IRESite_Id:117 summary record describing characteristics of DAP5 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `117`	Version: `4`
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský	Last change: `2009-09-02 01:47:02`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `hopefully_full-length_mRNA`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `DAP5`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
111494227

Synonyms of the gene name:

Synonym: p97

Synonym: AAG1

Synonym: NAT1

Synonym: FLJ41344

The mRNA/+RNA description:

Death-associated protein 5 (DAP5) (also named p97 and NAT1), a 97-kDa protein homologous to eukaryotic
translation initiation factor 4GI (eIF4GI)

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

gcagacggca accgggccgc tgattgggcg gcgaaggagc cattcgggga gactctggtg ggttcggctg ccccaagagt gataagttcg gcttcagaca 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cgccttagcg ccagcagtga gtcggagctc tatggaggtg gcagcgggta ccgagtggcg gctgcagcag cgactcctct gagctgagtt tgaggccgtc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cccgactcct tcctccccct tccctccccc ttttttttgt tttccgttcc cctttcccct cccttcccta tccccgacga ccggatcctg aggaggcagc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tgcggtggca gctgctgagt tctcggtgaa ggtatttcat ttctcctgtc ccctcccctc cccaccccat ctattaatat tattcttttg aagattcttc 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gttgtcaagc cgccaaaGTG GAGAGTGCGA TTGCAGAAGG GGGTGCTTCT CGTTTCAGTG CTTCTTCGGG CGGAGGAGGA AGTAGGGGTG CACCTCAGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CTATCCCAAG ACTGCTGGCA ACAGCGAGTT CCTGGGGAAA ACCCCAGGGC AAAACGCTCA GAAATGGATT CCTGCACGAA GCACTAGACG AGATGACAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCCGCAGCAA ACAACTCCGC AAACGAAAAA GAACGACATG ATGCAATCTT CAGGAAAGTA AGAGGCATAC TAAATAAGCT TACTCCTGAA AAGTTTGACA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGCTATGCCT TGAGCTCCTC AATGTGGGTG TAGAGTCTAA ACTCATCCTT AAAGGGGTCA TACTGCTGAT TGTGGACAAA GCCCTAGAAG AGCCAAAGTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TAGCTCACTG TATGCTCAGC TATGTCTGCG ATTGGCAGAA GATGCACCAA ACTTTGATGG CCCAGCAGCA GAGGGTCAAC CAGGACAGAA GCAAAGCACC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACATTCAGAC GCCTCCTAAT TTCCAAATTA CAAGATGAAT TTGAAAACCG AACTAGAAAT GTTGATGTCT ATGATAAGCG TGAAAATCCC CTCCTCCCCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGGAGGAGGA ACAGAGAGCC ATTGCTAAGA TCAAGATGTT GGGAAACATC AAATTCATTG GAGAGCTTGG CAAGCTTGAT CTTATTCACG AATCTATCCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCATAAGTGC ATCAAAACAC TTTTGGAAAA GAAGAAGAGA GTCCAACTCA AAGATATGGG AGAGGATTTG GAGTGCCTCT GTCAGATAAT GAGGACAGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GGACCTAGAT TAGACCATGA ACGAGCCAAG TCCTTAATGG ATCAGTACTT TGCCCGAATG TGCTCCTTGA TGTTAAGTAA GGAATTGCCA GCAAGGATTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTTTCCTGCT GCAGGATACC GTAGAGTTGC GAGAACACCA TTGGGTTCCT CGCAAGGCTT TTCTTGACAA TGGACCAAAG ACGATCAATC AAATTCGTCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGATGCAGTA AAAGATCTAG GGGTGTTTAT TCCTGCTCCT ATGGCTCAAG GGATGAGAAG TGACTTCTTT CTGGAGGGAC CGTTCATGCC ACCCAGGATG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAAATGGATA GGGACCCACT TGGAGGACTT GCTGATATGT TTGGACAAAT GCCAGGTAGC GGAATTGGTA CTGGTCCAGG AGTTATCCAG GATAGATTTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CACCCACCAT GGGACGTCAT CGTTCAAATC AACTCTTCAA TGGCCATGGG GGACACATCA TGCCTCCCAC ACAATCGCAG TTTGGAGAGA TGGGAGGCAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTTTATGAAA AGCCAGGGGC TAAGCCAGCT CTACCATAAC CAGAGTCAGG GACTCTTATC CCAGCTGCAA GGACAGTCGA AGGATATGCC ACCTCGGTTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCTAAGAAAG GACAGCTTAA TGCAGATGAG ATTAGCCTGA GGCCTGCTCA GTCGTTCCTA ATGAATAAAA ATCAAGTGCC AAAGCTTCAG CCCCAGATAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CTATGATTCC TCCTAGTGCA CAACCACCAC GCACTCAAAC ACCACCTCTG GGACAGACAC CTCAGCTTGG TCTCAAAACT AATCCACCGC TTATCCAGGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAAGCCTGCC AAGACCAGCA AAAAGCCACC ACCGTCAAAG GAAGAACTCC TTAAACTAAC TGAAACTGTT GTGACTGAAT ATCTAAATAG TGGAAATGCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AATGAGGCTG TCAATGGTGT AAGAGAAATG AGGGCTCCTA AACACTTTCT TCCTGAGATG TTAAGCAAAG TAATCATCCT GTCACTAGAT AGAAGCGATG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAGATAAAGA AAAAGCAAGT TCTTTGATCA GTTTACTCAA ACAGGAAGGG ATAGCCACAA GTGACAACTT CATGCAGGCT TTCCTGAATG TATTGGACCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GTGTCCCAAA CTGGAGGTTG ACATCCCTTT GGTGAAATCC TATTTAGCAC AGTTTGCAGC TCGTGCCATC ATTTCAGAGC TGGTGAGCAT TTCAGAACTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCTCAACCAC TAGAAAGTGG CACCCATTTT CCTCTCTTCC TACTTTGTCT TCAGCAGTTA GCTAAATTAC AAGATCGAGA ATGGTTAACA GAACTTTTTC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AACAAAGCAA GGTCAATATG CAGAAAATGC TCCCAGAAAT TGATCAGAAT AAGGACCGCA TGTTGGAGAT TTTGGAAGGA AAGGGACTGA GTTTCTTATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCCACTCCTC AAATTGGAGA AGGAACTGTT GAAGCAAATA AAGTTGGATC CATCCCCTCA AACCATATAT AAATGGATTA AAGATAACAT CTCTCCCAAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTTCATGTAG ATAAAGGATT TGTGAACATC TTAATGACTA GCTTCTTACA GTACATTTCT AGTGAAGTAA ACCCCCCCAG CGATGAAACA GATTCATCCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTGCTCCTTC CAAAGAACAG TTAGAGCAGG AAAAACAACT ACTACTATCT TTCAAGCCAG TAATGCAGAA ATTTCTTCAT GATCACGTTG ATCTACAAGT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAGTGCCCTG TATGCTCTCC AGGTGCACTG CTATAACAGC AACTTCCCAA AAGGCATGTT ACTTCGCTTT TTTGTGCACT TCTATGACAT GGAAATTATT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAAGAAGAAG CTTTCTTGGC TTGGAAAGAA GATATAACCC AAGAGTTTCC GGGAAAAGGC AAGGCTTTGT TCCAGGTGAA TCAGTGGCTA ACCTGGTTAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAACTGCTGA AGAAGAAGAA TCAGAGGAAG AAGCTGACTA Aagaaccagc caaagcctta aattgtgcaa aacatactgt tgctatgatg taactgcatt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tgacctaacc actgcgaaaa ttcattccgc tgtaatgttt tcacaatatt taaagcagaa gcacgtcagt taggatttcc ttctgcataa ggtttttttg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tagtgtaatg tcttaatcat agtctaccat caaatatttt aggagtatct ttaatgttta gatagtatat tagcagcatg caataattac atcataagtt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ctcaagcaga ggcagtctat tgcaaggacc ttctttgctg ccagttatca taggctgttt taagttagaa aactgaatag caacactgaa tactgtagaa 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

atgcactttg ctcagtaata cttgagttgt tgcaatattt gattatccat ttggttgtta cagaaaaatt cttaactgta attgatggtt gttgccgtaa 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tagtatattg cctgtatttc tacctctagt aatgggcttt atgtgctaga ttttaatatc cttgagcctg ggcaagtgca caagtctttt taaaagaaac 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

atggtttact tgcacaaaac tgatcagttt tgagagatcg ttaatgccct tgaagtggtt tttgtgggtg tgaaacaaat ggtgagaatt tgaattggtc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

cctcctatta tagtattgaa attaagtcta cttaatttat caagtcatgt tcatgccctg attttatata cttgtatcta tcaataaaca ttgtgatact 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tgatgtagtg a
^3901      ^3911

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:
not tested The total number of notable open-reading frames (ORFs):
1

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

ORF

ORF position:

1

Version: `1`	Last change: `2009-03-22 23:31:23`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
DAP5

The description of the protein encoded in this ORF:
death-associated protein 5

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):

418-3141

Remarks:

IRESite annotation is based on NM_001418.3 sequence. The record NM_001418.1 contained CDS between positions
307-3030 which matched the comments in the article by Henis-Korenblit et al. (2000) that the 5'-UTR was about
300 bp long and in Imataka et al. (1997) that the GUG-initiated CDS encodes 907 aa residues. A sequence of the
cloned cDNA was shown in Figure 2 in Levy-Strumpf et al. (1997) and aligns with this RefSeq sequence since its
position 127 (thus positions 1-7 shown in the Figure 2 do not have a counterpart). The sequence of p97/DAP5
published by Imataka is in AF104913 (GI:3941723).

The forward primer described in Henis-Korenblit et al. (2000) aligns well to both these RefSeq sequences while
the reverse primer mismatches in several positions. EST sequences confirm this NM_001418.3 sequence since
position 81 downstream while such ESTs begin at that position (GI:83041139).

Although RefSeq annotates this sequence as eIF4G2 we removed this gene name from this record because the DNA
sequence differs from both eIF4GI and eIF4GII. Probably because Shaughnessy et al. (1997) called this 907 aa
residues spanning CDS eIF4G2.

Citations:

Henis-Korenblit S., Strumpf N. L., Goldstaub D., Kimchi A. (2000) A novel form of DAP5 protein accumulates in apoptotic cells as a result of caspase cleavage and internal ribosome entry site-mediated translation. Mol. Cell. Biol. 20(2):496-506

Imataka H., Olsen H. S., Sonenberg N. (1997) A new translational regulator with homology to eukaryotic translation initiation factor 4G. EMBO J. 16(4):817-825

Levy-Strumpf N., Deiss L. P., Berissi H., Kimchi A. (1997) DAP-5, a novel homolog of eukaryotic translation initiation factor 4G isolated as a putative modulator of gamma interferon-induced programmed cell death. Mol. Cell. Biol. 17(3):1615-1625

Shaughnessy JD J. r., Jenkins N. A., Copeland N. G. (1997) cDNA cloning, expression analysis, and chromosomal localization of a gene with high homology to wheat eIF-(iso)4F and mammalian eIF-4G. Genomics. 39(2):192-197

IRESs:

IRES:

Version: `6`	Last change: `2009-03-22 23:40:09`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `DAP5`

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

112-416

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

cagcagtgag tcggagctct atggaggtgg cagcgggtac cgagtggcgg ctgcagcagc gactcctctg agctgagttt gaggccgtcc ccgactcctt 
^112       ^122       ^132       ^142       ^152       ^162       ^172       ^182       ^192       ^202       

cctccccctt ccctccccct tttttttgtt ttccgttccc ctttcccctc ccttccctat ccccgacgac cggatcctga ggaggcagct gcggtggcag 
^212       ^222       ^232       ^242       ^252       ^262       ^272       ^282       ^292       ^302       

ctgctgagtt ctcggtgaag gtatttcatt tctcctgtcc cctcccctcc ccaccccatc tattaatatt attcttttga agattcttcg ttgtcaagcc 
^312       ^322       ^332       ^342       ^352       ^362       ^372       ^382       ^392       ^402       

gccaa
^412

Remarks:

This IRES region is located on the NM_001418.1 sequence between positions 1-305.

Citations:

RNA:protein interactions:

The RNA:protein interaction:

Version: `1`	Last change: `2006-10-28 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
DAP5/p86

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

DAP5/p86 is a caspase cleaved DAP5 protein form. It has been shown that transient over-expression of the
DAP5/p86 truncated protein form supports internal ribosome entry site-mediated translation of DAP5, Apaf-1,
c-Myc and XIAP (so-called death proteins).

Citations:

Henis-Korenblit S., Shani G., Sines T., Marash L., Shohat G., Kimchi A. (2002) The caspase-cleaved DAP5 protein supports internal ribosome entry site-mediated translation of death proteins. Proc. Natl. Acad. Sci. U. S. A. 99(8):5400-5405

Nevins T. A., Harder Z. M., Korneluk R. G., Holcik M. (2003) Distinct regulation of internal ribosome entry site-mediated translation following cellular stress is mediated by apoptotic fragments of eIF4G translation initiation factor family members eIF4GI and p97/DAP5/NAT1. J. Biol. Chem. 278(6):3572-3579

The RNA:protein interaction:

Version: `1`	Last change: `2006-10-28 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
DAP5

The organism where this RNA:protein interaction occurs:

Homo sapiens SKW 6.4 (ATCC TIB-215)

Remarks:

The DAP5 protein mediates DAP5-IRES driven translation in vitro (in human SKW B-lymphoma cells).

Citations:

The RNA:protein interaction:

Version: `2`	Last change: `2009-03-22 23:31:23`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
DAP5

The organism where this RNA:protein interaction occurs:

Mus musculus

Remarks:

Direct binding of the DAP5 protein to DAP5 IRES was not demonstrated. DAP5 is not necessary for DAP5 IRES
driven translation in vivo (in mouse).

Citations:

Yamanaka S., Zhang X. Y., Maeda M., Miura K., Wang S., Farese RV J. r., Iwao H., Innerarity T. L. (2000) Essential role of NAT1/p97/DAP5 in embryonic differentiation and the retinoic acid pathway. EMBO J. 19(20):5533-5541

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