IRESite_Id:342 summary record describing characteristics of Apaf-1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `342`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-05-20 18:39:15`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `both_UTRs_incomplete`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `Apaf-1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
3694812

The mRNA/+RNA description:

Mus musculus apoptotic protease activating factor 1 mRNA, transcript variant 2

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

CGGCTTGAGG CAGAGACCAG GAGGCAGCTA GAGGAGCAGA CGTCTCACTC CGCTCGCGGA AGGGTGTGAG AGGGGTGTGT GGGGGTCGGC AGCGAGGGGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTGTGCCATC AGCCACCGGC GACGATCTGA GACAGTCGCA GCGGCTTTCC GAGCGGCGTC CGCTTCCCGC CCGGGCAGCT CCCGCCAGAG GGGTGAAGCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCGACTGGAG TGGCCGTGCT TTTGTGCCCT GGGTCCCGGT ACCCTCCCCT GGTGCGGCCC GAGGCAAGCC CACCGAGGTG ACCACCCCTC GACGCCGCTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGAGATCCCG GGCATCCACC CTGCGCCCCG AGCAGCTGAT ACCCAGGGAG GTGTCAGGAC CTGCCCGGGG CGCGGGGTCG CCGGAAGCCA GGCGGGAGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCGGCTGCTT TCTGGCAATC TAGTCTCATA AGTGACCCTC CCTGGGCTGC TTTCTTTCGA TTATCATCAG TGACCCTACC CCGGCTGCTC TTCCCAGCAC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACTCCGGTG CAAAGGCTTG GGCATCCTGG TGCTTTGCCT CTAGCCCATG CTCCACAGCG AGGAGAGAGA AAACCCTGAG GCACAATGGA TGCAAAGGCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGCAATTGTT TGCTTCAACA TAGAGAAGCT TTGGAAAAGG ACATCAAAAC ATCCTACATC ATGGATCACA TGATCAGTAA TGGCGTCTTG TCAGTGATAG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGGAGAA GGTCAAAAGT CAGGCCACTC AATATCAACG AGCAGCCGCT TTAATTAAAA TGATACTTAA TAAAGACAAC TGTGCCTACA TTTCATTCTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAACGCTCTG CTACACGAGG GCTATAAGGA CCTTGCTGCG CTTCTGCAGA GTGGCCTTCC TCTTGTGTCG TCTTCCAGTG CAAGGACAGT GCTGTGTGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGTGGAGTAC CCCAGAGGCC GGTTATTTTC GTTACTAGAA AGAAGCTGGT TCATGCGATT CAGCAGAAGC TCTGGAAACT GAATGGAGAA CCAGGGTGGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCACCATCTA TGGGATGGCA GGCTGCGGCA AGTCTGTGTT AGCTGCGGAA GCCGTTCGAG ATCACTCCCT CTTAGAAGGT TGCTTTTCAG GGGGTGTACA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTGGGTTTCC ATTGGAAAAC AAGACAAATC TGGGCTTCTC ATGAAACTGC AGAATCTGTG CATGCGCTTG GACCAAGATG AGAGTTTCTC TCAGAGGCTT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCACTTAATA TTGAGGAGGC CAAAGACCGC CTCCGTGTTC TGATGCTGCG CAAACACCCA AGGTCTCTGT TGATCTTGGA TGATGTTTGG GATCCTTGGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGTTAAAAGC TTTTGACAAT CAGTGTCAGA TTCTTCTTAC GACCAGAGAT AAGAGTGTTA CAGATTCAGT AATGGGTCCT AAGCATGTTG TCCCTGTGGA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAGTGGTCTA GGGAGAGAGA AAGGACTTGA GATCTTGTCA CTTTTTGTTA ATATGAAGAA AGAAGATCTG CCAGCGGAGG CTCACAGTAT TATAAAGGAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGCAAAGGTT CTCCTCTTGT AGTGTCTTTA ATTGGTGCAC TTTTACGTGA TTTTCCCAAT CGCTGGGCGT ACTACCTCAG ACAGCTTCAG AATAAGCAGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTAAGAGAAT AAGGAAGTCT TCATCTTATG ATTATGAGGC TCTAGATGAA GCCATGTCGA TAAGTGTTGA AATGCTCAGA GAAGACATCA AAGACTATTA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CACAGACCTT TCCATCCTTC AGAAGGACGT CAAGGTACCT ACAAAGGTGT TGTGCGTTCT CTGGGACTTG GAAACGGAAG AAGTTGAAGA CATCCTGCAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAGTTCGTTA ATAAGTCTCT CTTATTCTGT AATCGGAATG GAAAGTCATT TTGTTATTAT TTACACGATC TTCAAGTAGA TTTTCTTACA GAGAAGAATC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCAGTCAGCT TCAGGATCTG CACAGGAAGA TGGTCACTCA GTTTCAGAGG TATTACCAGC CCCACACGCT GTCTCCAGAC CAGGAGGACT GCATGTATTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTACAACTTC CTAGCCTATC ACATGGCTAG TGCCAATATG CACAAAGAAC TTTGTGCTTT AATGTTTTCC CTGGACTGGA TTAAAGCAAA AACAGAACTT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GTCGGCCCTG CCCATCTGAT TCACGAGTTC GTGGCATATA GGCATATATT GGATGAAAAG GATTGTGCAG TCTGTGAGAA TTTTCAAGAG TTTTTATCTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAAATGGACA CCTCCTTGGA CGACAGCCAT TTCCTAATAT TGTACAGCTG GGCCTCTGTG AACCAGAAAC TTCCGAAGTT TATCGACAAG CAAAGCTGCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGCCAAGCAG GAGGGGGATA CTGGGCCGCT TTACCTGGAA TGGATAAACA AAAAAACTAT CAAGAATCTG TCCCGCTTAG TCGTCCGCCC CCACACAGAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCTGTTTACC ACGCGTGTTT TTCTCAGGAT GGCCAGAGAA TAGCTTCTTG TGGGGCTGAT AAAACCTTAC AGGTGTTCAA AGCCGAGACA GGAGAGAAAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTCTTGACAT TAAAGCTCAT GAAGATGAGG TGCTCTGCTG CGCGTTCTCC TCAGACGACA GTTACATAGC GACCTGCTCA GCGGATAAGA AGGTTAAGAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTGGGATTCT GCGACTGGGA AGCTTGTGCA CACCTACGAC GAGCACTCGG AGCAAGTCAA TTGCTGCCAT TTCACCAACA GTAGTAACCA CCTTCTCTTG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCCACCGGGT CAAATGATTT CTTCCTCAAG CTCTGGGATT TGAATCAAAA AGAATGTCGA AATACCATGT TTGGTCACAC GAACTCAGTC AACCACTGCA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGTTCTCACC AGACGATGAG CTCTTGGCTA GCTGCTCAGC TGACGGGACT TTAAGGCTTT GGGATGTGAG ATCAGCAAAC GAGAGGAAAA GCATTAATGT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAGCGCTTC TTCCTGAGTT CAGAAGACCC TCCAGAGGAT GTGGAGGTGA TCGTGAAGTG TTGTTCCTGG TCTGCAGATG GTGACAAAAT AATAGTGGCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCAAAAAACA AAGTCCTCCT TTTTGATATT CATACTAGTG GCCTATTGGC AGAGATCCAC ACAGGCCATC ACAGCACCAT CCAGTACTGT GACTTCTCCC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCTATGACCA TTTGGCTGTG ATTGCCCTGT CTCAGTACTG TGTGGAGTTG TGGAACATAG ACTCCCGCCT AAAGGTGGCC GACTGCAGAG GACATTTGAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTGGGTTCAC GGTGTGATGT TTTCTCCCGA TGGCTCCTCA TTTTTGACAG CTTCTGATGA CCAAACAATA AGGGTCTGGG AGACAAAAAA GGTATGCAAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AACTCTGCTA TCGTGCTAAA GCAGGAAATA GACGTCGTGT TTCAAGAGAA CGAAACGATG GTCCTTGCAG TTGACAACAT AAGAGGCCTG CAACTCATTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CTGGAAAAAC AGGCCAGATT GATTACCTGC CTGAAGCCCA AGTGAGTTGC TGCTGCCTCA GTCCACACCT TGAGTACGTG GCATTCGGAG ATGAAGATGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCCATTAAG ATTATAGAAC TTCCAAACAA CAGAGTCTTC AGTTCTGGGG TTGGGCACAA GAAAGCTGTG CGGCACATCC AGTTCACAGC TGATGGGAAG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ACACTGATTT CAAGTTCTGA AGATTCTGTG ATTCAGGTAT GGAATTGGCA GACAGGGGAC TATGTATTTT TGCAAGCCCA CCAGGAAACG GTAAAGGACT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TCAGGCTCCT CCAAGATTCA AGATTGCTTT CTTGGTCATT TGATGGAACG GTGAAGGTGT GGAATGTCAT TACCGGAAGA ATAGAAAGAG ACTTTACTTG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TCATCAGGGC ACAGTGCTTT CCTGTGCTAT CTCTTCTGAT GCGACCAAGT TTTCCTCTAC CTCTGCTGAT AAGACTGCCA AGATCTGGAG TTTTGACCTC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTTTCCCCTC TTCATGAGCT GAAGGGCCAT AATGGCTGTG TCCGCTGCTC TGCCTTCTCG CTGGATGGCA TCCTGTTGGC AACTGGAGAT GACAATGGAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAATCCGGAT ATGGAATGTC TCAGATGGCC AGCTTCTTCA TTCGTGTGCT CCGATCTCGG TAGAGGAAGG AACTGCTACC CACGGCGGCT GGGTAACTGA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TGTGTGCTTC TCTCCCGACA GTAAAACGCT TGTCTCTGCT GGAGGATATC TCAAGTGGTG GAATGTTGCC ACTGGGGACT CCTCACAGAC CTTCTACACA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AATGGAACAA ACCTCAAGAA AATCCACGTG TCCCCTGACT TCAGAACCTA TGTGACTGTC GATAATCTCG GTATTTTATA TATTTTACAG GTTTTAGAGT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AAAATGGCTA AGCGTTAATG TAGTTCAGCT TCCTTAAGTT TGAATTGGAA AAAATCTAAA CCCTCTATAT CAACTTTTAT AAAGCTGTGA ATTGTACTGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGTATTGCAA CATTTACAAA GGTGGTTTAA CAGCTGGGCC AGTGCTCTGT ATAGTTGGGT GAATCATAGT ATATCTCCAC AAAGGAACAT ACTTTTACTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TATTTTTTTA AATATAGTCA TCATTGTTAT TAACAGTTTG TCCTTAACAT GCAAATGAAA TGGTAAATAT GTACCTTGTT ATGCTATTGG TAAATTCTTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GATGCATTCA AATTGGTTGG CAAAATTAGT GAGAATCATT TGAAGGCCTT CTATAGGTTG ATGCTGTCAT TATGTAGGCT ATGTCCCAAG GTAATGGTGG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TCAGTTTTCT GAACCACACT TACTCCCAGG GGGTATGGTT TTCCAAATAA ATCATGCTTA TTTGCACTCT TTAAATTTGC TTTAAGATAT TGTGTCATGG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TGCAAGCACA GTCTGCAACA TTTCTCTTGT TAACTCAGTG AGTATTGGTT TTCAACAGTT CTTCCTATGA GCTAGTCATG TGTTAGAGAG ATTTCTCTCT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTAGCTCTGT GTTTAGCTGG ACTCTGGCTG TCAGTGTCTG TGAATTGGGC ACCAACCACC TTGCACTCTT TTAGTTGTTT CGTTTATAAA GACAGGGTTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ATGTAGTCCT GGCTCTCTTG GCACTCAGCA TGTACACCAG GTTAGCCTTG AACTCAGAGC TCAGCCTGCC TCTCTGCCTC CTGAGTTCTG GAATTGAAGG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CGTGTGCCAA CAGCACCTCT CTCTCTCAGT TATACTCGAC TGAGCTTGAC CC
^5101      ^5111      ^5121      ^5131      ^5141      ^5151

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 Swiss-Webster/NIH

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

The abbreviated name of this ORF/gene:
Apaf-1

The description of the protein encoded in this ORF:
apoptotic protease activating factor

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):

586-4302

Remarks:

Current gene models in Gene database for mouse Apaf-1 present 2, alternatively spliced transcripts
(GI:110347464 and GI:110347470). They differ in a region which is optionally spliced out in variant 2. It
appears Coldwell et al. (2000) have used the second splice variant, with the optional intron excised as
they refer in their article to mouse Apaf-1 having 5'-UTR long 585bp (which is the case of GI:3694812) and
which aligns well with the second splice variant GI:110347470. The difference between the original record
GI:3694812 and current model for splice variant 2 is an extension of 5'-UTR by 40 bp at the 5'-extremity.
Below is shown the region with the optional intron (the alignment of 5'-ends of 5'UTRs is in the record with
pRMmAF plasmid annotation IRESiteID:343):

110347464       aactccggtgcaaaggcttggttacacatccggcgctcacacatcctgttgctcgtcatg
3694812         aactccggtgcaaaggcttg----------------------------------------
110347470       aactccggtgcaaaggcttg----------------------------------------
                ********************

110347464       acaggcatcctggtgctttgcctctagcccatgctccacagcgaggagagagaaaaccct
3694812         ---ggcatcctggtgctttgcctctagcccatgctccacagcgaggagagagaaaaccct
110347470       ---ggcatcctggtgctttgcctctagcccatgctccacagcgaggagagagaaaaccct
                   *********************************************************

Citations:

Coldwell M. J., Mitchell S. A., Stoneley M., MacFarlane M., Willis A. E. (2000) Initiation of Apaf-1 translation by internal ribosome entry. Oncogene. 19(7):899-905

IRESs:

IRES:

Version: `1`	Last change: `2008-05-20 18:39:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Apaf-1`

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

1-583

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

CGGCTTGAGG CAGAGACCAG GAGGCAGCTA GAGGAGCAGA CGTCTCACTC CGCTCGCGGA AGGGTGTGAG AGGGGTGTGT GGGGGTCGGC AGCGAGGGGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTGTGCCATC AGCCACCGGC GACGATCTGA GACAGTCGCA GCGGCTTTCC GAGCGGCGTC CGCTTCCCGC CCGGGCAGCT CCCGCCAGAG GGGTGAAGCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCGACTGGAG TGGCCGTGCT TTTGTGCCCT GGGTCCCGGT ACCCTCCCCT GGTGCGGCCC GAGGCAAGCC CACCGAGGTG ACCACCCCTC GACGCCGCTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGAGATCCCG GGCATCCACC CTGCGCCCCG AGCAGCTGAT ACCCAGGGAG GTGTCAGGAC CTGCCCGGGG CGCGGGGTCG CCGGAAGCCA GGCGGGAGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCGGCTGCTT TCTGGCAATC TAGTCTCATA AGTGACCCTC CCTGGGCTGC TTTCTTTCGA TTATCATCAG TGACCCTACC CCGGCTGCTC TTCCCAGCAC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACTCCGGTG CAAAGGCTTG GGCATCCTGG TGCTTTGCCT CTAGCCCATG CTCCACAGCG AGGAGAGAGA AAACCCTGAG GCA
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581

Remarks:

It appears only bases 1-583 have been actually cloned into pRMmAF vector. Please refer to the annotation of
the plasmids pRAF and pRMmAF).

Citations:

Coldwell M. J., Mitchell S. A., Stoneley M., MacFarlane M., Willis A. E. (2000) Initiation of Apaf-1 translation by internal ribosome entry. Oncogene. 19(7):899-905

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