IRESite_Id:258 summary record describing characteristics of CCND1 IRES

IRESite: The database of experimentally verified IRES structures

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:

CACACGGACT ACAGGGGAGT TTTGTTGAAG TTGCAAAGTC CTGGAGCCTC CAGAGGGCTG TCGGCGCAGT AGCAGCGAGC AGCAGAGTCC GCACGCTCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGAGGGGCA GAAGAGCGCG AGGGAGCGCG GGGCAGCAGA AGCGAGAGCC GAGCGCGGAC CCAGCCAGGA CCCACAGCCC TCCCCAGCTG CCCAGGAAGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCCCCAGCCA TGGAACACCA GCTCCTGTGC TGCGAAGTGG AAACCATCCG CCGCGCGTAC CCCGATGCCA ACCTCCTCAA CGACCGGGTG CTGCGGGCCA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGCTGAAGGC GGAGGAGACC TGCGCGCCCT CGGTGTCCTA CTTCAAATGT GTGCAGAAGG AGGTCCTGCC GTCCATGCGG AAGATCGTCG CCACCTGGAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCTGGAGGTC TGCGAGGAAC AGAAGTGCGA GGAGGAGGTC TTCCCGCTGG CCATGAACTA CCTGGACCGC TTCCTGTCGC TGGAGCCCGT GAAAAAGAGC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGCCTGCAGC TGCTGGGGGC CACTTGCATG TTCGTGGCCT CTAAGATGAA GGAGACCATC CCCCTGACGG CCGAGAAGCT GTGCATCTAC ACCGACAACT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCATCCGGCC CGAGGAGCTG CTGCAAATGG AGCTGCTCCT GGTGAACAAG CTCAAGTGGA ACCTGGCCGC AATGACCCCG CACGATTTCA TTGAACACTT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CCTCTCCAAA ATGCCAGAGG CGGAGGAGAA CAAACAGATC ATCCGCAAAC ACGCGCAGAC CTTCGTTGCC CTCTGTGCCA CAGATGTGAA GTTCATTTCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATCCGCCCT CCATGGTGGC AGCGGGGAGC GTGGTGGCCG CAGTGCAAGG CCTGAACCTG AGGAGCCCCA ACAACTTCCT GTCCTACTAC CGCCTCACAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCTTCCTCTC CAGAGTGATC AAGTGTGACC CGGACTGCCT CCGGGCCTGC CAGGAGCAGA TCGAAGCCCT GCTGGAGTCA AGCCTGCGCC AGGCCCAGCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GAACATGGAC CCCAAGGCCG CCGAGGAGGA GGAAGAGGAG GAGGAGGAGG TGGACCTGGC TTGCACACCC ACCGACGTGC GGGACGTGGA CATCTGAGGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CGCCAGGCAG GCGGGCGCCA CCGCCACCCG CAGCGAGGGC GGAGCCGGCC CCAGGTGCTC CCCTGACAGT CCCTCCTCTC CGGAGCATTT TGATACCAGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGGGAAAGCT TCATTCTCCT TGTTGTTGGT TGTTTTTTCC TTTGCTCTTT CCCCCTTCCA TCTCTGACTT AAGCAAAAGA AAAAGATTAC CCAAAAACTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCTTTAAAAG AGAGAGAGAG AAAAAAAAAA TAGTATTTGC ATAACCCTGA GCGGTGGGGG AGGAGGGTTG TGCTACAGAT GATAGAGGAT TTTATACCCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AATAATCAAC TCGTTTTTAT ATTAATGTAC TTGTTTCTCT GTTGTAAGAA TAGGCATTAA CACAAAGGAG GCGTCTCGGG AGAGGATTAG GTTCCATCCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTACGTGTTT AAAAAAAAGC ATAAAAACAT TTTAAAAACA TAGAAAAATT CAGCAAACCA TTTTTAAAGT AGAAGAGGGT TTTAGGTAGA AAAACATATT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTTGTGCTTT TCCTGATAAA GCACAGCTGT AGTGGGGTTC TAGGCATCTC TGTACTTTGC TTGCTCATAT GCATGTAGTC ACTTTATAAG TCATTGTATG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TTATTATATT CCGTAGGTAG ATGTGTAACC TCTTCACCTT ATTCATGGCT GAAGTCACCT CTTGGTTACA GTAGCGTAGC GTGCCCGTGT GCATGTCCTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGCGCCTGTG ACCACCACCC CAACAAACCA TCCAGTGACA AACCATCCAG TGGAGGTTTG TCGGGCACCA GCCAGCGTAG CAGGGTCGGG AAAGGCCACC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGTCCCACTC CTACGATACG CTACTATAAA GAGAAGACGA AATAGTGACA TAATATATTC TATTTTTATA CTCTTCCTAT TTTTGTAGTG ACCTGTTTAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAGATGCTGG TTTTCTACCC AACGGCCCTG CAGCCAGCTC ACGTCCAGGT TCAACCCACA GCTACTTGGT TTGTGTTCTT CTTCATATTC TAAAACCATT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCATTTCCAA GCACTTTCAG TCCAATAGGT GTAGGAAATA GCGCTGTTTT TGTTGTGTGT GCAGGGAGGG CAGTTTTCTA ATGGAATGGT TTGGGAATAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCATGTACTT GTTTGCAAGC AGGACTTTGA GGCAAGTGTG GGCCACTGTG GTGGCAGTGG AGGTGGGGTG TTTGGGAGGC TGCGTGCCAG TCAAGAAGAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAAGGTTTGC ATTCTCACAT TGCCAGGATG ATAAGTTCCT TTCCTTTTCT TTAAAGAAGT TGAAGTTTAG GAATCCTTTG GTGCCAACTG GTGTTTGAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTAGGGACCT CAGAGGTTTA CCTAGAGAAC AGGTGGTTTT TAAGGGTTAT CTTAGATGTT TCACACCGGA AGGTTTTTAA ACACTAAAAT ATATAATTTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TAGTTAAGGC TAAAAAGTAT ATTTATTGCA GAGGATGTTC ATAAGGCCAG TATGATTTAT AAATGCAATC TCCCCTTGAT TTAAACACAC AGATACACAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACACACACAC ACACACACAA ACCTTCTGCC TTTGATGTTA CAGATTTAAT ACAGTTTATT TTTAAAGATA GATCCTTTTA TAGGTGAGAA AAAAACAATC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGGAAGAAAA AAACCACACA AAGACATTGA TTCAGCCTGT TTGGCGTTTC CCAGAGTCAT CTGATTGGAC AGGCATGGGT GCAAGGAAAA TTAGGGTACT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CAACCTAAGT TCGGTTCCGA TGAATTCTTA TCCCCTGCCC CTTCCTTTAA AAAACTTAGT GACAAAATAG ACAATTTGCA CATCTTGGCT ATGTAATTCT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGTAATTTTT ATTTAGGAAG TGTTGAAGGG AGGTGGCAAG AGTGTGGAGG CTGACGTGTG AGGGAGGACA GGCGGGAGGA GGTGTGAGGA GGAGGCTCCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAGGGGAAGG GGCGGTGCCC ACACCGGGGA CAGGCCGCAG CTCCATTTTC TTATTGCGCT GCTACCGTTG ACTTCCAGGC ACGGTTTGGA AATATTCACA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCGCTTCTGT GTATCTCTTT CACATTGTTT GCTGCTATTG GAGGATCAGT TTTTTGTTTT ACAATGTCAT ATACTGCCAT GTACTAGTTT TAGTTTTCTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTAGAACATT GTATTACAGA TGCCTTTTTT GTAGTTTTTT TTTTTTTTAT GTGATCAATT TTGACTTAAT GTGATTACTG CTCTATTCCA AAAAGGTTGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGTTTCACAA TACCTCATGC TTCACTTAGC CATGGTGGAC CCAGCGGGCA GGTTCTGCCT GCTTTGGCGG GCAGACACGC GGGCGCGATC CCACACAGGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGGCGGGGGC CGGCCCCGAG GCCGCGTGCG TGAGAACCGC GCCGGTGTCC CCAGAGACCA GGCTGTGTCC CTCTTCTCTT CCCTGCGCCT GTGATGCTGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GCACTTCATC TGATCGGGGG CGTAGCATCA TAGTAGTTTT TACAGCTGTG TTATTCTTTG CGTGTAGCTA TGGAAGTTGC ATAATTATTA TTATTATTAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TATAACAAGT GTGTCTTACG TGCCACCACG GCGTTGTACC TGTAGGACTC TCATTCGGGA TGATTGGAAT AGCTTCTGGA ATTTGTTCAA GTTTTGGGTA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTTTAATCT GTTATGTACT AGTGTTCTGT TTGTTATTGT TTTGTTAATT ACACCATAAT GCTAATTTAA AGAGACTCCA AATCTCAATG AAGCCAGCTC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACAGTGCTGT GTGCCCCGGT CACCTAGCAA GCTGCCGAAC CAAAAGAATT TGCACCCCGC TGCGGGCCCA CGTGGTTGGG GCCCTGCCCT GGCAGGGTCA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TCCTGTGCTC GGAGGCCATC TCGGGCACAG GCCCACCCCG CCCCACCCCT CCAGAACACG GCTCACGCTT ACCTCAACCA TCCTGGCTGC GGCGTCTGTC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGAACCACGC GGGGGCCTTG AGGGACGCTT TGTCTGTCGT GATGGGGCAA GGGCACAAGT CCTGGATGTT GTGTGTATCG AGAGGCCAAA GGCTGGTGGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAGTGCACGG GGCACAGCGG AGTCTGTCCT GTGACGCGCA AGTCTGAGGG TCTGGGCGGC GGGCGGCTGG GTCTGTGCAT TTCTGGTTGC ACCGCGGCGC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTCCCAGCAC CAACATGTAA CCGGCATGTT TCCAGCAGAA GACAAAAAGA CAAACATGAA AGTCTAGAAA TAAAACTGGT AAAACCCC
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281

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):

CACACGGACT ACAGGGGAGT TTTGTTGAAG TTGCAAAGTC CTGGAGCCTC CAGAGGGCTG TCGGCGCAGT AGCAGCGAGC AGCAGAGTCC GCACGCTCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGAGGGGCA GAAGAGCGCG AGGGAGCGCG GGGCAGCAGA AGCGAGAGCC GAGCGCGGAC CCAGCCAGGA CCCACAGCCC TCCCCAGCTG CCCAGGAAGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCCCCAGCC
^201

Citations:

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