IRESite_Id:65 summary record describing characteristics of Ubx

IRESite: The database of experimentally verified IRES structures

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:

acgttcgttc gatggcaacg gattggataa caggcgcgcg ctttgtttta ttatccacat tatcagctgc attattgtta ttattggccc tcagcgcttt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

accgctcgcc cacgcgtccg cccgtgaatg ccgcgcggaa aagtcgcttt ccactagatt ggcgtccaga ttcgaggaaa tccgtcagca gacgcattcg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cgcccgttcg gtcagcacta tggctaataa tcgttcaaat cgttaaaacc ataaaaataa taataataat tgcaataaca ataaacatag taataatcgt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

aacgcttacg agcctttgat agtgccaagg caagcgcaat ccaagtattc aaattcgaat tcaattaaca gcaaagtgca attggctaaa aaccgaaacc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aaaacgcaac aaagtatacg aaacacttgt gaaaccgtac aaacaattgt ggaaaaaaat ttaaagatta ttaagattga agtctcaata aacattagtg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cttaaataaa tttaaaacga cccgcgtgga gagtgcaata aaaagaataa cttttgaaat aaatatttac caaacagaaa aatattttat aaatatttaa 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ataagtgaaa aacaaattgg ttactctgaa acaaagaaaa ttcaaattgg tgctaaaaca aaggagaaaa aatttcaaga atattttaca aataataaga 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

catatttaac tatataaaac caaacttaat caacaaagac ttggagtgaa aatataaaat aaattttaaa aagagtttaa caaaatttgt ttaaatccaa 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

aggaggcaaa ggaacagcac agaaagcgag gaaacactca aataaaatcc gccaaaaatc gcagatccct ggaaaccaat tcgtgtgaaa tcggtcaagc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ccccaacgac ttttagcccg tctcagacgg agcaccgcca agattcttac cgccagcagc gcaatgaact cgtactttga acaggcctcc ggcttttatg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gccatccgca ccaggccacc ggaatggcaa tgggcagcgg tggccaccac gaccagacgg ccagtgcagc ggcggccgcg tacagaggat tccctctctc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gctgggcatg agtccctatg ccaaccacca tctgcagcgc accacccagg actcgcccta cgatgccagc atcacggccg cctgcaacaa gatatacggc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gatggagccg gagcctacaa acaggactgc ctgaacatca aggcggatgc ggtgaatggc tacaaagaca tttggaacac gggcggctcg aatggcggcg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ggggtggcgg cggaggcggt ggtggcggcg gagcgggcgg aacaggtgga gccggcaatg ccaatggcgg taatgcggcc aatgcaaacg gacagaacaa 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tccggcgggc ggtatgcccg ttagaccctc cgcctgcacc ccagattccc gagtgggcgg ctatttggac acgtcgggcg gcagtcccgt tagccatcgc 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ggcggcagtg ccggcggtaa tgtgagtgtc agcggcggca acggcaacgc cggaggcgta cagagcggcg tgggcgtggc cggagcgggc actgcctgga 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

atgccaattg caccatctcg ggcgccgctg cccaaacggc ggccgccagc agtttacacc aggccagcaa tcacacattc tacccctgga tggctatcgc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aggtaagata agatctgatt taacacaata cggcggcata tcaacagaca tgggtaagag atactcagaa tctcttgcgg gctcacttct accagactgg 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ctaggtacaa atggtctgcg aagacgcggc cgacagacat acacccgcta ccagacgctc gagctggaga aggagttcca cacgaatcat tatctgaccc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gcagacggag aatcgagatg gcgcacgcgc tatgcctgac ggagcggcag atcaagatct ggttccagaa ccggcgaatg aagctgaaga aggagatcca 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ggcgatcaag gagctgaacg aacaggagaa gcaggcgcag gcccagaagg cggcggcggc agcggctgcg gcggcggcgg tccaaggtgg acacttagat 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

cagtagatcc ttagatcctt agatccttag atccgtaggg tgtatgtggg attgggcgaa atgacgcgga gacagataca aagcaactat attgtaacaa 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

atgaactatt tacttaaatg aataatattt aaatattttg atggtacttg tgcgaatacg aaacttaacc taaatcgaac ctaatggaat tatttcaagc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gtttgagcag caaccgaaaa tacgtaaatg aaacaaaact acaaactaat taactaggct aagtaaataa aagtagtgga aggagcgcag attataaacc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tacttagaat taaatgagca aaacaaacaa ttttaattta gttccaaacg aaaaaaaaat tcaagaggat tcgctcgaaa tggaaacctc tgtcctgccc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ctttgttgct tactgctatg tttaaattaa tttcgcgaaa aatactcaaa aattgaaaca caaagaaaac aaaaaatgaa agtataccat tataatgttg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

aatgcgagca aaattctgtt gatatgaatt tttggtaaaa acatgttcta aaccaattta agatacgtaa cgaaggatgc aaaaacaaaa tgaaaactat 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

taaactttaa cttaaatata aatagaattt gttagccaag taaacatatt acgacacgaa gaacaaacgt tttcgggagt atcgaatatt tgaatgtgta 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

tagtttgtgc ttattaaata aaataatgca attttagtta actctgttta tttgtaaacg aatttgttta gttctcgccc aaacgactag agtgaagctg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tttctttaag taatgtgtag tgtgtttact ttttaaatta aattaatgcc taattttatt attattatgt ttagtttaat gacaagcgtt tatgagatta 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

tccgacagaa gcggcgagaa gaggagtgcg acaaaccgtt tgccccggca aacgcaaata aattattggt tttgaaaaaa tctaaagaaa acaaaaaaaa 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

aaaacaatga gaaatcg
^3101      ^3111

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):

acgttcgttc gatggcaacg gattggataa caggcgcgcg ctttgtttta ttatccacat tatcagctgc attattgtta ttattggccc tcagcgcttt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

accgctcgcc cacgcgtccg cccgtgaatg ccgcgcggaa aagtcgcttt ccactagatt ggcgtccaga ttcgaggaaa tccgtcagca gacgcattcg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cgcccgttcg gtcagcacta tggctaataa tcgttcaaat cgttaaaacc ataaaaataa taataataat tgcaataaca ataaacatag taataatcgt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

aacgcttacg agcctttgat agtgccaagg caagcgcaat ccaagtattc aaattcgaat tcaattaaca gcaaagtgca attggctaaa aaccgaaacc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aaaacgcaac aaagtatacg aaacacttgt gaaaccgtac aaacaattgt ggaaaaaaat ttaaagatta ttaagattga agtctcaata aacattagtg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cttaaataaa tttaaaacga cccgcgtgga gagtgcaata aaaagaataa cttttgaaat aaatatttac caaacagaaa aatattttat aaatatttaa 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ataagtgaaa aacaaattgg ttactctgaa acaaagaaaa ttcaaattgg tgctaaaaca aaggagaaaa aatttcaaga atattttaca aataataaga 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

catatttaac tatataaaac caaacttaat caacaaagac ttggagtgaa aatataaaat aaattttaaa aagagtttaa caaaatttgt ttaaatccaa 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

aggaggcaaa ggaacagcac agaaagcgag gaaacactca aataaaatcc gccaaaaatc gcagatccct ggaaaccaat tcgtgtgaaa tcggtcaagc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ccccaacgac ttttagcccg tctcagacgg agcaccgcca agattcttac cgccagcagc gcaatg
^901       ^911       ^921       ^931       ^941       ^951       ^961

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:

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):

aaagtgcaat tggctaaaaa ccgaaaccaa aacgcaacaa agtatacgaa acacttgtga aaccgtacaa acaattgtgg aaaaaaattt aaagattatt 
^373       ^383       ^393       ^403       ^413       ^423       ^433       ^443       ^453       ^463       

aagattgaag tctcaataaa cattagtgct taaataaatt taaaacgacc cgcgtggaga gtgcaataaa aagaataact tttgaaataa atatttacca 
^473       ^483       ^493       ^503       ^513       ^523       ^533       ^543       ^553       ^563       

aacagaaaaa tattttataa atatttaaat aagtgaaaaa caaattggtt actctgaaac aaagaaaatt caaattggtg ctaaaacaaa ggagaaaaaa 
^573       ^583       ^593       ^603       ^613       ^623       ^633       ^643       ^653       ^663       

tttcaagaat attttacaaa taataagaca tatttaacta tataaaacca aacttaatca acaaagactt ggagtgaaaa tataaaataa attttaaaaa 
^673       ^683       ^693       ^703       ^713       ^723       ^733       ^743       ^753       ^763       

gagtttaaca aaatttgttt aaatccaaag gaggcaaagg aacagcacag aaagcgagga aacactcaaa taaaatccgc caaaaatcgc agatccctgg 
^773       ^783       ^793       ^803       ^813       ^823       ^833       ^843       ^853       ^863       

aaaccaattc gtgtgaaatc ggtcaagccc ccaacgactt ttagcccgtc tcagacggag caccgccaag attcttaccg ccagcagcg
^873       ^883       ^893       ^903       ^913       ^923       ^933       ^943       ^953

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: 2019-03-18 09:32:49 GMT+1