IRESite_Id:290 summary record describing characteristics of NDST4L IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `290`	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: `NDST4L`	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 NDST4L 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:

GAAAAGACCG ACTCCAGCTA AGCAAGAGGC ACAGCAGCAG TGGCAGAAGC AGACAGGAGC AGCTGGTATT CCGGTGATTA AATAGTTCTC ATAGCCTTTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCTGTACCC GGTCTGCTCC CTGGGGTAAG GCCTCGTGTC CGAGAAGGAA GCTGCATTTT AACGGTGTGC TGAACAGAGG TCTGAATCAT TCCAGCTGGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCTTGTTTT GAAAAGGACA ATGTGTGTAT AAATAAAAAG ACTGCTGGAA GGGTCCAGAC ACCGGCACCG GAGCTGAGGA GTGCTCTCAG AATCCTGTTG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGGCAGATGG CACGAACTGA AAGCTCCGCT AATTAACGTG GAGCCAAGTA AACCTGAATT CTGGATATCT CATTTTCTAA CTTCGGATAA ATTCAAGTTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCAAAAGAAA AAAAAATTGA AATGCTTCTC TAGATAATGC TTAAAGGACC CTGCAGCAGT TCTTGGTATT GGACATAGCA TCTCAGCTGT TGCCTCCTGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCCGTGACTA CCAGATTTGA CTCATTTGTG ATTCCTTCGA GAATCTCCCA TGATTTGCAA TGGTTACATG AATGTTTGGG AAGGAAAACT GGCAACATCT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TAGTATATGT TCTCCATGGC ACATTAGGGA AAGAAGCCAG AAAAGGCTCC CAACGCATTG ATTTTTAAAA TGAATCTTAT TTTAAAGTTT CGAAGAAGCT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTCGAACACT GATTGTTCTC TTAGCTACTT TTTGCTTGGT GAGCATCCTC ATTTCTGCCT ACTTCCTGTA CTCTGGCTAC AAACAGGAAA TGACACTTAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGAAACGACT GCAGAAGCAG AGTGTGCTGA CATCAAAGAC CTCCCTTATC GGTCTATAGA GCTGAGAACC ATCAAGCCTA TTGATACATC CAAAACTGAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCCACTGTCC TTCTCTTTGT AGAGAGCCAG TATTCGCAAC TTGGTCAAGA TATTATAGCA ATCTTGGAGT CCAGTCGGTT TCAATACCAG ATGGTCATTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTCCAGGCAA GGGAGACATA CCACCTCTTA CCGATAGTGG CAAAGGGAAG TACACATTGA TTATTTATGA AAATATTCTG AAGTACGTCA GCATGGACTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATGGAACCGG GAGCTTTTAG AAAAATACTG TATAGAATAC AGTGTTAGCA TAATTGGTTT TCATAAAGCC AATGAGAACA GTTTACCAAC TACACAACTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AAAGGGTTTC CTTTGAACTT ATTCAATAAC GTAGCTCTGA AGGACTGCTC TGTGAACCCC CAGTCTCCTC TGCTCCATAT TACCAAAGGC CCCAAAGTTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAAAGGGACC TCTTCCTGGG GAAGACTGGA CAATTTTCCA ATATAACCAT TCTACCTACC AGCCAGTGCT TTTAACTGAG TTACAGTCAG AAAAGTCCCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTCTTTCTTG TCCAGCCAAA CACTTTATGC GACAATTATT CAGGACCTGG GGCTTCATGA CGGGATTCAG CGAGTTCTTT TTGGTAACAA CTTGAACTTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGGTTGCACA AGCTCATTTT CATAGACGCC ATCTCTTTCT TGTCGGGGAA GAGGTTGACA CTGTCCTTGG ACAGGTACAT CCTTGTGGAC ATTGATGACA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TATTTGTGGG GAAGGAGGGC ACGAGAATGA ATGTCAAAGA TGTGAAGGCA TTACTAGAGA CTCAAAATTT ACTGCGCACT CAGGTTGCAA ATTTTACCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAACCTTGGA TTTTCAGGGA AGTTTTACCA CACAGGAACC GAAGAAGAGG ATGAAGGTGA CGACCTTCTG CTGAGGTCTG TGGATGAATT CTGGTGGTTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCTCACATGT GGAGTCACAT GCAGCCCCAC CTCTTCCACA ATGAATCATC TTTAGTTGAA CAGATGATTC TCAACAAAGA ATTTGCCCTG GAACATGGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTCCGATCAA CCTGGGCTAC GCAGTGGCCC CACATCACTC AGGGGTCTAC CCAGTCCATA TTCAGTTGTA TGCAGCTTGG AAGAAAGTCT GGGGTATTCA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGTCACCAGC ACTGAAGAGT ACCCACATCT GAAACCTGCG CGGTACAGGA AGGGCTTCAT TCATAATAGC ATCATGGTCC TCCCTCGACA GACCTGTGGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTGTTCACAC ATACTATTTT CTACAAGGAG TATCCAGGAG GACCTCAAGA ATTGGATAAA AGTATCAAAG GAGGTGAACT CTTCCTCACA ATCCTTCTAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATCCAATCAG CATTTTCATG ACACATCTGT CTAACTATGG AAATGACCGC CTCGGCTTAT ACACCTTTGT GAACTTGGCC AACTTTGTGC ACAGCTGGAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAACTTGAAA CTGCAGACCC TGCCTCCAGT GCAACTGGCC CACAAATACT TCGAGCTCTT CCCTGAGCAG AAAGACCCTC TCTGGCAGAA TCCATGCGAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GATAAACGAC ACAAAGACAT CTGGTCCAGG GAGAAAACCT GTGACCATTT ACCGAAATTC CTTGTGATTG GGCCACAGAA GACAGGAACA ACTGCACTTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATTTATTTCT TCTAATGCAC CCCTCCATCA TCAGCAATCT TCCTAGCCCC AAAACCTTTG AAGAAGTTCA ATTTTTTAAT GGCAACAACT ATCACAAGGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AATTGAGTGG TATATGGACT TTTTCCCCAC TCCTTCCAAC ATTACCAGTG ATTTCCTATT TGAAAAGAGT GCTAACTACT TCCACTCAGA AGAGGCTCCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGAGGGCTA CATCTCTTGT TCCCAAAGCC AAGATCATTA CTATCCTCAT AGACCCCTCG GACAGGGCAT ATTCTTGGTA CCAGCACCAA CGATCTCATG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AAGATCCAGC TGCCCTGAGG TTCAATTTCT ATGAAGTTAT CACAACAGGA CATTGGGCCC CTCCTGATTT AAAAACATTG CAGAGGAGAT GTCTGGTGCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGGGTGGTAT GCAGTGCACA TAGAAAGATG GCTGGCCTAC TTTTCTACTT CCCAGTTGCT AATTATTGAT GGACAACAGC TGAGATCTGA CCCAGCTACT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GTGATGGATG AAGTCCAGAA GTTTCTAGGA GTTACACCTC ATTATAATTA CTCGGAAGCA CTAACGTTTG ATCCCCAGAA AGGATTTTGG TGTCAGCTAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TAGAAGGAGG AAAAACCAAA TGCCTTGGGA AAAGCAAAGG CCGAAAATAC CCGCCCATGG ATTCAGAGTC CAGAACTTTC CTCTCCAGCT ACTACCGCGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCACAACGTG GAACTCTCGA AGCTGCTGCA CAGGCTGGGG CAGCCTCTGC CCTCGTGGCT GAGACAGGAG CTGCAGAAAG TGAGATAGCA CTGGAGA
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291

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:
yes 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:
heterogeneous_population_of_molecules_found

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:
NDST4L

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

670-3288

Remarks:

Hypothetical mRNA sequence of NDST4L 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 this NDST4L variant (Fig. 1) consisting of CAAT and TATA
boxes (5'-CAAT-GTGTG-TATAAAT-3').

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: `NDST4L`

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

1-672

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GAAAAGACCG ACTCCAGCTA AGCAAGAGGC ACAGCAGCAG TGGCAGAAGC AGACAGGAGC AGCTGGTATT CCGGTGATTA AATAGTTCTC ATAGCCTTTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCTGTACCC GGTCTGCTCC CTGGGGTAAG GCCTCGTGTC CGAGAAGGAA GCTGCATTTT AACGGTGTGC TGAACAGAGG TCTGAATCAT TCCAGCTGGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGCTTGTTTT GAAAAGGACA ATGTGTGTAT AAATAAAAAG ACTGCTGGAA GGGTCCAGAC ACCGGCACCG GAGCTGAGGA GTGCTCTCAG AATCCTGTTG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGGCAGATGG CACGAACTGA AAGCTCCGCT AATTAACGTG GAGCCAAGTA AACCTGAATT CTGGATATCT CATTTTCTAA CTTCGGATAA ATTCAAGTTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCAAAAGAAA AAAAAATTGA AATGCTTCTC TAGATAATGC TTAAAGGACC CTGCAGCAGT TCTTGGTATT GGACATAGCA TCTCAGCTGT TGCCTCCTGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCCGTGACTA CCAGATTTGA CTCATTTGTG ATTCCTTCGA GAATCTCCCA TGATTTGCAA TGGTTACATG AATGTTTGGG AAGGAAAACT GGCAACATCT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TAGTATATGT TCTCCATGGC ACATTAGGGA AAGAAGCCAG AAAAGGCTCC CAACGCATTG ATTTTTAAAA TG
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671

Citations:

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