The nucleic acid data:
IRESite Id: 258 Version: 6
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2009-09-01 22:04:06
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  CCND1
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
77628152
Synonyms of the gene name:
Synonym: BCL1
Synonym: PRAD1
Synonym: U21B31
Synonym: D11S287E
The mRNA/+RNA description: 
Homo sapiens cyclin D1 (CCND1), mRNA. Poly(A)-tail dropped from the sequence.
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:
Homo sapiens
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:
homogeneous_population_of_molecules_confirmed
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:
no_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:
Mus musculus MEF (C57BL/6) [MEF-BL/6-1] (ATCC SCRC-1008)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2009-09-01 21:18:41
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CCND1
The description of the protein encoded in this ORF:
cyclin D1
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):
  210-1097
Remarks:
It seems the sequence NM_053056.2 is exactly same in the 5'-UTR as the sequence published in the Supplementary
data. However, it is not sure that the RT-PCR-amplified and cloned sequence was exactly same.

From several mRNA hits and especially based on the hit to a cDNA prepared by oligo-capping method (AK313136)
it seems the 5'-UTR is usually shorter, in this case by 51bp. Anyway, it seems the annotation was based on
this record:

LOCUS       Z29078                  4585 bp    DNA     linear   PRI 05-MAY-1994
DEFINITION  H.sapiens cyclin D1 gene promoter region.
ACCESSION   Z29078
VERSION     Z29078.1  GI:483600
[cut]
COMMENT     On May 8, 1994 this sequence version replaced gi:469515.
FEATURES             Location/Qualifiers
     source          1..4585
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /clone="cyclin D1"
                     /cell_line="WI-38"
                     /cell_type="Fibroblast"
     promoter        <1..3015
     prim_transcript 2970..>4585
     exon            3016..3377
     CDS             3179..>3377
                     /codon_start=1
                     /product="cyclin D1"
                     /protein_id="CAA82318.1"
                     /db_xref="GI:483601"
                     /db_xref="UniProtKB/TrEMBL:Q14092"
                     /translation="MEHQLLCCEVETIRRAYPDANLLNDRVLRAMLKAEETCAPSVSY
                     FKCVQKEVLRPCGRSSPPGCWR"
     intron          3378..>4585
[cut]



And here is the alignment of the RefSeq sequence IRESite is using explaining why is the 5'-UTR so long:

>emb|Z29078.1| Gene info H.sapiens cyclin D1 gene promoter region
Length=4585

 GENE ID: 595 CCND1 | cyclin D1 [Homo sapiens] (Over 100 PubMed links)

 Score =  749 bits (405),  Expect = 0.0
 Identities = 408/409 (99%), Gaps = 1/409 (0%)
 Strand=Plus/Plus

Query  1     CACACGGACTACAGGGGAGTTTTGTTGAAGTTGCAAAGTCCTGGAGCCTCCAGAGGGCTG  60
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  2970  CACACGGACTACAGGGGAGTTTTGTTGAAGTTGCAAAGTCCTGGAGCCTCCAGAGGGCTG  3029

Query  61    TCGGCGCAGTAGCAGCGAGCAGCAGAGTCCGCACGCTCCGGCGAGGGGCAGAAGAGCGCG  120
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3030  TCGGCGCAGTAGCAGCGAGCAGCAGAGTCCGCACGCTCCGGCGAGGGGCAGAAGAGCGCG  3089

Query  121   AGGGAGCGCGGGGCAGCAGAAGCGAGAGCCGAGCGCGGACCCAGCCAGGACCCACAGCCC  180
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3090  AGGGAGCGCGGGGCAGCAGAAGCGAGAGCCGAGCGCGGACCCAGCCAGGACCCACAGCCC  3149

Query  181   TCCCCAGCTGCCCAGGAAGAGCCCCAGCCATGGAACACCAGCTCCTGTGCTGCGAAGTGG  240
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3150  TCCCCAGCTGCCCAGGAAGAGCCCCAGCCATGGAACACCAGCTCCTGTGCTGCGAAGTGG  3209

Query  241   AAACCATCCGCCGCGCGTACCCCGATGCCAACCTCCTCAACGACCGGGTGCTGCGGGCCA  300
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3210  AAACCATCCGCCGCGCGTACCCCGATGCCAACCTCCTCAACGACCGGGTGCTGCGGGCCA  3269

Query  301   TGCTGAAGGCGGAGGAGACCTGCGCGCCCTCGGTGTCCTACTTCAAATGTGTGCAGAAGG  360
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  3270  TGCTGAAGGCGGAGGAGACCTGCGCGCCCTCGGTGTCCTACTTCAAATGTGTGCAGAAGG  3329

Query  361   AGGTCCTGCCGTCCATGCGGAAGATCGTCGCCACCTGGATGCTGGAGGT  409
             ||||||| |||||||||||||||||||||||||||||||||||||||||
Sbjct  3330  AGGTCCT-CCGTCCATGCGGAAGATCGTCGCCACCTGGATGCTGGAGGT  3377





Regretfully, the experiments did not exclude the possibility of aberrantly spliced bicistronic mRNAs in the
cells. p27kip "IRES" was used as the positive control, known today to contain promoter. However, from the
different behavior of both CCND1 and c-myc IRESs from p27kip one could believe there is IRES in the former
two. Also increased presence of CCND1 and c-myc in polysomal fractions under low AKT activity cellular
conditions seems to confirm the presence of IRES.
Citations:
Shi Y., Sharma A., Wu H., Lichtenstein A., Gera J. (2005) Cyclin D1 and c-myc internal ribosome entry site (IRES)-dependent translation is regulated by AKT activity and enhanced by rapamycin through a p38 MAPK- and ERK-dependent pathway. J. Biol. Chem. 280(12):10964-10973
IRESs:
IRES:
Version: 2 Last change: 2007-01-23 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  CCND1
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-209
Conclusion:
  putative_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Shi Y., Sharma A., Wu H., Lichtenstein A., Gera J. (2005) Cyclin D1 and c-myc internal ribosome entry site (IRES)-dependent translation is regulated by AKT activity and enhanced by rapamycin through a p38 MAPK- and ERK-dependent pathway. J. Biol. Chem. 280(12):10964-10973
Last change to the database: 2015-04-16 16:45:23 GMT+1