IRESite_Id:291 summary record describing characteristics of NDST4S IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `291`	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: `NDST4S`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
12000418

The mRNA/+RNA description:

Hypothetical mRNA sequence of NDST4S 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:

GGTCCAGACA CCGGCACCGG AGCTGAGGAG TGCTCTCAGA ATCCTGTTGA GGCAGATGGC ACGAACTGAA AGCTCCGCTA ATTAACGTGG AGCCAAGTAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ACCTGAATTC TGGATATCTC ATTTTCTAAC TTCGGATAAA TTCAAGTTAG CAAAAGAAAA AAAAATTGAA ATGCTTCTCT AGATAATGCT TAAAGGACCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCAGCAGTT CTTGGTATTG GACATAGCAT CTCAGCTGTT GCCTCCTGGT CCGTGACTAC CAGATTTGAC TCATTTGTGA TTCCTTCGAG AATCTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATTTGCAAT GGTTACATGA ATGTTTGGGA AGGAAAACTG GCAACATCTT AGTATATGTT CTCCATGGCA CATTAGGGAA AGAAGCCAGA AAAGGCTCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AACGCATTGA TTTTTAAAAT GAATCTTATT TTAAAGTTTC GAAGAAGCTT TCGAACACTG ATTGTTCTCT TAGCTACTTT TTGCTTGGTG AGCATCCTCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTTCTGCCTA CTTCCTGTAC TCTGGCTACA AACAGGAAAT GACACTTATT GAAACGACTG CAGAAGCAGA GTGTGCTGAC ATCAAAGACC TCCCTTATCG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTCTATAGAG CTGAGAACCA TCAAGCCTAT TGATACATCC AAAACTGACC CCACTGTCCT TCTCTTTGTA GAGAGCCAGT ATTCGCAACT TGGTCAAGAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATTATAGCAA TCTTGGAGTC CAGTCGGTTT CAATACCAGA TGGTCATTGC TCCAGGCAAG GGAGACATAC CACCTCTTAC CGATAGTGGC AAAGGGAAGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACACATTGAT TATTTATGAA AATATTCTGA AGTACGTCAG CATGGACTCA TGGAACCGGG AGCTTTTAGA AAAATACTGT ATAGAATACA GTGTTAGCAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AATTGGTTTT CATAAAGCCA ATGAGAACAG TTTACCAACT ACACAACTGA AAGGGTTTCC TTTGAACTTA TTCAATAACG TAGCTCTGAA GGACTGCTCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GTGAACCCCC AGTCTCCTCT GCTCCATATT ACCAAAGGCC CCAAAGTTGA AAAGGGACCT CTTCCTGGGG AAGACTGGAC AATTTTCCAA TATAACCATT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTACCTACCA GCCAGTGCTT TTAACTGAGT TACAGTCAGA AAAGTCCCTC TCTTTCTTGT CCAGCCAAAC ACTTTATGCG ACAATTATTC AGGACCTGGG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCTTCATGAC GGGATTCAGC GAGTTCTTTT TGGTAACAAC TTGAACTTTT GGTTGCACAA GCTCATTTTC ATAGACGCCA TCTCTTTCTT GTCGGGGAAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGGTTGACAC TGTCCTTGGA CAGGTACATC CTTGTGGACA TTGATGACAT ATTTGTGGGG AAGGAGGGCA CGAGAATGAA TGTCAAAGAT GTGAAGGCAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TACTAGAGAC TCAAAATTTA CTGCGCACTC AGGTTGCAAA TTTTACCTTC AACCTTGGAT TTTCAGGGAA GTTTTACCAC ACAGGAACCG AAGAAGAGGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGAAGGTGAC GACCTTCTGC TGAGGTCTGT GGATGAATTC TGGTGGTTTC CTCACATGTG GAGTCACATG CAGCCCCACC TCTTCCACAA TGAATCATCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTAGTTGAAC AGATGATTCT CAACAAAGAA TTTGCCCTGG AACATGGAAT TCCGATCAAC CTGGGCTACG CAGTGGCCCC ACATCACTCA GGGGTCTACC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAGTCCATAT TCAGTTGTAT GCAGCTTGGA AGAAAGTCTG GGGTATTCAG GTCACCAGCA CTGAAGAGTA CCCACATCTG AAACCTGCGC GGTACAGGAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GGGCTTCATT CATAATAGCA TCATGGTCCT CCCTCGACAG ACCTGTGGGC TGTTCACACA TACTATTTTC TACAAGGAGT ATCCAGGAGG ACCTCAAGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTGGATAAAA GTATCAAAGG AGGTGAACTC TTCCTCACAA TCCTTCTAAA TCCAATCAGC ATTTTCATGA CACATCTGTC TAACTATGGA AATGACCGCC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCGGCTTATA CACCTTTGTG AACTTGGCCA ACTTTGTGCA CAGCTGGACC AACTTGAAAC TGCAGACCCT GCCTCCAGTG CAACTGGCCC ACAAATACTT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGAGCTCTTC CCTGAGCAGA AAGACCCTCT CTGGCAGAAT CCATGCGACG ATAAACGACA CAAAGACATC TGGTCCAGGG AGAAAACCTG TGACCATTTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCGAAATTCC TTGTGATTGG GCCACAGAAG ACAGGAACAA CTGCACTTTA TTTATTTCTT CTAATGCACC CCTCCATCAT CAGCAATCTT CCTAGCCCCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAACCTTTGA AGAAGTTCAA TTTTTTAATG GCAACAACTA TCACAAGGGA ATTGAGTGGT ATATGGACTT TTTCCCCACT CCTTCCAACA TTACCAGTGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTCCTATTT GAAAAGAGTG CTAACTACTT CCACTCAGAA GAGGCTCCCA AGAGGGCTAC ATCTCTTGTT CCCAAAGCCA AGATCATTAC TATCCTCATA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GACCCCTCGG ACAGGGCATA TTCTTGGTAC CAGCACCAAC GATCTCATGA AGATCCAGCT GCCCTGAGGT TCAATTTCTA TGAAGTTATC ACAACAGGAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATTGGGCCCC TCCTGATTTA AAAACATTGC AGAGGAGATG TCTGGTGCCT GGGTGGTATG CAGTGCACAT AGAAAGATGG CTGGCCTACT TTTCTACTTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCAGTTGCTA ATTATTGATG GACAACAGCT GAGATCTGAC CCAGCTACTG TGATGGATGA AGTCCAGAAG TTTCTAGGAG TTACACCTCA TTATAATTAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCGGAAGCAC TAACGTTTGA TCCCCAGAAA GGATTTTGGT GTCAGCTACT AGAAGGAGGA AAAACCAAAT GCCTTGGGAA AAGCAAAGGC CGAAAATACC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CGCCCATGGA TTCAGAGTCC AGAACTTTCC TCTCCAGCTA CTACCGCGAC CACAACGTGG AACTCTCGAA GCTGCTGCAC AGGCTGGGGC AGCCTCTGCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTCGTGGCTG AGACAGGAGC TGCAGAAAGT GAGATAGCAC TGGAGA
^3001      ^3011      ^3021      ^3031      ^3041

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:
not tested The total number of notable open-reading frames (ORFs):
1

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
NDST4S

The description of the protein encoded in this ORF:
N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 4S (shorter) isoform

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):

419-3037

Remarks:

Hypothetical mRNA sequence of NDST4S assembled in silico by two-step multiple sequence alignment polished by
manual editing. First, EST sequences matching the cloned 5'-UTR region from brain and embryonic (and deposited
to GenBank under GI:21780283, 669bp) were aligned and resulting 5'-UTR region consensus sequence
partly overlapping to ORF region was created. The ORF overlapping sequence was used to find NDST4 protein
records, and their mRNA sequences were aligned to the consensus sequence created previously. The final
consensus sequence is this hypothetical mRNA. The NDST4S variant has shorter 5'-UTR region as it is
transcribed from a promoter P2 located in 5'-UTR of the NDST4L variant (Fig. 1) consisting of CAAT and TATA
boxes (5'-CAAT-GTGTG-TATAAAT-3'). Therefore, NDST4L sequence was trimmed from 5'-end to match the plasmid
pCAT-NDST4S-eGFP sequence provided by original author. Somehow, the resulting 5'-UTR is not 377 bp as
described in Fig. 1 (140bp+237bp for short variant) but is 418 bp instead.

For consensus sequence of 5'-UTR were used records GI# 26415164, 21780283 (the one published by Grobe et al.,
2002), 17092388, 27141716, 16482267, 32466133. For consensus sequence of ORF and 3'-UTR was used record
GI:12000418.

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: `NDST4S`

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

1-418

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GGTCCAGACA CCGGCACCGG AGCTGAGGAG TGCTCTCAGA ATCCTGTTGA GGCAGATGGC ACGAACTGAA AGCTCCGCTA ATTAACGTGG AGCCAAGTAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ACCTGAATTC TGGATATCTC ATTTTCTAAC TTCGGATAAA TTCAAGTTAG CAAAAGAAAA AAAAATTGAA ATGCTTCTCT AGATAATGCT TAAAGGACCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCAGCAGTT CTTGGTATTG GACATAGCAT CTCAGCTGTT GCCTCCTGGT CCGTGACTAC CAGATTTGAC TCATTTGTGA TTCCTTCGAG AATCTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATTTGCAAT GGTTACATGA ATGTTTGGGA AGGAAAACTG GCAACATCTT AGTATATGTT CTCCATGGCA CATTAGGGAA AGAAGCCAGA AAAGGCTCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AACGCATTGA TTTTTAAA
^401       ^411

Citations:

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