IRESite_Id:122 summary record describing characteristics of FMR1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `122`	Version: `7`
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský	Last change: `2007-07-24 00:00:00`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `nonexisting_chimera_of_GenBank_record_and_tested_IRES_fragment`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `FMR1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
50053960

Synonyms of the gene name:

Synonym: FMRP

Synonym: FRAXA

Synonym: MGC87458

The mRNA/+RNA description:

Homo sapiens fragile X mental retardation 1 (FMR1), mRNA.

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

GGCCTCAGTC AGGCCTCAGC TCCGTTTCGG TTTCACTTCC GGTGGAGGGC CGCCTCTGAG CGGGCGGCGG GCCGACGGCG AGCGCGGGCG GCGGCGGTGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGGAGGCGCC GCTGCCAGGG GGCGTGCGGC AGCGCGGCGG CGGCGGCGGC GGCGGCGGCG GCGGCGGCGG CGGCGGCGGC GGCTGGGCCT CGAGCGCCCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAGCCCACCT CTCGGGGGCG GGCTCCCGGC GCTAGCAGGG CTGAAGAGAA CATGATGGAG GAGCTGGTGG TGGAAGTGCG GGGCTCCAAT GGCGCTTTCT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACAAGGCATT TGTAAAGGAT GTTCATGAAG ATTCAATAAC AGTTGCATTT GAAAACAACT GGCAGCCTGA TAGGCAGATT CCATTTCATG ATGTCAGATT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCACCTCCT GTAGGTTATA ATAAAGATAT AAATGAAAGT GATGAAGTTG AGGTGTATTC CAGAGCAAAT GAAAAAGAGC CTTGCTGTTG GTGGTTAGCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AAAGTGAGGA TGATAAAGGG TGAGTTTTAT GTGATAGAAT ATGCAGCATG TGATGCAACT TACAATGAAA TTGTCACAAT TGAACGTCTA AGATCTGTTA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATCCCAACAA ACCTGCCACA AAAGATACTT TCCATAAGAT CAAGCTGGAT GTGCCAGAAG ACTTACGGCA AATGTGTGCC AAAGAGGCGG CACATAAGGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTTTAAAAAG GCAGTTGGTG CCTTTTCTGT AACTTATGAT CCAGAAAATT ATCAGCTTGT CATTTTGTCC ATCAATGAAG TCACCTCAAA GCGAGCACAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGCTGATTG ACATGCACTT TCGGAGTCTG CGCACTAAGT TGTCTCTGAT AATGAGAAAT GAAGAAGCTA GTAAGCAGCT GGAGAGTTCA AGGCAGCTTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCTCGAGATT TCATGAACAG TTTATCGTAA GAGAAGATCT GATGGGTCTA GCTATTGGTA CTCATGGTGC TAATATTCAG CAAGCTAGAA AAGTACCTGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGTCACTGCT ATTGATCTAG ATGAAGATAC CTGCACATTT CATATTTATG GAGAGGATCA GGATGCAGTG AAAAAAGCTA GAAGCTTTCT CGAATTTGCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAAGATGTAA TACAAGTTCC AAGGAACTTA GTAGGCAAAG TAATAGGAAA AAATGGAAAG CTGATTCAGG AGATTGTGGA CAAGTCAGGA GTTGTGAGGG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGAGGATTGA GGCTGAAAAT GAGAAAAATG TTCCACAAGA AGAGGAAATT ATGCCACCAA ATTCCCTTCC TTCCAATAAT TCAAGGGTTG GACCTAATGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCCAGAAGAA AAAAAACATT TAGATATAAA GGAAAACAGC ACCCATTTTT CTCAACCTAA CAGTACAAAA GTCCAGAGGG TGTTAGTGGC TTCATCAGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTAGCAGGGG AATCCCAGAA ACCTGAACTC AAGGCTTGGC AGGGTATGGT ACCATTTGTT TTTGTGGGAA CAAAGGACAG CATCGCTAAT GCCACTGTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTTTGGATTA TCACCTGAAC TATTTAAAGG AAGTAGACCA GTTGCGTTTG GAGAGATTAC AAATTGATGA GCAGTTGCGA CAGATTGGAG CTAGTTCTAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACCACCACCA AATCGTACAG ATAAGGAAAA AAGCTATGTG ACTGATGATG GTCAAGGAAT GGGTCGAGGT AGTAGACCTT ACAGAAATAG GGGGCACGGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGACGCGGTC CTGGATATAC TTCAGGAACT AATTCTGAAG CATCAAATGC TTCTGAAACA GAATCTGACC ACAGAGACGA ACTCAGTGAT TGGTCATTAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCCAACAGA GGAAGAGAGG GAGAGCTTCC TGCGCAGAGG AGACGGACGG CGGCGTGGAG GGGGAGGAAG AGGACAAGGA GGAAGAGGAC GTGGAGGAGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CTTCAAAGGA AACGACGATC ACTCCCGAAC AGATAATCGT CCACGTAATC CAAGAGAGGC TAAAGGAAGA ACAACAGATG GATCCCTTCA GATCAGAGTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GACTGCAATA ATGAAAGGAG TGTCCACACT AAAACATTAC AGAATACCTC CAGTGAAGGT AGTCGGCTGC GCACGGGTAA AGATCGTAAC CAGAAGAAAG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGAAGCCAGA CAGCGTGGAT GGTCAGCAAC CACTCGTGAA TGGAGTACCC TAAACTGCAT AATTCTGAAG TTATATTTCC TATACCATTT CCGTAATTCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TATTCCATAT TAGAAAACTT TGTTAGGCCA AAGACAAATA GTAGGCAAGA TGGCACAGGG CATGAAATGA ACACAAATTA TGCTAAGAAT TTTTTATTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGGTATTGG CCATAAGCAA CAATTTTCAG ATTTGCACAA AAAGATACCT TAAAATTTGA AACATTGCTT TTAAAACTAC TTAGCACTTC AGGGCAGATT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTAGTTTTAT TTTCTAAAGT ACTGAGCAGT GATATTCTTT GTTAATTTGG ACCATTTTCC TGCATTGGGT GATCATTCAC CAGTACATTC TCAGTTTTTC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTAATATATA GCATTTATGG TAATCATATT AGACTTCTGT TTTCAATCTC GTATAGAAGT CTTCATGAAA TGCTATGTCA TTTCATGTCC TGTGTCAGTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TATGTTTTGG TCCACTTTTC CAGTATTTTA GTGGACCCTG AAATGTGTGT GATGTGACAT TTGTCATTTT CATTAGCAAA AAAAGTTGTA TGATCTGTGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTTTTTTATA TCTTGGCAGG TAGGAATATT ATATTTGGAT GCAGAGTTCA GGGAAGATAA GTTGGAAACA CTAAATGTTA AAGATGTAGC AAACCCTGTC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AAACATTAGT ACTTTATAGA AGAATGCATG CTTTCCATAT TTTTTTCCTT ACATAAACAT CAGGTTAGGC AGTATAAAGA ATAGGACTTG TTTTTGTTTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGTTTTGTTG CACTGAAGTT TGATAAATAG TGTTATTGAG AGAGATGTGT AATTTTTCTG TATAGACAGG AGAAGAAAGA ACTATCTTCA TCTGAGAGAG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCTAAAATGT TTTCAGCTAG GAACAAATCT TCCTGGTCGA AAGTTAGTAG GATATGCCTG CTCTTTGGCC TGATGACCAA TTTTAACTTA GAGCTTTTTT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTTTAATTTT GTCTGCCCCA AGTTTTGTGA AATTTTTCAT ATTTTAATTT CAAGCTTATT TTGGAGAGAT AGGAAGGTCA TTTCCATGTA TGCATAATAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCCTGCAAAG TACAGGTACT TTGTCTAAGA AACATTGGAA GCAGGTTAAA TGTTTTGTAA ACTTTGAAAT ATATGGTCTA ATGTTTAAGC AGAATTGGAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AAGACTAAGA TCGGTTAACA AATAACAACT TTTTTTTCTT TTTTTCTTTT GTTTTTTGAA GTGTTGGGGT TTGGTTTTGT TTTTTGAGTC TTTTTTTTTT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AAGTGAAATT TATTGAGGAA AAATATGTGA AGGACCTTCA CTCTAAGATG TTATATTTTT CTTAAAAAGT AACTCCTAGT AGGGGTACCA CTGAATCTGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACAGAGCCGT AAAAACTGAA GTTCTGCCTC TGATGTATTT TGTGAGTTTG TTTCTTTGAA TTTTCATTTT ACAGTTACTT TTCCTTGCAT ACAAACAAGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATATAAAATG GCAACAAACT GCACATGATT TCACAAATAT TAAAAAGTCT TTTAAAAAGT ATTGCCAAAC ATTAATGTTG ATTTCTAGTT ATTTATTCTG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GGAATGTATA GTATTTGAAA ACAGAAATTG GTACCTTGCA CACATCATCT GTAAGCTGTT TGGTTTTAAA ATACTGTAGA TAATTAACCA AGGTAGAATG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACCTTGTAAT GTAACTGCTC TTGGGCAATA TTCTCTGTAC ATATTAGCGA CAACAGATTG GATTTTATGT TGACATTTGT TTGGTTATAG TGCAATATAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTTGTATGCA AGCAGTTTCA ATAAAGTTTG ATCTTCCTCT GCTAAATTGA TGTTGATGCA ATCCTTACAA ATGATTGCTT TTAAAATTTT AAGCTAGGAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAGAAATCTA TAGAAAGTGT TCTGTTACAA AATGTAACTG TTACCATTGG AAATTTCACG TCATAGGAAG TTAGCCTTTA TCTACCCAAC TTTCAAGAAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTTCTTTAAT AAAGCGAAAA CTCAACCAAA TGGTACTTTT CCACAGTGTA CCATTAAAAT ATGCACTAGT CTCTTTTTAC AAGGCTGTAT TCAGCAAGGG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CCTAACTTGC TTAAAGTGTA ATTACTAACT TCTAAAACTG TACTTTGATT CACATGTTTT CAAATGGAGT TGGAGTTCAT TCATATTACA ATATTTGTGT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCTAAACGTG TATGTTTTTC AGTTCAAAGT CATGATGTTT TTAAAATCTT ATTAAAGTTT CAAAAATCTG AAGATTGTTT ATCTAGATGT AAATTTT
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

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

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:
heterogeneous_population_of_molecules_found

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:
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 SK-N-MC (ATCC HTB-10)

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

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
FMR1

The description of the protein encoded in this ORF:
fragile X mental retardation 1

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):

252-2153

OPTIONAL: The function of the encoded protein

RNA-binding protein. Associated to polysomes and might be involved in the transport of mRNA from the nucleus
to the cytoplasm.

GO:0005737;  Cellular component: cytoplasm
GO:0005730;  Cellular component: nucleolus
GO:0005654;  Cellular component: nucleoplasm
GO:0005625;  Cellular component: soluble fraction
GO:0003729;  Molecular function: mRNA binding
GO:0005515;  Molecular function: protein binding

Remarks:

This sequence is composed of Figure 1 (L29074) in cited article (5' UTR) and GenBank sequence number 50053960
(the rest of the mRNA) by curator [it does not start at the base 251 but at the base 252].

Citations:

Chiang P. W., Carpenter L. E., Hagerman P. J. (2001) The 5'-untranslated region of the FMR1 message facilitates translation by internal ribosome entry. J. Biol. Chem. 276(41):37916-37921

IRESs:

IRES:

Version: `5`	Last change: `2007-07-24 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `FMR1`

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

1-252

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GGCCTCAGTC AGGCCTCAGC TCCGTTTCGG TTTCACTTCC GGTGGAGGGC CGCCTCTGAG CGGGCGGCGG GCCGACGGCG AGCGCGGGCG GCGGCGGTGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGGAGGCGCC GCTGCCAGGG GGCGTGCGGC AGCGCGGCGG CGGCGGCGGC GGCGGCGGCG GCGGCGGCGG CGGCGGCGGC GGCTGGGCCT CGAGCGCCCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAGCCCACCT CTCGGGGGCG GGCTCCCGGC GCTAGCAGGG CTGAAGAGAA CA
^201       ^211       ^221       ^231       ^241       ^251

Remarks:

Sequences between -223 and -209 [bases 29 to 43 here in database] appear to contribute most of the observed
IRES activity of the FMR1 5'-UTR in the dicistronic context. This sequence is located mainly within a
21-nucleotide, pyrimidine-rich region spanning nucleotides -232 through -212 [bases 20 to 40 here in
database].

Citations:

Chiang P. W., Carpenter L. E., Hagerman P. J. (2001) The 5'-untranslated region of the FMR1 message facilitates translation by internal ribosome entry. J. Biol. Chem. 276(41):37916-37921

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