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:


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):


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
Last change to the database: 2015-04-16 16:45:23 GMT+1