCT TCGAGAATCT CCCATGATTT GCAAATGGAT CCACCGGTCG CCACCATGGT GAGCAAGGGC GAGGAGCTGT TCACCGGGGT GGTGCCCATC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTGGTCGAGC TGGACGGCGA CGTAAACGGC CACAAGTTCA GCGTGTCCGG CGAGGGCGAG GGCGATGCCA CCTACGGCAA GCTGACCCTG AAGTTCATCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCACCACCGG CAAGCTGCCC GTGCCCTGGC CCACCCTCGT GACCACCCTG ACCTACGGCG TGCAGTGCTT CAGCCGCTAC CCCGACCACA TGAAGCAGCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGACTTCTTC AAGTCCGCCA TGCCCGAAGG CTACGTCCAG GAGCGCACCA TCTTCTTCAA GGACGACGGC AACTACAAGA CCCGCGCCGA GGTGAAGTTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAGGGCGACA CCCTGGTGAA CCGCATCGAG CTGAAGGGCA TCGACTTCAA GGAGGACGGC AACATCCTGG GGCACAAGCT GGAGTACAAC TACAACAGCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACAACGTCTA TATCATGGCC GACAAGCAGA AGAACGGCAT CAAGGTGAAC TTCAAGATCC GCCACAACAT CGAGGACGGC AGCGTGCAGC TCGCCGACCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTACCAGCAG AACACCCCCA TCGGCGACGG CCCCGTGCTG CTGCCCGACA ACCACTACCT GAGCACCCAG TCCGCCCTGA GCAAAGACCC CAACGAGAAG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGCGATCACA TGGTCCTGCT GGAGTTCGTG ACCGCCGCCG GGATCACTCT CGGCATGGAC GAGCTGTACA AGTAAAGCGG CCGCGACTCT AGATCATAAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAGCCATACC ACATTTGTAG AGGTTTTACT TGCTTTAAAA AACCTCCCAC ACCTCCCCCT GAACCTGAAA CATAAAATGA ATGCAATTGT TGTTGTTAAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTGTTTATTG CAGCTTATAA TGGTTACAaa taaagcaata gcatcacaaa tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

aactcatcaa tgtatcttaa ggcgtaaatt gtaagcgtta atattttgtt aaaattcgcg ttaaattttt gttaaatcag ctcatttttt aaccaatagg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ccgaaatcgg caaaatccct tataaatcaa aagaatagac cgagataggg ttgagtgttg ttccagtttg gaacaagagt ccactattaa agaacgtgga 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ctccaacgtc aaagggcgaa aaaccgtcta tcagggcgat ggcccactac gtgaaccatc accctaatca agttttttgg ggtcgaggtg ccgtaaagca 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ctaaatcgga accctaaagg gagcccccga tttagagctt gacggggaaa gccggcgaac gtggcgagaa aggaagggaa gaaagcgaaa ggagcgggcg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ctagggcgct ggcaagtgta gcggtcacgc tgcgcgtaac caccacaccc gccgcgctta atgcgccgct acagggcgcg tcaggtggca cttttcgggg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

aaatgtgcgc ggaaccccta tttgtttatt tttctaaata cattcaaata tgtatccgct catgagacaa taaccctgat aaatgcttca ataatattga 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

aaaaggaaga gtcctgaggc ggaaagaacc agctgtggaa tgtgtgtcag ttagggtgtg gaaagtcccc aggctcccca gcaggcagaa gtatgcaaag 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

catgcatctc aattagtcag caaccaggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccata 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gtcccgcccc taactccgcc catcccgccc ctaactccgc ccagttccgc ccattctccg ccccatggct gactaatttt ttttatttat gcagaggccg 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

aggccgcctc ggcctctgag ctattccaga agtagtgagg aggctttttt ggaggcctag gcttttgcaa agatcgatca agagacagga tgaggatcgt 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ttcgcatgat tgaacaagat ggattgcacg caggttctcc ggccgcttgg gtggagaggc tattcggcta tgactgggca caacagacaa tcggctgctc 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

tgatgccgcc gtgttccggc tgtcagcgca ggggcgcccg gttctttttg tcaagaccga cctgtccggt gccctgaatg aactgcaaga cgaggcagcg 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

cggctatcgt ggctggccac gacgggcgtt ccttgcgcag ctgtgctcga cgttgtcact gaagcgggaa gggactggct gctattgggc gaagtgccgg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ggcaggatct cctgtcatct caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg gctgcatacg cttgatccgg ctacctgccc 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

attcgaccac caagcgaaac atcgcatcga gcgagcacgt actcggatgg aagccggtct tgtcgatcag gatgatctgg acgaagagca tcaggggctc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

gcgccagccg aactgttcgc caggctcaag gcgagcatgc ccgacggcga ggatctcgtc gtgacccatg gcgatgcctg cttgccgaat atcatggtgg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

aaaatggccg cttttctgga ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc gttggctacc cgtgatattg ctgaagagct 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

tggcggcgaa tgggctgacc gcttcctcgt gctttacggt atcgccgctc ccgattcgca gcgcatcgcc ttctatcgcc ttcttgacga gttcttctga 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

gcgggactct ggggttcgaa atgaccgacc aagcgacgcc caacctgcca tcacgagatt tcgattccac cgccgccttc tatgaaaggt tgggcttcgg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

aatcgttttc cgggacgccg gctggatgat cctccagcgc ggggatctca tgctggagtt cttcgcccac cctaggggga ggctaactga aacacggaag 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

gagacaatac cggaaggaac ccgcgctatg acggcaataa aaagacagaa taaaacgcac ggtgttgggt cgtttgttca taaacgcggg gttcggtccc 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agggctggca ctctgtcgat accccaccga gaccccattg gggccaatac gcccgcgttt cttccttttc cccaccccac cccccaagtt cgggtgaagg 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

cccagggctc gcagccaacg tcggggcggc aggccctgcc atagcctcag gttactcata tatactttag attgatttaa aacttcattt ttaatttaaa 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

aggatctagg tgaagatcct ttttgataat ctcatgacca aaatccctta acgtgagttt tcgttccact gagcgtcaga ccccgtagaa aagatcaaag 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gatcttcttg agatcctttt tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc ggtggtttgt ttgccggatc aagagctacc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

aactcttttt ccgaaggtaa ctggcttcag cagagcgcag ataccaaata ctgtccttct agtgtagccg tagttaggcc accacttcaa gaactctgta 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

gcaccgccta catacctcgc tctgctaatc ctgttaccag tggctgctgc cagtggcgat aagtcgtgtc ttaccgggtt ggactcaaga cgatagttac 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg agatacctac agcgtgagct 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

aacgcctggt atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ccagcaacgc ggccttttta cggttcctgg ccttttgctg gccttttgct cacatgttct ttcctgcgtt atcccctgat tctgtggata accgtattac 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

cgccatgcat
^6001

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:
enahnced 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):

1374-2093

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: `NDST4L-delta100`	The functional status of IRES: `defective`

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

793-1352

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: `623`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-581`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-22`

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

GAAAAGACCG ACTCCAGCTA AGCAAGAGGC ACAGCAGCAG TGGCAGAAGC AGACAGGAGC AGCTGGTATT CCGGTGATTA AATAGTTCTC ATAGCCTTTT 
^793       ^803       ^813       ^823       ^833       ^843       ^853       ^863       ^873       ^883       

TGCTGTACCC GGTCTGCTCC CTGGGGTAAG GcTCGTGTCC GAGAAGGAAG CTGCATTTTA ACGGTGTGCT GAACAGAGGT CTGAATCATT CCAGCTGGCT 
^893       ^903       ^913       ^923       ^933       ^943       ^953       ^963       ^973       ^983       

GCTTGTTTTG AAAAGGACAA TGTGTGTATA AATAAAAAGA CTGCTGGAAG GGTCCAGACA CCGGCACCGG AGCTGAGGAG TGCTCTCAGA ATCCTGTTGA 
^993       ^1003      ^1013      ^1023      ^1033      ^1043      ^1053      ^1063      ^1073      ^1083      

GGCAGATGGC ACGAACTGAA AGCTCCGCTA ATTAACGTGG AGCCAAGTAA ACCTGAATTC TGGATATCTC ATTTTCTAAC TTCGGATAAA TTCAAGTTAG 
^1093      ^1103      ^1113      ^1123      ^1133      ^1143      ^1153      ^1163      ^1173      ^1183      

CAAAAGAAAA AAAAATTGAA ATGCTTCTCT AGATAATGCT TAAAGGACCC TGCAGCAGTT CTTGGTATTG GACATAGCAT CTCAGCTGTT GCCTCCTGGT 
^1193      ^1203      ^1213      ^1223      ^1233      ^1243      ^1253      ^1263      ^1273      ^1283      

CCGTTGACTA CCAGATTTGA CTCATTTGTG ATTCCTTCGA GAATCTCCCA TGATTTGCAA
^1293      ^1303      ^1313      ^1323      ^1333      ^1343

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 336

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:

5.000

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