The nucleic acid data:
IRESite Id: 65 Version: 7
Originaly submitted by: Petra Sekyrová Submission date: 2005-08-10 00:00:00
Reviewed by: Martin Mokrejš Last change: 2009-09-01 17:39:46
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  end-to-end_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  Ubx
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
33636522
Synonyms of the gene name:
Synonym: Hm
Synonym: bx
Synonym: Cbx
Synonym: UBx
Synonym: abx
Synonym: bxd
Synonym: bxl
Synonym: pbx
Synonym: BX-C
Synonym: DUbx
Synonym: DmUbx
Synonym: Ubx1b
Synonym: bx[D]
Synonym: bxd[D]
Synonym: CG10388
Synonym: bithorax
Synonym: l(3)89Eb
Synonym: Ultraabdom
Synonym: Ultrabithorax
The mRNA/+RNA description: 
Full-length mRNA of Ubx, 3.2kb splice variant. Poly(A)-tail sequence dropped.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The organism containing this mRNA with IRES segment in its genome:
Drosophila melanogaster
A promoter reported in cDNA corresponding to IRES sequence:
  no
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:
heterogeneous_population_of_molecules_found
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:
Drosophila melanogaster
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 4 Last change: 2007-09-07 00:00:00
Originaly submitted by: Petra Sekyrová Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
Ubx
The description of the protein encoded in this ORF:
ultrabithorax, a sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis. Binds the consensus region 5'-TTAAT[GT][GA]-3'. This homeotic protein controls development of the cells in the posterior thoracic and first abdominal segments. It activates the synthesis of the decapentaplegic (DPP) growth factor. (www.expasy.org)
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  964-2106
Remarks:
Three splice variants were known to Saari and Bienz (1987): 4.7kb, 4.3kb, 3.2kb. The promoter region sequenced
is deposited under GI:8794.

GI:24647526 corresponds to Ubx A isoform mRNA, 4.7kb mRNA. The +372 to +965 region of the 3.2kb transcript was
used by Ye et al. (1997) in IRES-oriented experiments and it corresponds to bases 3518-4110 of GI:8794.
Please note the region is A-rich and contains TATA regions. However, the two closely adjacent transcription
sites were found by S1 nuclease-based mapping and primer extension and the upper was defined as +1 (Saari and
Bienz, 1987). This mRNA sequence seems to arise from the 3nt downstream located +1 site. It has some sequence
mismatches in the region sequenced by Saari but overall identity is very good. But beware the numbering
compared to Hart and Bienz (1996) is shifted by 3 at the 5'-end.
Citations:
Ye X., Fong P., Iizuka N., Choate D., Cavener D. R. (1997) Ultrabithorax and Antennapedia 5' untranslated regions promote developmentally regulated internal translation initiation. Mol. Cell. Biol. 17(3):1714-1721
Saari G., Bienz M. (1987) The structure of the Ultrabithorax promoter of Drosophila melanogaster. EMBO. J. 6(6):1775-1779
Struhl G., Basler K. (1993) Organizing activity of wingless protein in Drosophila. Cell. 72(4):527-540
IRESs:
IRES:
Version: 12 Last change: 2009-09-01 17:39:46
Originaly submitted by: Petra Sekyrová Reviewed by: Martin Mokrejš
The IRES name:
  Ubx_1-966
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-966
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Ye et al. (1997) studied functionality first 970nt (not this transcript starts from the downstream
transcription start site located 3 bases downstream) of Ubx in Drosophila flies and stated:
However, the embryonic central nervous system and larval imaginal tissues, two major sites of UBX and ANTP
expression (8, 40), did not exhibit Antp and Ubx IRES activity in our assays despite high levels of
dicistronic mRNAs in these tissues. Further worrisome are the results showing that a minor transcript is
produced in flies from the empty vector as well as from its derivatives containing 5'-UTR of Ubx. In summary,
at least in some developmental stages IRES presence was NOT proved although mRNA was present. And, although
activity of the product of the first cistron was detected and correlated with presence of dicistronic mRNA,
the activity of the second cistron product was dependent upon the presence of Antp 5'-UTR and had complex
tissue-specific expression pattern.
Citations:
Ye X., Fong P., Iizuka N., Choate D., Cavener D. R. (1997) Ultrabithorax and Antennapedia 5' untranslated regions promote developmentally regulated internal translation initiation. Mol. Cell. Biol. 17(3):1714-1721
IRES:
Version: 8 Last change: 2007-09-07 00:00:00
Originaly submitted by: Petra Sekyrová Reviewed by: Martin Mokrejš
The IRES name:
  Ubx_373-961
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  373-961
Conclusion:
  weakly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
This region of Ubx 5'UTR has IRES activity in transgenic flies (larval imaginal discs and adult
wings). In transgenic flies (Drosophila) insertion of the retrotransposon was induced by crossing with line
expressing flp recombinase. Only cells expressing Ubx protein (1st cistron) and galactosidase (2nd cistron,
under the control of putative Ubx IRES placed in the intercistronic region) were detected microscopically.
Further, no neighbouring cells expressing only galactosidase were detected, confirming the Ubx IRES does not
get activated by Ubx expression from surrounding cells and that no promoter is present in the intercistronic
region. [Hart and Bienz, 1996]
Citations:
Hart K., Bienz M. (1996) A test for cell autonomy, based on di-cistronic messenger translation. Development. 122(3):747-751
Last change to the database: 2015-04-16 16:45:23 GMT+1