The description of the protein encoded in this ORF: Mus musculus RNA-binding motif protein 3 mRNA
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): 721-1182
The whole 5'UTR was not tested for promoter activity. The only parts tested were:
- the 100nt long region containing the 22-nt IRES module (fragment III)
- the 22-nt module itself (-286 to -265, i.e. bases 435-456 in IRESite annotation)
and none of these contained promoter activity.
The Rbm3 5'leader sequence contains 13 uORF and none of them overlapped the Rbm3 coding sequence. Seven of the
uAUGs contain a purine at position -3 and might be therefore in good context to function as initiation codons.
Sequence comparisons of the Rbm3 5'leader identified several matches with different ESTs, which may indicate
that there are several alternatively spliced variations of the Rbm3 5'leader. Reporter mRNAs containing the
Rbm3 5'leader are translated relatively efficiently, the full length 5'leader has more IRES activity than
5'deleted fragments that contain fewer uORFs. One uORF overlaps the 22-nt IRES module and its translation
seems to mask an inhibitory activity.
Possible presence of a cryptic promoter was ruled out using promoter-less plasmid (Chappel et al., 2003 Fig.
Baranick et al. (2008) in Supplementary Figure 11 report that the sequence reported as Rbm3 IRES is a cloning
artifact and is actually a reverse-complementary sequence of Thoc1 mRNA. Moreover, they report aberrantly
GenBankId of the rRNA that interacts with this mRNA/+RNA: 53990
The name of the rRNA interacting with this mRNA/+RNA: 18S
The base range located on rRNA where this interaction occurs in 3'-5' direction. 819-808
The number of bases within that range which actually do interact. 9
The experimental validation of this interaction between mRNA and rRNA in these regions is available: no
The base range located on mRNA where this interaction occurs in 5'-3' direction. 439-448
IRES: 3' AAGACC-TTCTTCTTTAATATTT 5'
18S: 5' TT-TACTTTGAAAAAATTAGAGT 3'
The above schema represents the 22-nt IRES module and predicted interaction of nucleotides 439-448 of Rbm3
mRNA with bases 819-808 of 18S rRNA (GI:53990). 9 base-pairs are denoted by colons.
The 22nt IRES module ranging from 435-456 was tested to bind purified 40S ribosomal subunit and ribosomes, but
it was not tested yet whether the complementary sequence match contributes to the binding of ribosomes.
Several other complementary sequence matches between Rbm3 5'UTR and mouse 18S rRNA were also predicted (none
of these sequences overlap with the 22nt IRES module):
rRNA in 3'-5'direction mRNA in 5'-3'direction
All sequence matches listed above were predicted in-silico and none of them was experimentally tested.
The IRES absolute position (the range includes START and STOP codons or their equivalents): 435-456
How IRES boundaries were determined: experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):
IRES activity was studied in transiently transfected cells and also T7 bicistronic (capped) transcripts in C6
cell-free lysates. Integrity of the mRNAs was verified by Northern blot.
435-456 is a 22-nt IRES module, which functions as IRES when it is tested in isolation. This 22-nt IRES module
is part of a larger but not further described IRES, containing at least 9 cis-acting sequences. The whole IRES
appears within the 5'UTR of Rbm3 mRNA.
Experimentally tested were: the 22-nt IRES module, 5' and 3' IRES inhibitory sequences and IRES enhancer, all
spanning the region 424-493 nt on mRNA:
22-nt IRES module
^______uORF______^ ^ ^ ^ ^
424 441 464 473 480 493
5'inhibitor 3'enhancer 3'inhibitor
Baranick et al., 2008 and they postulate that most of the "IRES" activity observed so far was due to the
splice artifacts (Fig. 3D).
Interacting protein was not further described. RNP complexes were detected using mobility shift assay. The
22-nt IRES module, used as the probe was incubated with extracts from NIH-3T3, C6 and N2a cell lines. In the
N2a lysate two RNP complexes formed. Interactions were shown to be sequence specific.