IRESite_Id:289 summary record describing characteristics of NDST3 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `289`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `nonexisting_chimera_of_GenBank_record_and_tested_IRES_fragment`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `NDST3`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
71043952

The mRNA/+RNA description:

Hypothetical mRNA sequence of NDST3 assembled in silico by two-step multiple sequence alignment of selected
GenBank EST and mRNA sequences.

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

GGTCCTGCCA GCCCCTCCCG CCCCACGCGC CTAGCCCACT CCGGCTCAGG AGCCGATGCT GGGGGAGGCG GCTGCAGCCG TGGCTCTGCA GCGAGAGCGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AGAGAAGCAG AGGACCAAGA GGCAGAATGC CGGCGCTCCA CCGCCCGAGA CTGTGTTTCC TGTGAGTCCA GATGTGTGAT CCAGATATGC TGCAATGGTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACATAAACTG TTGACTGAGA CTAGGAGCGT GCCTGAAACT CCATCCCTCC TCCTATTATT TTTTAATGGT GCTTCTACTG GAATAGTCAA CAAAGTGCAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCAACATGAG TTTTATCATG AAACCTCACA GACACTTTCA GAGAACACTG ATTCTGCTTG CCACCTTTTG TATGGTAAGC ATTATTATTT CTGCTTACTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCTGTACAGC GGCTACAAAC AGGAAAGTGA AGTCTCCGGG CGGGCTTCGG AAGTGGACTG TGGTGACCTC CAGCACATAC CATCCAGGCT GATGGAAGTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGGAGGACAA TGATTTCCGA TGCTTCAAGG ACAGACCCCA CAGTCCTGGT GTTTGTGGAG AGCCAGTACT CATCCCTTGG TCAAGACATC ATTATGATGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TAGAATCCAT CCGGTTCCAT TATCACACTG AAATCGCTCC TGGAAAAGGA GATCTTCCGG CACTTACAGA CAATGTGAAG GGCAAATATG TTCTCATTAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATATGAGAAT ATTCTAAAGT ATATAAACAT GGACTCTTGG AATAGAAGCC TTTTAGATAA ATACTGTATA GAGTATGGTG TGGGTATCAT TGGATTCCAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAAACCAGTG AGAAAAATCT ACAGAGCTTT CAGTTCAGGG GCTTCCCCTT TTCCATAAGT GGAAACCTGG CAGTAAAAGA TTGCTGTATT AATCCTCACT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCCCACTCCT TCGTGTGACC AAATCATCCA AGCTGGACAG AGGTTCTCTA CCTGGAACTG ACTGGACAGT TTTTCAGATT AACCACTCCA CCTACCAGCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGTAATATTT GCCAAAGTTA AGACTCCAGA AAACCTTTCT CCTCCCATCT CTAAACATGC ATTTTATGCC ACTATCATAC ACGACCTGGG GCTTCATGAC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGGATCCAGC GAGTTCTTTT TGGCAACAAC TTGAACTTCT GGCTACACAA GCTCATCTTC ATAGACGCCA TCTCCTTCTT GTCGGGGAAG AGGCTGACAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGTCCTTGGA CAGGTACATC CTTGTGGACA TTGACGACAT ATTTGTAGGG AAGGAGGGCA CAAGGATGAA CACCAATGAT GTGAAGGCCC TGCTTGACAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCAGAATCTT TTGCGCACAC AAATCACAAA TTTTACATTC AACCTTGGAT TTTCAGGGAA ATTTTATCAC ACAGGAACTG AAGAGGAAGA TGAAGGGGAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GATTGTCTGC TGGGTTCTGT GGACGAGTTC TGGTGGTTTC CTCACATGTG GAGTCACATG CAGCCCCACC TCTTCCACAA TGAGTCGTCT TTAATAGAGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGATGATTCT CAACAAAAAG TTTGCCTTAG AGCACGGCAT CCCTACCGAT ATGGGATATG CAGTGTCCCC TCACCATTCA GGTGTCTACC CTGTCCATGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCAGCTTTAT GAGGCCTGGA AGAAGGTTTG GAATATTAAA ATCACCAGCA CTGAAGAATA TCCACATCTG AAACCAGCTA GATATCGGAG AGGCTTCATT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CACAAAAACA TCATGGTTCT CCCAAGACAA ACCTGTGGGC TCTTCACCCA CACAATTTTC TACAAGGAGT ATCCAGGGGG TCCCAGGGAA CTGGACAAGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTATTCATGG AGGGGAGCTC TTCTTCACTG TGGTTCTCAA CCCAATCAGT ATTTTCATGA CCCATTTGTC TAACTATGGA AACGACCGAC TGGGATTATA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACATTTGTG AATCTAGCCA ATTTTGTGCA GACCTGGACC AACCTGCGTC TTCAGACCTT GCCTCCAGCT CAGCTGGCTC ACAAGTATTT TGAGCTCTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCTGATCAGA AAGACCCTCT CTGGCAGAAC CCCTGTGATG ACAAACGCCA CAGAGACATT TGGTCTAAAG AGAAAACCTG CGATCGTTTA CCAAAATTCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGGTAATAGG ACCCCAGAAA ACTGGTACCA CTGCCTTGTG TCTGTTCCTG ATTATGCATC CTTCCATCCT TAGTAACTCC CCCAGCCCAA AATCCTTTGA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGAGGTACAG TTCTTTAATA GAAATAACTA CCACAGGGGG ATTGATTGGT ACATGGATTT CTTCCCAGTC CCATCTAATG TCACCACTGA CTTTCTGTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAGAAGAGTG CTAATTACTT CCATTCAGAG GACGCTCCCA AGAGGGCTGC TTCTCTAGTC CCGAAAGCCA AAATCATCAC CATACTCATT GACCCGTCAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACCGAGCGTA CTCCTGGTAT CAGCATCAGC GATCCCATGA AGACCCTGCA GCTCTGAAAT TTAGCTTCTA TGAAGTGATC TCTGCTGGGC CCAATGCACC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTGGGAACTC CGAACCCTGC AGAAGAGATG CCTGGTCCCT GGGTGGTATG CCAACCACAT CGAGAGATGG CTTGTTTATT TCCCTCCATT TCAGTTGCTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATCATTGATG GACAGCAGCT AAGAACTACC CCTGCGACAG TGATGGATGA AGTCCAGAAG TTTCTAGGAG TCTCACCTCA TTATAATTAC TCCGAAGCTT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TAACGTTTGA TTCTCATAAA GGCTTCTGGT GTCAGCTGCT GGAAGAAGGG AAAACAAAAT GCCTTGGGAA GAGTAAAGGA AGAAAATACC CCCCGATGGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTCTGATAGC AGAGCGTTTC TGTCCAGCTA CTACCGCGAC CACAACGTGG AGCTCTCGAA GCTGCTGCAC AGGCTGGGGC AGCCTCTGCC CTCCTGGCTG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGACAGGAGC TGCAGAAAGT GAGGTAGCAT GGAGAAAAGA AGCAGACCTC ATCTAGAGCT CACAGACGAC ACTACCAAAA AGCTGTGGAA CACATACCTC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGCATCACAG AAAACGAGCA AGGCTCTTCC ATGTGCTGGC ATGTGGATGA TTGTGGAGGG TCAGGCATAA AATATATATA TATCTTTAAG AAGCTTCCAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCCTATGGCC TTCCTCTTAA CCCTTATCTG ATTTGTGTGG AACAGCAACC AACATAAATT TTAAAACAAA ACAGAAAACA GAAACACTGA CGCAGTCCTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TACCATTTCA TAGTAATATT TACAATTTTG TATATTTCGG CTACAGTTGT TATTTCTGTA GATTTCTGGA CCACTATTTG ACTGTAAAAA TGTTTTCTGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTCGATTCTG TGAAGTAGCC TATAAACATC ACGATGGAGA ATTACAAGTG TCGGAAAATG CTGCCAGCAT AGGCCATGGC TGTGTGAGAG CAGGGTCGGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAGCAATCTG TGGACTTTGT CTCCAAACAG GGAAGCAAAG GGGGTGGTTC TCCTTGTACA TAGTCCAGCG AGCTCGTGCT GATGTAGCTC TGTATTGTAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACTTGGCAGA CAGCAAACAG TAACACATCC TTACATCAAA ATACTGAACA TTAATGGCAG AGTATTGACT AAATCCTCTG AGAAAGAGAA CTGGTGAACT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCTAAAGATA CGCCATACAG ATACATAAAA ATACACTGAG AACTCTTTGC TTTCTGATGT AAGCTGCCGG TCTATTCTGG CCACCTCCAG TTGCACCGAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ATGCATGTGG AGCCTGCAGG AAGTATTCTC TCTGAGTCAG AGTGACCTTT AAATTTGCAG AGCAGAGACT GGAGAAATGG CTCCACAGTG GGGGGCACTG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACTCTTCTTC TAGAGGACTC AGGTTTAAAT CCCAGCACCC ACATGGCAGC TCACAACTGC CTGTATCTCC CAAGATCTGA CACTCTCACA TAGACAAACA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TACAGGCAAA ACACCAATGC ACATAAAATA AAGGTTAAAA AATTAATTTA AAGTCCTCAT AAATGAGCAG AGCAGCTGCT GAACAAACTT ATTAACTGGA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AACTAAGGAC AGTTCCTTGA GCTGCTTAAA GTACTCAGAT TTAAATTATT GCAAAACTGT GTTTTTCCAG GTAATCCCAA AGCAAACTGT GTAATATACA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGCTTGTGGG ACAATGGACT CATATACAAA TTTTCATCTA ATATATAAAA CGATGGTTGT GCTTCGAGGT GGAACAAGCA GGTGAAGTAC CATGATGGAG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GATACCTCGC ATATTGCCCA CATCTTTGCC CAACAACAGA ACATTGCCAA CTGTATGAAC TACCTACGAT AAGAATCACA GGGAGTACAA AGATGAGCAT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGCTCAGGAA ATATATCTAA TTTAAATTAG ACACGTGATG AGTGAAGGAT TCGAAACAAG AGTACGGGAG ATCACACTTT CCTGTGTTAG TATAGACTTA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ATCTTGTATT GTGATTGACC CATATGTAAA CATAAGGAGA ATGTTCCTCG CTGTGACTGC ACACAATTCT AGAAAGTATT CTATAAGGTG TGTTTAGAGA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CACAATATGC CACAAAACCA AAGGCCTGAA TACGTCTATC TGTCATTTCA GTGCACAAAA CGGTACTCTT GCAGCTATTT GCCAGTTTAA AAAACAAAAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CAAAAAAGAA TGAAGCACCC CCACTCGCGC TGCTTAATTC CTTACATCCT TATTCCCACA ATTACCAGTT TCTCTAAAGT TTTTCCATCT TTTATGAACT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CAAAGAATAC AGTGACTTTT TTTTAAAGCA CATACCGGAA AGAGTTGGCT AAACAACCAA ATTTTAAGAG CCCTGATTGA GAGGCCAAAT CAAAATACAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TGAAAGGACT CTTCCCTCCT AACCGCTGCC ACTTTGGCAG TGACACCTGC CATGCCCAGC GGGGAAATCA CCCCTCACAT CCACGTCCAT TAATTTAAGA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AAATTGGCTC AAGGGGTCAT AAGACCCAGC GCTCCAGCTG TTACAGTCTC ACTGGTGACA GTGTGTCAGC TCAGGAAATA AGCTGACATA CATCTCCACA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTTGAACCTC TGTAGATAAA TTGGCTACTG ACATCCTTTA ATGTAGGGAG ACAGTGCCTG TAAAATAAAT GGCAAAAAAT AGCACTTATA ATGAATCAGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AAAAAAAGAG AGAGAAACGG TATTCCGACC TGCTCATTCC CAAGTCCATG TCAGATGCCG TGTAGACCAG CAGCCCTTTC AAAGGGTTTT GACCACTGGG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CGTGTCAAAG AGGCAGCTCC CAATTCAGGA GGGCAACCAC ACATCTCACA CTGTGAGCTC CAGCTGGCCA TTATGCTACC CTGAAATCGA CAGAAGTCCA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GGAGAAAAGA ATGGGAGAGA ACATGATTCC AAACTAGCTT TGTATAGAAT TCCCTTTTTC CTGACTTATA ATACGGGGCT TCCTCAGGAA GAAATGAAAT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GGTTATTTCA ATGTTTATAG CTATAATATT CTTGTCATTC ACATTGAATG AAAACTACTG GGAACATTTT TTTCTCTGGG TTTTTTAAAA GGAAAACAAA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AAACCCCTCT ATATAATTCT AAAAGTGGCA TGATACCTCA TATGTATAAC AATAAACTGG T
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The organism containing this mRNA with IRES segment in its genome:

Mus musculus C57BL/6

A promoter reported in cDNA corresponding to IRES sequence:
no (not convincing) The total number of notable open-reading frames (ORFs):
1

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:
unclear_result

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)

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:
NDST3

The description of the protein encoded in this ORF:
N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3

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):

306-2927

Remarks:

Hypothetical mRNA sequence of NDST1 assembled in silico by two-step multiple sequence alignment polished by
manual editing. First, EST sequences matching the cloned 5'-UTR region from mouse skin, brain and testis (and
deposited to GenBank under GI:21780279, 418bp) were aligned and resulting 5'-UTR region consensus sequence
partly overlapping to ORF region was created. The ORF overlapping sequence was used to find NDST1 protein
records, and their mRNA sequences were aligned to the consensus sequence created previously. The final
consensus sequence is this hypothetical mRNA. Please note several EST were longer at the 5'-end while having
different alignment in largers blocks (could be different exons). Therefore, the actually cloned sequence by
Grobe was only extended at the 5'-end using the sequence from highly similar sequences.

For consensus sequence of 5'-UTR were used records GI#  16490862, 11492647, 21780282 (the one published by
Grobe et al., 2002), 16484896, 16464127. For consensus sequence of ORF and 3'-UTR were used records GI#
71043952, 50927496, 12854230.

The sequence deposited in IRESite is the final consensus sequence but was trimmed at the 3'-end from poly(A)
sequence.

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: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NDST3`

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

59-305

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

CTGGGGGAGG CGGCTGCAGC CGTGGCTCTG CAGCGAGAGC GCAGAGAAGC AGAGGACCAA GAGGCAGAAT GCCGGCGCTC CACCGCCCGA GACTGTGTTT 
^59        ^69        ^79        ^89        ^99        ^109       ^119       ^129       ^139       ^149       

CCTGTGAGTC CAGATGTGTG ATCCAGATAT GCTGCAATGG TGACATAAAC TGTTGACTGA GACTAGGAGC GTGCCTGAAA CTCCATCCCT CCTCCTATTA 
^159       ^169       ^179       ^189       ^199       ^209       ^219       ^229       ^239       ^249       

TTTTTTAATG GTGCTTCTAC TGGAATAGTC AACAAAGTGC ACCCAAC
^259       ^269       ^279       ^289       ^299

Citations:

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