IRESite_Id:457 summary record describing characteristics of p27kip1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `457`	Version: `3`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 21:43:52`

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: `p27kip1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
17978497

Synonyms of the gene name:

Synonym: KIP1

Synonym: CDKN1B

Synonym: MEN4

Synonym: CDKN4

Synonym: MEN1B

The mRNA/+RNA description:

Homo sapiens cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B), mRNA. Poly(A)-tail sequence was
dropped.

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

GTCAGCCTCC CTTCCACCGC CATATTGGGC CACTAAAAAA AGGGGGCTCG TCTTTTCGGG GTGTTTTTCT CCCCCTCCCC TGTCCCCGCT TGCTCACGGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCTGCGACTC CGACGCCGGC AAGGTTTGGA GAGCGGCTGG GTTCGCGGGA CCCGCGGGCT TGCACCCGCC CAGACTCGGA CGGGCTTTGC CACCCTCTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCTTGCCTGG TCCCCTCTCC TCTCCGCCCT CCCGCTCGCC AGTCCATTTG ATCAGCGGAG ACTCGGCGGC CGGGCCGGGG CTTCCCCGCA GCCCCTGCGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCTCCTAGAG CTCGGGCCGT GGCTCGTCGG GGTCTGTGTC TTTTGGCTCC GAGGGCAGTC GCTGGGCTTC CGAGAGGGGT TCGGGCCGCG TAGGGGCGCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTGTTTTGTT CGGTTTTGTT TTTTTGAGAG TGCGAGAGAG GCGGTCGTGC AGACCCGGGA GAAAGATGTC AAACGTGCGA GTGTCTAACG GGAGCCCTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTGGAGCGG ATGGACGCCA GGCAGGCGGA GCACCCCAAG CCCTCGGCCT GCAGGAACCT CTTCGGCCCG GTGGACCACG AAGAGTTAAC CCGGGACTTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GAGAAGCACT GCAGAGACAT GGAAGAGGCG AGCCAGCGCA AGTGGAATTT CGATTTTCAG AATCACAAAC CCCTAGAGGG CAAGTACGAG TGGCAAGAGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGAGAAGGG CAGCTTGCCC GAGTTCTACT ACAGACCCCC GCGGCCCCCC AAAGGTGCCT GCAAGGTGCC GGCGCAGGAG AGCCAGGATG TCAGCGGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CCGCCCGGCG GCGCCTTTAA TTGGGGCTCC GGCTAACTCT GAGGACACGC ATTTGGTGGA CCCAAAGACT GATCCGTCGG ACAGCCAGAC GGGGTTAGCG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GAGCAATGCG CAGGAATAAG GAAGCGACCT GCAACCGACG ATTCTTCTAC TCAAAACAAA AGAGCCAACA GAACAGAAGA AAATGTTTCA GACGGTTCCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAAATGCCGG TTCTGTGGAG CAGACGCCCA AGAAGCCTGG CCTCAGAAGA CGTCAAACGT AAACAGCTCG AATTAAGAAT ATGTTTCCTT GTTTATCAGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TACATCACTG CTTGATGAAG CAAGGAAGAT ATACATGAAA ATTTTAAAAA TACATATCGC TGACTTCATG GAATGGACAT CCTGTATAAG CACTGAAAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAACAACACA ATAACACTAA AATTTTAGGC ACTCTTAAAT GATCTGCCTC TAAAAGCGTT GGATGTAGCA TTATGCAATT AGGTTTTTCC TTATTTGCTT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CATTGTACTA CCTGTGTATA TAGTTTTTAC CTTTTATGTA GCACATAAAC TTTGGGGAAG GGAGGGCAGG GTGGGGCTGA GGAACTGACG TGGAGCGGGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TATGAAGAGC TTGCTTTGAT TTACAGCAAG TAGATAAATA TTTGACTTGC ATGAAGAGAA GCAATTTTGG GGAAGGGTTT GAATTGTTTT CTTTAAAGAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTAATGTCCC TTTCAGAGAC AGCTGATACT TCATTTAAAA AAATCACAAA AATTTGAACA CTGGCTAAAG ATAATTGCTA TTTATTTTTA CAAGAAGTTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATTCTCATTT GGGAGATCTG GTGATCTCCC AAGCTATCTA AAGTTTGTTA GATAGCTGCA TGTGGCTTTT TTAAAAAAGC AACAGAAACC TATCCTCACT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCCCTCCCCA GTCTCTCTTA AAGTTGGAAT TTACCAGTTA ATTACTCAGC AGAATGGTGA TCACTCCAGG TAGTTTGGGG CAAAAATCCG AGGTGCTTGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAGTTTTGAA TGTTAAGAAT TGACCATCTG CTTTTATTAA ATTTGTTGAC AAAATTTTCT CATTTTCTTT TCACTTCGGG CTGTGTAAAC ACAGTCAAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TAATTCTAAA TCCCTCGATA TTTTTAAAGA TCTGTAAGTA ACTTCACATT AAAAAATGAA ATATTTTTTA ATTTAAAGCT TACTCTGTCC ATTTATCCAC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGAAAGTGT TATTTTTAAA GGAAGGTTCA TGTAGAGAAA AGCACACTTG TAGGATAAGT GAAATGGATA CTACATCTTT AAACAGTATT TCATTGCCTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGTATGGAAA AACCATTTGA AGTGTACCTG TGTACATAAC TCTGTAAAAA CACTGAAAAA TTATACTAAC TTATTTATGT TAAAAGATTT TTTTTAATCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGACAATATA CAAGCCAAAG TGGCATGTTT TGTGCATTTG TAAATGCTGT GTTGGGTAGA ATAGGTTTTC CCCTCTTTTG TTAAATAATA TGGCTATGCT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAAAAGGTTG CATACTGAGC CAAGTATAAT TTTTTGTAAT GTGTGAAAAA GATGCCAATT ATTGTTACAC ATTAAGTAAT CAATAAAGAA AACTTCCATA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCT
^2401

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:
not_tested

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 :
heterogeneous_population_of_molecules_found

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:

Homo sapiens

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
CDKN1B

The description of the protein encoded in this ORF:
cyclin-dependent kinase inhibitor 1B

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):

466-1062

Remarks:

The sequence used in IRESite was obtained from IRESdb database to which it has been provided by S. Pyronnet.
Although the sequence appears to be an incomplete mRNA sequence when aligned to current GenBank RefSeq record
the base #1 of the query is the first base of the transcript as determined by primer extension (Minami et al.
(1997):

>NM_004064.2 Homo sapiens cyclin-dependent kinase inhibitor 1B (p27, Kip1) (CDKN1B), mRNA
Length=2422

 GENE ID: 1027 CDKN1B | cyclin-dependent kinase inhibitor 1B (p27, Kip1)
[Homo sapiens] (Over 100 PubMed links)

 Score =  281 bits (152),  Expect = 2e-75
 Identities = 154/155 (99%), Gaps = 0/155 (0%)
 Strand=Plus/Plus

Query  1    GGGCCGTGGCTCGTCGGGGTCAGTGTCTTTTGGCTCCGAGGGCAGTCGCTGGGCTTCCGA  60
            ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct  314  GGGCCGTGGCTCGTCGGGGTCTGTGTCTTTTGGCTCCGAGGGCAGTCGCTGGGCTTCCGA  373

Query  61   GAGGGGTTCGGGCCGCGTAGGGGCGCtttgttttgttcggttttgtttttttgAGAGTGC  120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  374  GAGGGGTTCGGGCCGCGTAGGGGCGCTTTGTTTTGTTCGGTTTTGTTTTTTTGAGAGTGC  433

Query  121  GAGAGAGGCGGTCGTGCAGACCCGGGAGAAAGATG  155
            |||||||||||||||||||||||||||||||||||
Sbjct  434  GAGAGAGGCGGTCGTGCAGACCCGGGAGAAAGATG  468

The transcription start site of mouse p27kip1 is 23 bp upstream of the one from human (Minami et al. (1997),
Figure 5.

A human sequence with just 153 bp long 5'-UTR is GI:9652559.

Citations:

Minami S., Ohtani-Fujita N., Igata E., Tamaki T., Sakai T. (1997) Molecular cloning and characterization of the human p27Kip1 gene promoter. FEBS. Lett. 411(1):1-6

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `p27kip1`

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

314-465

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GGGCCGTGGC TCGTCGGGGT CTGTGTCTTT TGGCTCCGAG GGCAGTCGCT GGGCTTCCGA GAGGGGTTCG GGCCGCGTAG GGGCGCTTTG TTTTGTTCGG 
^314       ^324       ^334       ^344       ^354       ^364       ^374       ^384       ^394       ^404       

TTTTGTTTTT TTGAGAGTGC GAGAGAGGCG GTCGTGCAGA CCCGGGAGAA AG
^414       ^424       ^434       ^444       ^454       ^464

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