IRESite_Id:268 characteristics of NDST2 IRES studied in pCAT-NDST2-eGFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `268`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-04-16 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:
our_best_guess

The mRNA/+RNA description:

Putative in vivo transcript of pCAT-NDST2-eGFP plasmid from CMV promoter up to 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 TTTGCCACCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGCGTGGAGG ACGGGGTCCA CCCTGGTGGG CTGAGCGCGA GGCCGGAGGG CTGGGAGGCT GCGGCTGGGC TGAGCACTGC GGAGGGCCGT CGGCTTATCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CAGGTCCCGG TCACGCAGCG GCCACGCTCG GGGAGCGCGC GGACCTGAGC GGGCACCACG AGCCGCAGCG CGCCGCCTCC CCCTGGTGGG AGCGGTACTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGGCCCGACT GCGGCGGAGC GTTCGCTCGG AGATGGCGGA GCCGCCGCGA CGCGGCCCGA GGCCCCGCGA GCAGGGAAGC CGGGCAGCCC CGGGACGCGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CAGGGCCCGG GGACAGCGGG GACGCCGCCC ACTCCACCGG GTATGAAGCT AAAATACAGT GGTTACAACA CAGGAGGTTG ACAGGCCTGA CCTTTGAATC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCAGTTCATC CACAAACGGA GCTTTGTAAT CTCGGATTGT AAGGGCCAAG CTTGTGGACT TTACTGACTT CTGATCTAAG AACCTCCACC AGGGCTGAGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GAGCTCAAGT TTCAGCCTGA GGCATGGGCC AGGAGGCCAT GGTGACCTGA GACCCGTGGA TTCTGTCCAG TACACCCTGT TGCTCCTTCT GCCTCCCCTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCCTGTATTG AAAGCGTTTG TGTTCATCTT ATCAGGGACC TGACCCTAAG AGAATCCTTc CCCTGCCAAG GCAGTTCCAG CCTcCAGAAC TCATCACCCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATCTCCTGAG GTGGTTCCTA TACTCCCTCT CTTCTCCTCG CCATGGATCC ACCGGTCGCC ACCATGGTGA GCAAGGGCGA GGAGCTGTTC ACCGGGGTGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGCCCATCCT GGTCGAGCTG GACGGCGACG TAAACGGCCA CAAGTTCAGC GTGTCCGGCG AGGGCGAGGG CGATGCCACC TACGGCAAGC TGACCCTGAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTTCATCTGC ACCACCGGCA AGCTGCCCGT GCCCTGGCCC ACCCTCGTGA CCACCCTGAC CTACGGCGTG CAGTGCTTCA GCCGCTACCC CGACCACATG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAGCAGCACG ACTTCTTCAA GTCCGCCATG CCCGAAGGCT ACGTCCAGGA GCGCACCATC TTCTTCAAGG ACGACGGCAA CTACAAGACC CGCGCCGAGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGAAGTTCGA GGGCGACACC CTGGTGAACC GCATCGAGCT GAAGGGCATC GACTTCAAGG AGGACGGCAA CATCCTGGGG CACAAGCTGG AGTACAACTA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CAACAGCCAC AACGTCTATA TCATGGCCGA CAAGCAGAAG AACGGCATCA AGGTGAACTT CAAGATCCGC CACAACATCG AGGACGGCAG CGTGCAGCTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCGACCACT ACCAGCAGAA CACCCCCATC GGCGACGGCC CCGTGCTGCT GCCCGACAAC CACTACCTGA GCACCCAGTC CGCCCTGAGC AAAGACCCCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACGAGAAGCG CGATCACATG GTCCTGCTGG AGTTCGTGAC CGCCGCCGGG ATCACTCTCG GCATGGACGA GCTGTACAAG TAAAGCGGCC GCGACTCTAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATCATAATCA GCCATACCAC ATTTGTAGAG GTTTTACTTG CTTTAAAAAA CCTCCCACAC CTCCCCCTGA ACCTGAAACA TAAAATGAAT GCAATTGTTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTGTTAACTT GTTTATTGCA GCTTATAATG GTTACAaata aagcaatagc atcacaaatt tcacaaataa agca
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pCAT-NDST2-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?):

no (not convincing)

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

no (not convincing)

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Cricetulus griseus CHO-K1 (ATCC CCL-61)

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 GCTTTGCCAC CCAGCGTGGA GGACGGGGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CACCCTGGTG GGCTGAGCGC GAGGCCGGAG GGCTGGGAGG CTGCGGCTGG GCTGAGCACT GCGGAGGGCC GTCGGCTTAT CCCAGGTCCC GGTCACGCAG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CGGCCACGCT CGGGGAGCGC GCGGACCTGA GCGGGCACCA CGAGCCGCAG CGCGCCGCCT CCCCCTGGTG GGAGCGGTAC TTGGGCCCGA CTGCGGCGGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCGTTCGCTC GGAGATGGCG GAGCCGCCGC GACGCGGCCC GAGGCCCCGC GAGCAGGGAA GCCGGGCAGC CCCGGGACGC GGCAGGGCCC GGGGACAGCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGGACGCCGC CCACTCCACC GGGTATGAAG CTAAAATACA GTGGTTACAA CACAGGAGGT TGACAGGCCT GACCTTTGAA TCCCAGTTCA TCCACAAACG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAGCTTTGTA ATCTCGGATT GTAAGGGCCA AGCTTGTGGA CTTTACTGAC TTCTGATCTA AGAACCTCCA CCAGGGCTGA GGGAGCTCAA GTTTCAGCCT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAGGCATGGG CCAGGAGGCC ATGGTGACCT GAGACCCGTG GATTCTGTCC AGTACACCCT GTTGCTCCTT CTGCCTCCCC TCTCCTGTAT TGAAAGCGTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGTGTTCATC TTATCAGGGA CCTGACCCTA AGAGAATCCT TcCCCTGCCA AGGCAGTTCC AGCCTcCAGA ACTCATCACC CCATCTCCTG AGGTGGTTCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TATACTCCCT CTCTTCTCCT CGCCATGGAT CCACCGGTCG CCACCATGGT GAGCAAGGGC GAGGAGCTGT TCACCGGGGT GGTGCCCATC CTGGTCGAGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGGACGGCGA CGTAAACGGC CACAAGTTCA GCGTGTCCGG CGAGGGCGAG GGCGATGCCA CCTACGGCAA GCTGACCCTG AAGTTCATCT GCACCACCGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAAGCTGCCC GTGCCCTGGC CCACCCTCGT GACCACCCTG ACCTACGGCG TGCAGTGCTT CAGCCGCTAC CCCGACCACA TGAAGCAGCA CGACTTCTTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGTCCGCCA TGCCCGAAGG CTACGTCCAG GAGCGCACCA TCTTCTTCAA GGACGACGGC AACTACAAGA CCCGCGCCGA GGTGAAGTTC GAGGGCGACA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCCTGGTGAA CCGCATCGAG CTGAAGGGCA TCGACTTCAA GGAGGACGGC AACATCCTGG GGCACAAGCT GGAGTACAAC TACAACAGCC ACAACGTCTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TATCATGGCC GACAAGCAGA AGAACGGCAT CAAGGTGAAC TTCAAGATCC GCCACAACAT CGAGGACGGC AGCGTGCAGC TCGCCGACCA CTACCAGCAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AACACCCCCA TCGGCGACGG CCCCGTGCTG CTGCCCGACA ACCACTACCT GAGCACCCAG TCCGCCCTGA GCAAAGACCC CAACGAGAAG CGCGATCACA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGGTCCTGCT GGAGTTCGTG ACCGCCGCCG GGATCACTCT CGGCATGGAC GAGCTGTACA AGTAAAGCGG CCGCGACTCT AGATCATAAT CAGCCATACC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ACATTTGTAG AGGTTTTACT TGCTTTAAAA AACCTCCCAC ACCTCCCCCT GAACCTGAAA CATAAAATGA ATGCAATTGT TGTTGTTAAC TTGTTTATTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAGCTTATAA TGGTTACAaa taaagcaata gcatcacaaa tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

tgtatcttaa ggcgtaaatt gtaagcgtta atattttgtt aaaattcgcg ttaaattttt gttaaatcag ctcatttttt aaccaatagg ccgaaatcgg 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

caaaatccct tataaatcaa aagaatagac cgagataggg ttgagtgttg ttccagtttg gaacaagagt ccactattaa agaacgtgga ctccaacgtc 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

aaagggcgaa aaaccgtcta tcagggcgat ggcccactac gtgaaccatc accctaatca agttttttgg ggtcgaggtg ccgtaaagca ctaaatcgga 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

accctaaagg gagcccccga tttagagctt gacggggaaa gccggcgaac gtggcgagaa aggaagggaa gaaagcgaaa ggagcgggcg ctagggcgct 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ggcaagtgta gcggtcacgc tgcgcgtaac caccacaccc gccgcgctta atgcgccgct acagggcgcg tcaggtggca cttttcgggg aaatgtgcgc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggaaccccta tttgtttatt tttctaaata cattcaaata tgtatccgct catgagacaa taaccctgat aaatgcttca ataatattga aaaaggaaga 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gtcctgaggc ggaaagaacc agctgtggaa tgtgtgtcag ttagggtgtg gaaagtcccc aggctcccca gcaggcagaa gtatgcaaag catgcatctc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

aattagtcag caaccaggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccata gtcccgcccc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

taactccgcc catcccgccc ctaactccgc ccagttccgc ccattctccg ccccatggct gactaatttt ttttatttat gcagaggccg aggccgcctc 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ggcctctgag ctattccaga agtagtgagg aggctttttt ggaggcctag gcttttgcaa agatcgatca agagacagga tgaggatcgt ttcgcatgat 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

tgaacaagat ggattgcacg caggttctcc ggccgcttgg gtggagaggc tattcggcta tgactgggca caacagacaa tcggctgctc tgatgccgcc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

gtgttccggc tgtcagcgca ggggcgcccg gttctttttg tcaagaccga cctgtccggt gccctgaatg aactgcaaga cgaggcagcg cggctatcgt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ggctggccac gacgggcgtt ccttgcgcag ctgtgctcga cgttgtcact gaagcgggaa gggactggct gctattgggc gaagtgccgg ggcaggatct 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

cctgtcatct caccttgctc ctgccgagaa agtatccatc atggctgatg caatgcggcg gctgcatacg cttgatccgg ctacctgccc attcgaccac 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

caagcgaaac atcgcatcga gcgagcacgt actcggatgg aagccggtct tgtcgatcag gatgatctgg acgaagagca tcaggggctc gcgccagccg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aactgttcgc caggctcaag gcgagcatgc ccgacggcga ggatctcgtc gtgacccatg gcgatgcctg cttgccgaat atcatggtgg aaaatggccg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

cttttctgga ttcatcgact gtggccggct gggtgtggcg gaccgctatc aggacatagc gttggctacc cgtgatattg ctgaagagct tggcggcgaa 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tgggctgacc gcttcctcgt gctttacggt atcgccgctc ccgattcgca gcgcatcgcc ttctatcgcc ttcttgacga gttcttctga gcgggactct 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ggggttcgaa atgaccgacc aagcgacgcc caacctgcca tcacgagatt tcgattccac cgccgccttc tatgaaaggt tgggcttcgg aatcgttttc 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cgggacgccg gctggatgat cctccagcgc ggggatctca tgctggagtt cttcgcccac cctaggggga ggctaactga aacacggaag gagacaatac 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

cggaaggaac ccgcgctatg acggcaataa aaagacagaa taaaacgcac ggtgttgggt cgtttgttca taaacgcggg gttcggtccc agggctggca 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ctctgtcgat accccaccga gaccccattg gggccaatac gcccgcgttt cttccttttc cccaccccac cccccaagtt cgggtgaagg cccagggctc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gcagccaacg tcggggcggc aggccctgcc atagcctcag gttactcata tatactttag attgatttaa aacttcattt ttaatttaaa aggatctagg 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tgaagatcct ttttgataat ctcatgacca aaatccctta acgtgagttt tcgttccact gagcgtcaga ccccgtagaa aagatcaaag gatcttcttg 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

agatcctttt tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc ggtggtttgt ttgccggatc aagagctacc aactcttttt 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ccgaaggtaa ctggcttcag cagagcgcag ataccaaata ctgtccttct agtgtagccg tagttaggcc accacttcaa gaactctgta gcaccgccta 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

catacctcgc tctgctaatc ctgttaccag tggctgctgc cagtggcgat aagtcgtgtc ttaccgggtt ggactcaaga cgatagttac cggataaggc 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta caccgaactg agatacctac agcgtgagct atgagaaagc 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca ggagagcgca cgagggagct tccaggggga aacgcctggt 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct cgtcaggggg gcggagccta tggaaaaacg ccagcaacgc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ggccttttta cggttcctgg ccttttgctg gccttttgct cacatgttct ttcctgcgtt atcccctgat tctgtggata accgtattac cgccatgcat
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191

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):

1564-2283

Remarks:

The NDST2 variant shares overlaps with the exon1 of NDST4L, which contains a promoter used to transcribe the
NDST4S variant. The promoter in NDST2 thus might have escaped detection.

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: `NDST2`	The functional status of IRES: `functional`

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

793-1545

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: `816`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-771`	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):

TGCCACCCAG CGTGGAGGAC GGGGTCCACC CTGGTGGGCT GAGCGCGAGG CCGGAGGGCT GGGAGGCTGC GGCTGGGCTG AGCACTGCGG AGGGCCGTCG 
^793       ^803       ^813       ^823       ^833       ^843       ^853       ^863       ^873       ^883       

GCTTATCCCA GGTCCCGGTC ACGCAGCGGC CACGCTCGGG GAGCGCGCGG ACCTGAGCGG GCACCACGAG CCGCAGCGCG CCGCCTCCCC CTGGTGGGAG 
^893       ^903       ^913       ^923       ^933       ^943       ^953       ^963       ^973       ^983       

CGGTACTTGG GCCCGACTGC GGCGGAGCGT TCGCTCGGAG ATGGCGGAGC CGCCGCGACG CGGCCCGAGG CCCCGCGAGC AGGGAAGCCG GGCAGCCCCG 
^993       ^1003      ^1013      ^1023      ^1033      ^1043      ^1053      ^1063      ^1073      ^1083      

GGACGCGGCA GGGCCCGGGG ACAGCGGGGA CGCCGCCCAC TCCACCGGGT ATGAAGCTAA AATACAGTGG TTACAACACA GGAGGTTGAC AGGCCTGACC 
^1093      ^1103      ^1113      ^1123      ^1133      ^1143      ^1153      ^1163      ^1173      ^1183      

TTTGAATCCC AGTTCATCCA CAAACGGAGC TTTGTAATCT CGGATTGTAA GGGCCAAGCT TGTGGACTTT ACTGACTTCT GATCTAAGAA CCTCCACCAG 
^1193      ^1203      ^1213      ^1223      ^1233      ^1243      ^1253      ^1263      ^1273      ^1283      

GGCTGAGGGA GCTCAAGTTT CAGCCTGAGG CATGGGCCAG GAGGCCATGG TGACCTGAGA CCCGTGGATT CTGTCCAGTA CACCCTGTTG CTCCTTCTGC 
^1293      ^1303      ^1313      ^1323      ^1333      ^1343      ^1353      ^1363      ^1373      ^1383      

CTCCCCTCTC CTGTATTGAA AGCGTTTGTG TTCATCTTAT CAGGGACCTG ACCCTAAGAG AATCCTTcCC CTGCCAAGGC AGTTCCAGCC TcCAGAACTC 
^1393      ^1403      ^1413      ^1423      ^1433      ^1443      ^1453      ^1463      ^1473      ^1483      

ATCACCCCAT CTCCTGAGGT GGTTCCTATA CTCCCTCTCT TCTCCTCGCC ATG
^1493      ^1503      ^1513      ^1523      ^1533      ^1543

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 341

Version: `1`	Last change: `2007-02-21 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:

Cercopithecus aethiops COS-7 (ATCC CRL-1651)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

57.400

Name of IRES used as the positive control:

NDST4L

Name of the plasmid used as the positive control. `pCAT-NDST4L-eGFP`
`IRESite Id` of the plasmid used as positive control. `265`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `753`

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. 3

Citations:

Translation results:

IRESite Translation Id: 342

Version: `0`
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:

84.000

Name of IRES used as the positive control:

NDST4L

Name of the plasmid used as the positive control. `pCAT-NDST4L-eGFP`
`IRESite Id` of the plasmid used as positive control. `265`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `753`

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. 3

Citations:

Translation results:

IRESite Translation Id: 343

Version: `1`	Last change: `2007-02-21 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:

Mus musculus Neuro-2a [N2a] (ATCC CCL-131)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

71.400

Name of IRES used as the positive control:

NDST4L

Name of the plasmid used as the positive control. `pCAT-NDST4L-eGFP`
`IRESite Id` of the plasmid used as positive control. `265`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `753`

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. 3

Citations:

Translation results:

IRESite Translation Id: 344

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens 293T (ATCC CRL-1573)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

45.000

Name of IRES used as the positive control:

NDST4L

Name of the plasmid used as the positive control. `pCAT-NDST4L-eGFP`
`IRESite Id` of the plasmid used as positive control. `265`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `753`

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. 3

Citations:

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