IRESite_Id:1 summary record describing characteristics of HIF1a IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `1`	Version: `9`
Originaly submitted by: Martin Pospíšek	Submission date: `2005-06-26 00:00:00`
Reviewed by: Martin Pospíšek	Last change: `2009-09-03 13:38:32`

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: `Hif1a`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
7363432

The mRNA/+RNA description:

Mus musculus hypoxia inducible factor 1, alpha subunit (Hif1a), mRNA. Poly(A) tail dropped.

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

CGCGAGGACT GTCCTCGCCG CCGTCGCGGG CAGTGTCTAG CCAGGCCTTG ACAAGCTAGC CGGAGGAGCG CCTAGGAACC CGAGCCGGAG CTCAGCGAGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCAGCCTGCA CGCCCGCCTC GCGTCCCGGG GGGGTCCCGC CTCCCACCCC GCCTCTGGAC TTGTCTCTTT CCCCGCGCGC GCGGACAGAG CCGGCGTTTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGCCCGAGCG AGCCCGGGGG CCGCCGGCCG GGAAGACAAC GCGGGCACCG ATTCGCCATG GAGGGCGCCG GCGGCGAGAA CGAGAAGAAA AAGATGAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CTGAACGTCG AAAAGAAAAG TCTAGAGATG CAGCAAGATC TCGGCGAAGC AAAGAGTCTG AAGTTTTTTA TGAGCTTGCT CATCAGTTGC CACTTCCCCA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CAATGTGAGC TCACATCTTG ATAAAGCTTC TGTTATGAGG CTCACCATCA GTTATTTACG TGTGAGAAAA CTTCTGGATG CCGGTGGTCT AGACAGTGAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATGAGATGA AGGCACAGAT GGACTGTTTT TATCTGAAAG CCCTAGATGG CTTTGTGATG GTGCTAACAG ATGACGGCGA CATGGTTTAC ATTTCTGATA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACGTGAACAA ATACATGGGG TTAACTCAGT TTGAACTAAC TGGACACAGT GTGTTTGATT TTACTCATCC ATGTGACCAT GAGGAAATGA GAGAAATGCT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TACACACAGA AATGGCCCAG TGAGAAAAGG GAAAGAACTA AACACACAGC GGAGCTTTTT TCTCAGAATG AAGTGCACCC TAACAAGCCG GGGGAGGACG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGAACATCA AGTCAGCAAC GTGGAAGGTG CTTCACTGCA CGGGCCATAT TCATGTCTAT GATACCAACA GTAACCAACC TCAGTGTGGG TACAAGAAAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CACCCATGAC GTGCTTGGTG CTGATTTGTG AACCCATTCC TCATCCGTCA AATATTGAAA TTCCTTTAGA TAGCAAGACA TTTCTCAGTC GACACAGCCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGATATGAAA TTTTCTTACT GTGATGAAAG AATTACTGAG TTGATGGGTT ATGAGCCGGA AGAACTTTTG GGCCGCTCAA TTTATGAATA TTATCATGCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTGGATTCTG ATCATCTGAC CAAAACTCAC CATGATATGT TTACTAAAGG ACAAGTCACC ACAGGACAGT ACAGGATGCT TGCCAAAAGA GGTGGATATG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCTGGGTTGA AACTCAAGCA ACTGTCATAT ATAATACGAA GAACTCCCAG CCACAGTGCA TTGTGTGTGT GAATTATGTT GTAAGTGGTA TTATTCAGCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGACTTGATT TTCTCCCTTC AACAAACAGA ATCTGTGCTC AAACCAGTTG AATCTTCAGA TATGAAGATG ACTCAGCTGT TCACCAAAGT TGAATCAGAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GATACAAGCT GCCTTTTTGA TAAGCTTAAG AAGGAGCCTG ATGCTCTCAC TCTGCTGGCT CCAGCTGCCG GCGACACCAT CATCTCTCTG GATTTTGGCA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCGATGACAC AGAAACTGAA GATCAACAAC TTGAAGATGT TCCATTATAT AATGATGTAA TGTTTCCCTC TTCTAATGAA AAATTAAATA TAAACCTGGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AATGTCTCCT TTACCTTCAT CGGAAACTCC AAAGCCACTT CGAAGTAGTG CTGATCCTGC ACTGAATCAA GAGGTTGCAT TAAAATTAGA ATCAAGTCCA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGTCACTGG GACTTTCTTT TACCATGCCC CAGATTCAAG ATCAGCCAGC AAGTCCTTCT GATGGAAGCA CTAGACAAAG TTCACCTGAG AGACTTCTTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGGAAAACGT AAACACTCCT AACTTTTCCC AGCCTAACAG TCCCAGTGAA TATTGCTTTG ATGTGGATAG CGATATGGTC AATGTATTCA AGTTGGAACT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGTGGAAAAA CTGTTTGCTG AAGACACAGA GGCAAAGAAT CCATTTTCAA CTCAGGACAC TGATTTAGAT TTGGAGATGC TGGCTCCCTA TATCCCAATG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GATGATGATT TCCAGTTACG TTCCTTTGAT CAGTTGTCAC CATTAGAGAG CAATTCTCCA AGCCCTCCAA GTATGAGCAC AGTTACTGGG TTCCAGCAGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCCAGTTACA GAAACCTACC ATCACTGCCA CTGCCACCAC AACTGCCACC ACTGATGAAT CAAAAACAGA GACGAAGGAC AATAAAGAAG ATATTAAAAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACTGATTGCA TCTCCATCTT CTACCCAAGT ACCTCAAGAA ACGACCACTG CTAAGGCATC AGCATACAGT GGCACTCACA GTCGGACAGC CTCACCAGAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGAGCAGGAA AGAGAGTCAT AGAACAGACA GACAAAGCTC ATCCAAGGAG CCTTAAGCTG TCTGCCACTT TGAATCAAAG AAATACTGTT CCTGAGGAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AATTAAACCC AAAGACAATA GCTTCGCAGA ATGCTCAGAG GAAGCGAAAA ATGGAACATG ATGGCTCCCT TTTTCAAGCA GCAGGAATTG GAACATTATT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCAGCAACCA GGTGACTGTG CACCTACTAT GTCACTTTCC TGGAAACGAG TGAAAGGATT CATATCTAGT GAACAGAATG GAACGGAGCA AAAGACTATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATTTTAATAC CCTCCGATTT AGCATGCAGA CTGCTGGGGC AGTCAATGGA TGAGAGTGGA TTACCACAGC TGACCAGTTA CGATTGTGAA GTTAATGCTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCATACAAGG CAGCAGAAAC CTACTGCAGG GTGAAGAATT ACTCAGAGCT TTGGATCAAG TTAACTGAGC GTTTCCTAAT CTCATTCCTT TTGATTGTTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATGTTTTTGT TCAGTTGTTG TTGTTTGTTG GGTTTTTGTT TCTGTTGGTT ATTTTTGGAC ACTGGTGGCT CAGCAGTCTA TTTATATTTT CTATATCTAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTTTAGAAGC CTGGCTACAA TACTGCACAA ACTCAGATAG TTTAGTTTTC ATCCCCTTTC TACTTAATTT TCATTAATGC TCTTTTTAAT ATGTTCTTTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AATGCCAGAT CACAGCACAT TCACAGCTCC TCAGCATTTC ACCATTGCAT TGCTGTAGTG TCATTTAAAA TGCACCTTTT TATTTATTTA TTTTTGGTGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGGAGTTTGT CCCTTATTGA ATTATTTTTA ATGAAATGCC AATATAATTT TTTAAGAAAG CAGTAAATTC TCATCATGAT CATAGGCAGT TGAAAACTTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTACTCATTT TTTTCATGTT TTACATGAAA ATAATGCTTT GTCAGCAGTA CATGGTAGCC ACAATTGCAC AATATATTTT CTTTAAAAAA CCAGCAGTTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTCATGCAAT ATATTCTGCA TTTATAAAAC TAGTTTTTAA GAAATTTTTT TTGGCCTATG GAATTGTTAA GCCTGGATCA TGAAGCGTTG ATCTTATAAT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GATTCTTAAA CTGTATGGTT TCTTTATATG GGTAAAGCCA TTTACATGAT ATAAAGAAAT ATGCTTATAT CTGGAAGGTA TGTGGCATTT ATTTGGATAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AATTCTCAAT TCAGAGAAGT TATCTGGTGT TTCTTGACTT TACCAACTCA AAACAGTCCC TCTGTAGTTG TGGAAGCTTA TGCTAATATT GTGTAATTGA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTATGAAACA TAAATGTTCT GCCCACCCTG TTGGTATAAA GACATTTTGA GCATACTGTA AACAAACAAA CAAAAAATCA TGCTTTGTTA GTAAAATTGC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CTAGTATGTT GATTTGTTGA AAATATGATG TTTGGTTTTA TGCACTTTGT CGCTATTAAC ATCCTTTTTT CATATAGATT TCAATAAGTG AGTAATTTTA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GAAGCATTAT TTTAGGAATA TAGAGTTGTC ATAGTAAACA TCTTGTTTTT TCTATGTACA CTGTATAAAT TTTTCGTTCC CTTGCTCTTT GTGGTTGGGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTAACACTAA CTGTACTGTT TTGTTATATC AAATAAACAT CTTCTGTGGA CCAGG
^3901      ^3911      ^3921      ^3931      ^3941      ^3951

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:

Mus musculus

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:
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:
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

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
Hif1a

The description of the protein encoded in this ORF:
Mus musculus hypoxia inducible factor 1, alpha subunit (Hif1a).

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):

258-2768

Remarks:

Transiently transfected cells with pRF based vector. Integrity of the bicistronic transcripts verified by
RNase protection assay and Northern blot (Lang et al., 2002).

Bert et al. (2006) tested Hif1a IRES in HeLa cells using promoter-less plasmids with or without the enhancer
left in (Figure 2). They showed there is a cryptic promoter activatable when the enhancer is left in.

Also Young et al. (2008) report in Figure 2 a cryptic promoter in NIH3T3 cells.

Citations:

Luo G., Gu Y. Z., Jain S., Chan W. K., Carr K. M., Hogenesch J. B., Bradfield C. A. (1997) Molecular characterization of the murine Hif-1 alpha locus. Gene Expr. 6(5):287-299

Bert AG, Grépin R, Vadas MA, Goodall GJ (2006) Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 12(6):1074-1083

IRESs:

IRES:

Version: `9`	Last change: `2009-09-03 13:33:06`
Originaly submitted by: Martin Pospíšek	Reviewed by: Martin Pospíšek
The IRES name: `HIF1a`

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

1-257

Conclusion:
disproved_IRES

How IRES boundaries were determined:
guessed

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

CGCGAGGACT GTCCTCGCCG CCGTCGCGGG CAGTGTCTAG CCAGGCCTTG ACAAGCTAGC CGGAGGAGCG CCTAGGAACC CGAGCCGGAG CTCAGCGAGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCAGCCTGCA CGCCCGCCTC GCGTCCCGGG GGGGTCCCGC CTCCCACCCC GCCTCTGGAC TTGTCTCTTT CCCCGCGCGC GCGGACAGAG CCGGCGTTTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GGCCCGAGCG AGCCCGGGGG CCGCCGGCCG GGAAGACAAC GCGGGCACCG ATTCGCC
^201       ^211       ^221       ^231       ^241       ^251

Remarks:

This mRNA remains bound to polysomes both in normoxia and hypoxia. Exact IRES region was not determined.
Values represent length of the 5' UTR.

Bert et al. (2006) reported that despite the contribution of the cryptic promoter in in vivo-based
assays Hif1a IRES has "some" activity.

Young et al. (2008 reported that Hif1a IRES is not functional in directly transfected RNAs (Figure 3) nor in
NIH3T3 cells transfected by a plasmid encoding a bicistronic mRNA when subtracted the IRES-like activity
contributed by the promoter (Figure 2B vs. 2C).

Citations:

Lang K. J. D., Kappel A., Goodall G. J. (2002) Hypoxia-inducible factor-1alpha mRNA contains an internal ribosome entry site that allows efficient translation during normoxia and hypoxia. Mol. Biol. Cell. 13(5):1792-1801

Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, Simon MC (2008) Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J. Biol. Chem. 283(24):16309-16319

Bert AG, Grépin R, Vadas MA, Goodall GJ (2006) Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 12(6):1074-1083

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