IRESite_Id:102 summary record describing characteristics of PDGF2/c-sis IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `102`	Version: `17`
Originaly submitted by: Martin Mokrejš	Submission date: `2005-12-20 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 13:40:48`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `only_IRES_fragment`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `PDGF2/c-sis`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
189727

Synonyms of the gene name:

Synonym: SIS

Synonym: SSV

Synonym: PDGF2

Synonym: c-sis

Synonym: PDGF-B

The mRNA/+RNA description:

Homo sapiens platelet-derived growth factor beta polypeptide, promoter with 5'-UTR and part of ORF. The
sequence does not match currently annotated PDGF sequences in GenBank (nonred) nor EST/RefSeq databases and
probably should not be called PDGF2/cSIS at all.

The mRNA/+RNA sequence represented in the +DNA notation:

GGTGGCAACT TCTCCTCCTG CAGCCGGGAG CGGCCTGCCT GCCTCCCTGC GCACCCGCAG CCTCCCCCGC TGCCTCCCTA GGGCTCCCCT CCGGCCGCCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGCCCATTT TTCATTCCCT AGATAGAGAT ACTTTGCGCG CACACACATA CATACGCGCG CAAAAAGGAA AAAAAAAAAA AAAAGCCCAC CCTCCAGCCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGCTGCAAAG AGAAAACCGG AGCAGCCGCA GCTCGCAGCT CGCAGCTCGC AGCCCGCAGC CCGCAGAGGA CGCCCAGAGC GGCGAGCAGG CGGGCAGACG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GACCGACGGA CTCGCGCCGC GTCCACCTGT CGGCCGGGCC CAGCCGAGCG CGCAGCGGGC ACGCCGCGCG CGCGGAGCAG CCGTGCCCGC CGCCCGGGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGCCGCCAGG GCGCACACGC TCCCGCCCCC CTACCCGGCC CGGGCGGGAG TTTGCACCTC TCCCTGCCCG GGTGCTCGAG CTGCCGTTGC AAAGCCAACT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTGGAAAAAG TTTTTTGGGG GAGACTTGGG CCTTGAGGTG CCCAGCTCCG CGCTTTCCGA TTTTGGGGGC CTTTCCAGAA AATGTTGCAA AAAAGCTAAG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCGGCGGGCA GAGGAAAACG CCTGTAGCCG GCGAGTGAAG ACGAACCATC GACTGCCGTG TTCCTTTTCC TCTTGGAGGT TGGAGTCCCC TGGGCGCCCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CACACCGGTA GACGCCTCGG CTGGTTCGCG ACGCAGCCCC CCGGCCGTGG ATGCTCACTC GGGCTCGGGA TCCGCCCAGG TAGCCGGCTC GGACCCAGGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CCTGCGCCCA GGTCCTCCCC TGCCCCCCAG CGACGGAGCC GGGGCCGGGG GCGGCGGCGC CCGGGGGCCA TGCGGGTGAG CCGCGGCTGC AGAGGCCTGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCGCCTGATC GCCGCGGACC CGAGCCGAGC CCACCCCCCT CCCCAGCCCC CCACCCTGGC CGCGGGGGCG GCGCGCTCGA TCTACGCGTC CGGGGCCCCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGGGGCCGGG CCCGGAGTCG GCATGAATCG CTGCTGGGCG CTCTTCCTGT CTCTCTGCTG CTACCTGCGT CTGGTCAGCG CCGA
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081

Credibility of mRNA sequence:

reverse_engineered_fragment_only

The organism containing this mRNA with IRES segment in its genome:

Homo sapiens K-562 (ATCC CCL-243)

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:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
heterogeneous_population_of_molecules_found

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:
promoter_confirmed

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:

Homo sapiens NCI-H1299 [H1299] (ATCC CRL-5803)

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `3`	Last change: `2008-10-22 16:24:11`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
PDGF-B

The description of the protein encoded in this ORF:
fragment of platelet-derived growth factor beta isoform 1, preproprotein

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):

1023-1082

OPTIONAL: The function of the encoded protein

isoform 1, preproprotein is encoded by transcript variant 1;
Platelet-derived growth factor, beta polypeptide (oncogene SIS);
platelet-derived growth factor, B chain; PDGF, B chain; becaplermin;
v-sis platelet-derived growth factor beta polypeptide (simian sarcoma viral oncogene homolog);
PDGF-B VORLAEUFERSEQUENZ;
HUMANES PDGF-B GEN AUS PGEM2-PDGF-B, FLANKIERT VON 5'-ECORI UND 3'-HINDIII RESTRIKTIONSSCHNITTSTELLEN;
platelet-derived growth factor 2;
go_component: membrane [goid 0016020] [evidence IEA];
go_component: extracellular region [goid 0005576] [evidence NAS] [pmid 1661670];
go_function: growth factor activity [goid 0008083] [evidence IEA];
go_function: platelet-derived growth factor receptor binding [goid 0005161] [evidence NAS] [pmid 1661670];
go_process: cell proliferation [goid 0008283] [evidence IEA];
go_process: response to wounding [goid 0009611] [evidence NAS] [pmid 1661670];
go_process: regulation of progression through cell cycle [goid 0000074] [evidence IEA]

Remarks:

Bernstein et al., 1997 have used GI:189727 (alias M19719.1, 1482 b, 10-JAN-1995) record which contains
chromosomal DNA region. The size of UTRs does not match the description in the article. In contrast, the
GI:4505680 (3373 b, 27-NOV-2005) record matches the description of both UTR lengths (5'-UTR 1022b and 3'-UTR
1625b) quite well. This sequence aligns with the GI:189727 (alias M19719.1, 1482 b, 10-JAN-1995) with only 3
mismatches. Sella et al., 1999 refer to M19719.1 record and pinpoint discrepancies of their gene to it.
Therefore it seems in the original work from 1997 they used essentially the same cDNA fragment. Unfortunately,
they did not submit the sequence into GenBank. We have modified the M19719.1 sequence hopefully in the way as
described in Sella et al., 1999 as used throughout this IRESite record: "Referring to the RNA start site as nt
1 (which corresponds to nt 398 of human c-sis, accession no. M19719), the updated sequence includes the
following seven changes: nt 706 and 707 are GG (not CC), nt 921 is C (not U), nt 756 (G) and nt 786 (C) are
absent, and immediately following nt 863 and nt 868 there is an insertion of C. The nucleotide numbering
throughout the present study includes the above corrections." Surprisingly, the sequence we came up with
differs slightly (few isolated insertions/deletions) from the sequence in IRESdb database which received
the updated sequence directly from O. Elroy-Stein.

Bernstein et al., 1997 verified integrity of the bicistronic transcripts after in vivo transcription using
Northern blot analysis.

Han et al., 2003 refers to 2.8kb PDGF-B mRNA (GI:20987438) being produced from an internal promoter located
within the 5'-UTR region of the 3.8 kb mRNA studied by Bernstein et al., 1997 and Sella et al., 1999. The
promoter had activity of about 15/48 activity of control SV40 promoter with enhancer and contributed all
reported IRES-like activity from the second cistron.

Citations:

Bernstein J., Sella O., Le S. Y., Elroy-Stein O. (1997) PDGF2/c-sis mRNA leader contains a differentiation-linked internal ribosomal entry site (D-IRES). J. Biol. Chem. 272(14):9356-9362

Fen Z., Daniel T. O. (1991) 5' untranslated sequences determine degradative pathway for alternate PDGF B/c-sis mRNA's. Oncogene. 6(6):953-959

Sella O., Gerlitz G., Le S. Y., Elroy-Stein O. (1999) Differentiation-induced internal translation of c-sis mRNA: analysis of the cis elements and their differentiation-linked binding to the hnRNP C protein. Mol. Cell. Biol. 19(8):5429-5440

Han B., Dong Z., Zhang J. T. (2003) Tight control of platelet-derived growth factor B/c-sis expression by interplay between the 5'-untranslated region sequence and the major upstream promoter. J. Biol. Chem. 278(47):46983-46993

The rRNA complementarities:

The rRNA complementarity:

Version: `1`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The organism where this rRNA:RNA interaction occurred:

Homo sapiens K-562 (ATCC CCL-243)

GenBankId of the rRNA that interacts with this mRNA/+RNA:
36162

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.
1838-1826

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.
1010-1022

Remarks:

The publication refers to bases 1010-1022 [5'-GCCcggaGUCGGC-3'] of the PDGF2/c-sis mRNA interacting with
the 3'-end of the 18S rRNA [5'-GUCGuaACaaGGU-3'] (9 bases in uppercase letters are basepaired).

There are many other complementary regions, mainly in the GC-rich regions. To name just a few at least close
to the 3'-end mentioned in the paper (base ranges in format mRNA:rRNA):

1015-1019:1249-1245, 5 bases
1012-1016:1740-1736, 5 bases
1012-1016:1752-1748, 5 bases

IRESs:

IRES:

Version: `11`	Last change: `2009-09-01 13:40:48`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `PDGF2/c-sis`

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

1-1022

Conclusion:
disproved_IRES

How IRES boundaries were determined:
experimentally_determined

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

GGTGGCAACT TCTCCTCCTG CAGCCGGGAG CGGCCTGCCT GCCTCCCTGC GCACCCGCAG CCTCCCCCGC TGCCTCCCTA GGGCTCCCCT CCGGCCGCCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGCCCATTT TTCATTCCCT AGATAGAGAT ACTTTGCGCG CACACACATA CATACGCGCG CAAAAAGGAA AAAAAAAAAA AAAAGCCCAC CCTCCAGCCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGCTGCAAAG AGAAAACCGG AGCAGCCGCA GCTCGCAGCT CGCAGCTCGC AGCCCGCAGC CCGCAGAGGA CGCCCAGAGC GGCGAGCAGG CGGGCAGACG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GACCGACGGA CTCGCGCCGC GTCCACCTGT CGGCCGGGCC CAGCCGAGCG CGCAGCGGGC ACGCCGCGCG CGCGGAGCAG CCGTGCCCGC CGCCCGGGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGCCGCCAGG GCGCACACGC TCCCGCCCCC CTACCCGGCC CGGGCGGGAG TTTGCACCTC TCCCTGCCCG GGTGCTCGAG CTGCCGTTGC AAAGCCAACT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTGGAAAAAG TTTTTTGGGG GAGACTTGGG CCTTGAGGTG CCCAGCTCCG CGCTTTCCGA TTTTGGGGGC CTTTCCAGAA AATGTTGCAA AAAAGCTAAG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCGGCGGGCA GAGGAAAACG CCTGTAGCCG GCGAGTGAAG ACGAACCATC GACTGCCGTG TTCCTTTTCC TCTTGGAGGT TGGAGTCCCC TGGGCGCCCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CACACCGGTA GACGCCTCGG CTGGTTCGCG ACGCAGCCCC CCGGCCGTGG ATGCTCACTC GGGCTCGGGA TCCGCCCAGG TAGCCGGCTC GGACCCAGGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CCTGCGCCCA GGTCCTCCCC TGCCCCCCAG CGACGGAGCC GGGGCCGGGG GCGGCGGCGC CCGGGGGCCA TGCGGGTGAG CCGCGGCTGC AGAGGCCTGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCGCCTGATC GCCGCGGACC CGAGCCGAGC CCACCCCCCT CCCCAGCCCC CCACCCTGGC CGCGGGGGCG GCGCGCTCGA TCTACGCGTC CGGGGCCCCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGGGGCCGGG CCCGGAGTCG GC
^1001      ^1011      ^1021

Remarks:

Bernstein et al., 1997 stated in the article: "The D-IRES activity was conferred by the full-length (1022 nt)
5'-UTR or by a 395 nt segment spanning nucleotides 475–870 of the 5'-UTR. In contrast, the 273-nt
segment spanning nucleotides 215–488 of the 5'-UTR did not confer D-IRES activity and thereby served as
a negative control in our experiments (Fig. 3)."


The integrity of the bicistronic transcripts obtained in vivo in recombinant vaccinia virus infected cells
was verified by Northern blot.

Han et al. (2003) state that the cryptic promoter contributed all reported IRES-like activity from second
cistron.

Citations:

Bernstein J., Sella O., Le S. Y., Elroy-Stein O. (1997) PDGF2/c-sis mRNA leader contains a differentiation-linked internal ribosomal entry site (D-IRES). J. Biol. Chem. 272(14):9356-9362

RNA:protein interactions:

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The description of the protein interacting with the RNA:
hnRNP C

The interacting RNA base range: 215-846

The organism where this RNA:protein interaction occurs:

Homo sapiens K-562 (ATCC CCL-243)

Remarks:

In vitro UV-crosslinking assay has shown p43 protein. Subsequent antibody assay confirmed the p43 protein has
hnRNP C epitope, seems to be hnRNP C1 and except its nuclear localization p43 also exists in cytoplasm of
differentiated cells (human chronic myelogenous leukemia cell line K562). In addition, antibody assay also
revealed p44 protein (nuclear only) which seems to be hnRNP C2.

The interaction region might be a U-rich region in the range 500-680.

Citations:

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