IRESite_Id:243 summary record describing characteristics of NRF_-653

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `243`	Version: `9`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2009-09-01 21:15:02`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
7406601

Synonyms of the gene name:

Synonym: NF-kappaB-repressing factor

The mRNA/+RNA description:

Homo sapiens mRNA for transcription factor NRF (NF-kappaB-repressing factor), a nuclear inhibitor of
NF-kappaB. Poly(A)-tail was dropped from the sequence.

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

cagagtaatg acatggttcc ttccatcctc caaaggtgac caataatagt ttgtaagtat cattatgaac taatgaattt tcaacatatt tgatatattt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

caatccattg ccatcattgt tcttatcgat atttgagttg gctcactttg ccagtaagag tctattcaaa ttggcttctg agtccatttg acacaacacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tttgatcttt gacagtttcc ttggttttag gtgctagatg atttctcagg ctcaccttag acatttcctg ccacagactt agaatcagcc atttctctaa 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ggaccctgat tccatttcat gagaaatgat agagaccaca atcaaaacaa gtcatgaatt tatactgata ttttcaattc aaattaaaga tgaggttttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gctaaatttt tttgagttta tatttgtatg tcttatgctg aaaaatcttg tttcctaatt agtaacataa ttattcattt gatgggtaaa tattttaggg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ccgattcttt ggttttatag ccaagatacc ctgttgataa agtcttgtgg gagcaattat aagactggct tattttgaag ctttttaaaa aagacatcct 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tacctgtttt aactgtagat tatattaact taaatagGTA CAGCCCACGC TTGATGGAAA AAATTCTCCA AATGGCTGAA GGTATTGATA TTGGGGAGAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCCTTCATAT GATCTGGTGC TGTCCAAACC TTCCAAAGGT CAAAAACGCC ACCTCTCAAC ATGTGATGGT CAAAATCCTC CTAAAAAGCA AGCCGGTTCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AAATTCCATG CGAGACCTCG TTTTGAGCCT GTACATTTTG TAGCTAGTAG TTCAAAAGAT GAAGGACAGG AAGATCCTTA TGGCCCTCAA ACAAAAGAGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TAAATGAACA AACACATTTT GCCAGCATGC CAAGAGACAT CTACCAAGAT TATACTCAAG ACTCTTTCAG TATACAAGAT GGGAATTCTC AGTATTGTGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTCATCAGGA TTCATTCTCA CAAAAGACCA GCCTGTAACA GCCAACATGT ATTTTGACAG TGGGAACCCT GCCCCAAGCA CCACATCACA GCAGGCAAAC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCTCAGTCAA CTCCTGAGCC TTCACCATCA CAGACATTTC CCGAGTCTGT GGTAGCCGAG AAGCAGTATT TTATTGAAAA ATTAACGGCG ACAATCTGGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGAACCTTTC TAATCCAGAA ATGACTTCTG GATCTGATAA AATTAATTAT ACATATATGT TAACTCGTTG TATTCAGGCG TGTAAGACAA ATCCTGAGTA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TATATATGCT CCTTTAAAGG AAATTCCTCC TGCCGACATC CCCAAAAATA AAAAACTTCT AACTGATGGC TATGCTTGTG AAGTTAGATG CCAAAATATC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TACTTAACTA CAGGTTATGC TGGCAGCAAG AATGGGTCCA GGGATCGAGC TACAGAGCTA GCTGTAAAAC TCTTGCAGAA ACGTATTGAA GTTAGAGTTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCCGGCGGAA ATTCAAGCAT ACATTTGGAG AGGACCTCGT GGTGTGTCAG ATTGGCATGT CCTCCTATGA ATTTCCTCCA GCTCTGAAGC CACCAGAAGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCTGGTGGTG CTGGGTAAAG ATGCTTCCGG GCAGCCAATT TTTAATGCTT CTGCCAAACA CTGGACCAAT TTTGTCATTA CAGAAAATGC AAATGATGCA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATTGGTATCC TTAACAATTC TGCCTCATTC AACAAGATGT CAATTGAATA CAAATATGAG ATGATGCCAA ATCGCACATG GCGTTCGTCG AGTGTTTTTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CAAGATCACT GCTTAGCTGA AGGTTATGGA ACCAAGAAAA CAAGTAAACA TGCAGCTGCC GACGAGTTTG AAAATTCTTC AAAAACACAG CCCACTTATC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CATCTGTCAA AAGTTCACAA TGCCATACAG GCTCTTCACC CAGAGGATCT GGAAAGAAGA AAGATATAAA GGCTCTGTAG TTTATGAGAA TTCTTCAAAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCCGTGTGCA CGCTGAACGA CACAGCTCAG TTTAACCGAA TGACAGTTGA GTATGTCTAT GAAAGGATGA CAGGCCTCCG CTGGAAATGC AAAGTGATTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TAGAGAGTGA AGTAATTGCA GAAGCAGTTG GGGTGAAGAA AACTGTCAAA TATAAGCTGC TGGGGAAGCT GTGAAAACCC TCAAAAAGAC CCAGCAACTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCATTAACAA CTTGAAGAAA GGAGCTGTTG AAGATGTGAT TTCAAGAAAT GAAATTCAGG GCCGCTCAGC AGAGGAGGCT TACAAACAGC AAATCAAAGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGATAATATT GGAAATCAGC TGCTGAGAAA GATGGGTTGG ACTGGTGGTG GTTTAGGTAA ATCTGGTGAG GGCATACGGG AGCCTATCTC AGTGAAAGAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGCATAACG GAAGGGCTTG GTCTGGATGT AGAGAGGGTG ATAAAATGCC AAGAGAGATA TTGAACAGAT CATCAGAAAC TACGAAAGCT CCGAGAGCCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CACAGATTTG ACTTTCTCTA GAGAGCTGAC TAATGATGAA CGGAAGCAAA TACATCAGAT TGCCCAGAAG TATGGTCTTA AGAGTAAGTC TCATGGGGTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGCCATGATA GGTACCTAGT GGTAGGTAGA AAAAGACGGA AGGAAGACCT ACTAGATCAG CTCAAACAGG AAGGCCAAGT GGGCATTACG AGCTTGTTAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCCTCAAGCA AATTGAGATC TTACTAATTT ATTTTGTAAA TGCCTAATGA GGTAGATTTT TGAATTAAAG AAATGCTACA TGTTCCGGTT GCAGAGTATA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTCATAAGAT GTCTCACCTT GTTCATTTCA CATAGTGGTT TATTAGATAT TGGAACCTAA AGAATTCTGT CCACTTGTAT TAGCTTAATC CAGCAGATGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TATTGTGCAG TTACTGTTTG TGTCTTTGAT ATTGCTGTGT CCCTCAGATT TTAGTAGTTT GACAAGCAAG AACACATATC CAAATGGAAT TTTACCCTGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAAATTAGCA TTTTAAAGGG CATAGCACAG CAATCTGCAA CAATATGTAA AGTTGATATT GACTACAATA AAAATCCAGT CTTAATTCCA GATTTACTGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAATGTCAGA TCATTTTGTA TTAATCTATT TTCATCTTTG TGTGAAGCCA GTTATAGAAT GTTTGACAAT AAATTGTGCT GTACATGTCC TTACCAACAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ATGATGTAAA ACTTTCTTAA AGTAATTTTA GTGTTATTTA TTTATAACTT CTACCATGTG ATTTCCAGAC TATTGGAAGT GATTTACTGT ATCTTGTGGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GATATATTTT TAACAAATTC TACTCTTCAC GCTGAGAGAG CACTACTTGA GAGAGCAGTT GAAAGTTTCA AAAACTTTGG TTCAATCTGA AGAAAGGAAG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CTTGAACTGT TTGTTCTTGG TGCCTTGCAG AGAGACTCAC AGCAACTCTC CATTATAGCT TTCACACGGT TTGGATGTGC AGCACATCCA AGGCACACCA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CAGCTGTGGT AGAGCTTGGT AAAAGACTGA ATACATTGGT GCTTTGATGA AAAGGTCAGT TGGCTGGTCC CTCTCTCAAA AAGCTTATTA AGCCTGAAAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GCCAACTTTG TAACATATTT AAAACTGCTA TTTTCGCTTA TTTCTGGAAT GTAAAAAAAA AATGTATAAA AAGAATTAGT GTATGCTTCC TGAATAAAAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GGAGCCAAAG TTGATCAG
^3701      ^3711

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The organism containing this mRNA with IRES segment in its genome:

Homo sapiens

A promoter reported in cDNA corresponding to IRES sequence:
no (not convincing) 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:
homogeneous_population_of_molecules_confirmed

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:

Mus musculus C243

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:
NRF

The description of the protein encoded in this ORF:
transcription factor NRF

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):

654-1820

Remarks:

Please refer also to GI:119960145 (EF158333.1) submitted by Oumard et al. (2000).

The 5'-most sequence of this mRNA (AJ011812.2, GI:7406601, 3736 bp) is confirmed by the following EST
since position 144 and downstream:


>gb|DR002872.1| UniGene info TC114069 Human fetal brain, large insert, pCMV expression library
Homo sapiens cDNA clone TC114069 5' similar to Homo sapiens NF-kappaB repressing factor (NKRF), mRNA sequence.
Length=756

 Score = 1369 bits (741),  Expect = 0.0
 Identities = 746/748 (99%), Gaps = 1/748 (0%)
 Strand=Plus/Plus

Query  144  CACTTTGCCAGTAAGAGTCTATTCAAATTGGCTTCTGAGTCCATTTGACACAACACCTTT  203
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  9    CACTTTGCCAGTAAGAGTCTATTCAAATTGGCTTCTGAGTCCATTTGACACAACACCTTT  68

[cut]

However, several additional mRNA records confirm this exon (all three from the same lab):
EF216688.1  GI:124431166, Nourbakhsh,M., 2809bp
EF216689.1  GI:124431168, Nourbakhsh,M., 3764bp
EF158333.1  GI:119960145, Nourbakhsh,M., 988bp (missing part of CDS and whole 3'-UTR)

There is one clone with genomic DNA insert:
AC004913.2  GI:5523836, Waterston,R.H. (genomic DNA)




There is one more entry confiming existence of the  5'-end sequence:

>gb|ES316131.1| UniGene info Met-p03-C12 Metastatic Melanoma SSH Library (Met Library) Homo  sapiens cDNA
Length=473

 Score =  601 bits (325),  Expect = 1e-168
 Identities = 364/383 (95%), Gaps = 1/383 (0%)
 Strand=Plus/Plus

Query  1    CAGAGTAATGACATGGTTCCTTCCATCCTCCAAAGGTGACCAATAATAGTTTGTAAGTAT  60
            |||| |||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct  91   CAGAATAATGACATGGTTCCTTCCATCCTCCAAAGGTGACCAATAATAGTTGGTAAGTAT  150

Query  61   CATTATGAACTAATGAATTTTCAACATATTTGATATATTTCAATCCATTGCCATCATTGT  120
            ||||||||||||||||||| |||||||||||||||||||||||||||| |||||||||||
Sbjct  151  CATTATGAACTAATGAATTGTCAACATATTTGATATATTTCAATCCATGGCCATCATTGT  210

Query  121  TCTTATCGATATTTGAGTTGGCTCACTTTGCCAGTAAGAGTCTATTCAAATTGGCTTCTG  180
            ||||||||||||| |||| |||||||||||||||||||||||||||||||| ||||||||
Sbjct  211  TCTTATCGATATTGGAGTGGGCTCACTTTGCCAGTAAGAGTCTATTCAAATGGGCTTCTG  270

Query  181  AGTCCATTTGACACAACACCTTTGATCTTTGACAGTTTCCTTGGTTTTAGGTGCTAGATG  240
            |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||
Sbjct  271  AGTCCATTTGACACAACACCTTTGATCTTTGAGAGTTTCCTTGGTTTGAGGTGCTAGATG  330

Query  241  ATTTCTCAGGCTCACCTTAGACATTTCC-TGCCACAGACTTAGAATCAGCCATTTCTCTA  299
            |||||||||||||||||||||||||| | ||||| ||| |||||||||| ||||||||||
Sbjct  331  ATTTCTCAGGCTCACCTTAGACATTTGCGTGCCATAGATTTAGAATCAGGCATTTCTCTA  390

Query  300  AGGACCCTGATTCCATTTCATGAGAAATGATAGAGACCACAATCAAAACAAGTCATGAAT  359
            ||||||||||||||||| |||||||||||||||||| || |||||||||||||||||| |
Sbjct  391  AGGACCCTGATTCCATTGCATGAGAAATGATAGAGAGCAAAATCAAAACAAGTCATGAGT  450

Query  360  TTATACTGATATTTTCAATTCAA  382
             ||||||||||||||||||||||
Sbjct  451  GTATACTGATATTTTCAATTCAA  473


There is yet one more match to DR002872 (not shown).

All other ESTs confirm only the sequence downstream since the position 636:

>gb|BI544578.1| UniGene info 603242218F1 NIH_MGC_95 Homo sapiens cDNA clone IMAGE:5284565
5', mRNA sequence.
Length=740

 Score = 1022 bits (553),  Expect = 0.0
 Identities = 580/591 (98%), Gaps = 10/591 (1%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  155   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  214

[cut]

>emb|AL539002.3| UniGene info AL539002 Homo sapiens FETAL BRAIN Homo sapiens cDNA clone CS0DF030YI23
5-PRIME, mRNA sequence.
Length=1101

 Score = 1498 bits (811),  Expect = 0.0
 Identities = 825/833 (99%), Gaps = 3/833 (0%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  179   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  238

[cut]

>gb|BI554152.1| UniGene info 603235573F1 NCI_CGAP_Brn67 Homo sapiens cDNA clone IMAGE:5309490
5', mRNA sequence.
Length=702

 Score =  835 bits (452),  Expect = 0.0
 Identities = 496/515 (96%), Gaps = 11/515 (2%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  190   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  249

[cut]

>gb|BG705887.1| UniGene info 602669385F1 NIH_MGC_96 Homo sapiens cDNA clone IMAGE:4792052
5', mRNA sequence.
Length=791

 Score = 1149 bits (622),  Expect = 0.0
 Identities = 648/659 (98%), Gaps = 7/659 (1%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  135   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  194

[cut]

>gb|BI599571.1| UniGene info 603247745F1 NIH_MGC_96 Homo sapiens cDNA clone IMAGE:5299667
5', mRNA sequence.
Length=572

 Score =  795 bits (430),  Expect = 0.0
 Identities = 436/439 (99%), Gaps = 1/439 (0%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  135   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  194

[cut]

>gb|BI836552.1| UniGene info 603089514F1 NIH_MGC_120 Homo sapiens cDNA clone IMAGE:5228666
5', mRNA sequence.
Length=889

 Score = 1319 bits (714),  Expect = 0.0
 Identities = 756/774 (97%), Gaps = 11/774 (1%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  119   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  178

[cut]

>gb|BG741433.1| UniGene info 602632215F1 NCI_CGAP_Skn3 Homo sapiens cDNA clone IMAGE:4777539
5', mRNA sequence.
Length=913

 Score = 1262 bits (683),  Expect = 0.0
 Identities = 741/766 (96%), Gaps = 15/766 (1%)
 Strand=Plus/Plus

Query  636   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  695
             ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct  134   AGGTACAGCCCACGCTTGATGGAAAAAATTCTCCAAATGGCTGAAGGTATTGATATTGGG  193

[cut]





Baranick et al. (2008) studied shorter region -163 to -1 (relative to initiator ATG) whereas Oumard et al.
(2000) studied -653 to -1. Baranick et al. (2008) in Supplementary Figure 9B showed a putative mammalian
branching site YNYTRAC (the actual sequence -47_TTTTAAC_-41).

The exon containing this putative IRES is always the first exon, probably different promoter is involved
than the one discussed further in this text. The many other ESTs in dbEST covering a different splice
variant utilizing the 3'-splice acceptor site of this putative IRES appear to be transcribed from an
upstream promoter and therefore their second exon overlaps in tiny part with the 3'-border of the "IRES"
(from -17 downstream) (Baranick et al. (2008), Supplementary Figure 13).

Citations:

Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759

IRESs:

IRES:

Version: `7`	Last change: `2009-04-08 16:46:36`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NRF_-653_-17`

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

1-637

Conclusion:
probably_not_IRES

How IRES boundaries were determined:
experimentally_determined

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

cagagtaatg acatggttcc ttccatcctc caaaggtgac caataatagt ttgtaagtat cattatgaac taatgaattt tcaacatatt tgatatattt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

caatccattg ccatcattgt tcttatcgat atttgagttg gctcactttg ccagtaagag tctattcaaa ttggcttctg agtccatttg acacaacacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tttgatcttt gacagtttcc ttggttttag gtgctagatg atttctcagg ctcaccttag acatttcctg ccacagactt agaatcagcc atttctctaa 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ggaccctgat tccatttcat gagaaatgat agagaccaca atcaaaacaa gtcatgaatt tatactgata ttttcaattc aaattaaaga tgaggttttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gctaaatttt tttgagttta tatttgtatg tcttatgctg aaaaatcttg tttcctaatt agtaacataa ttattcattt gatgggtaaa tattttaggg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ccgattcttt ggttttatag ccaagatacc ctgttgataa agtcttgtgg gagcaattat aagactggct tattttgaag ctttttaaaa aagacatcct 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tacctgtttt aactgtagat tatattaact taaatag
^601       ^611       ^621       ^631

Remarks:

Reboll et al. (2007) studied "IRES" activity of many mutants spanning the "IRES" region and determined a
secondary structure of 77bp long region immediately preceding the initiator ATG.

Baranick et al. (2008) postulate that the "IRES" activity observed was mainly due to the splice artifacts
(Fig. 3D). The sequence originally reported as the 5'-UTR contains -18_agGT_-16 (the 3'-splice acceptor site
is in lowercase) based on several EST records lacking the region -653 to -17. Mutation affecting the 3'-splice
acceptor site decreased "IRES" activity of NRF to about 50% of EMCV, about 8-fold drop. It is unclear why
mutations to the putative branching site caused only marginal decrease whereas a mutation to the region
preceding the 3'-splice acceptor site caused in contrast much deeper drop (Fig. 4B). Similarly puzzling
results of the mutations shown in Supplementary Figure 10 (mutant4 should have been close to parental control
if one expects that the changes were not to be affecting splicing).

Citations:

Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
578-639

ITAF protein characteristics:

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

ITAF abbreviated name:
JKTBP1

ITAF fullname:
JKTBP1

ITAF description (long):
JKTBP1 binds AU-rich elements of 3'-UTRs, related to hnRNP D/AUF1

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens HeLa (ATCC CCL-2)

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
HeLa cell lysate

Remarks:

Authors mention the JKTBP1 protein is abundant in many cell lines. Binding was shown in Figure 5B.

Citations:

Reboll M. R., Oumard A., Gazdag A. C., Renger I., Ritter B., Schwarzer M., Hauser H., Wood M., Yamada M., Resch K., Nourbakhsh M. (2007) NRF IRES activity is mediated by RNA binding protein JKTBP1 and a 14-nt RNA element. RNA. 13(8):1328-1340

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 32

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `unknown`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
577-656

The underlying nucleic acid sequence and structure of the mapped region:

gaagcttttt aaaaaagaca tccttacctg ttttaactgt agattatatt aacttaaata gGTACAGCCC ACGCTTGATG
.....(((.. ...))).... .....(((.. .(((...... .......... .....))).. )))..(((.. ..))).....
^577       ^587       ^597       ^607       ^617       ^627       ^637       ^647

Rendering structure of NRF mRNA 80 nt long with energy of 4.90 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Citations:

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