IRESite_Id:81 summary record describing characteristics of UNR IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `81`	Version: `4`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-10-21 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2007-01-24 00:00:00`

IRESite record type:

natural_transcript

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
56117851

Synonyms of the gene name:

Synonym: CSDE1

Synonym: D1S155E

Synonym: DKFZp779B0247

Synonym: DKFZp779J1455

Synonym: RP5-1000E10.3

The mRNA/+RNA description:

Homo sapiens cold shock domain containing E1, RNA-binding (CSDE1), transcript variant 1, mRNA.

In transcript variant 2 lacks an in-frame exon, compared to variant 1, resulting in a shorter protein (isoform
2) that is missing an internal segment relative to isoform 1.

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

GAGAGAAGCG AGATTTATTC CTACGTACCG GGCCGTGCTG CTTATGGCGG CGCTGGAGAG GGGGCGCTGA GCTGTTGGGT ATGAAGTGTA ACAGAACAGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CTTTACCACC TGAAACTGCT GCTTCAAGTT CAGATCAGGC AAGGAACAAA CCTCGTAACA ACTAACAAGA CCAAAGAAGA GTACACTTAA GTTGAAGACA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAACACTTGA TCTGAAACAA GAAGTTTGTG CCTACTCAAC AGCTTTGAAA GAGCACTTCC CAACGCTGCT AGTAGTCTTT GTTTTCTTCA GTGCTGTACT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGAGATTGC CCGGTACAGC AGCAGTTGTA TTCTTTATTA GCTTGGTAGA TCATTTTCTC TCGCTCTTTT TTTTAATACT AGCAACTTTC ATCCTTTGAA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACGTGTGCTG AAAAAGAAGA ATCAGCAAAT ACTACTGAAA GTGCAATATT TGAGTATCAC TGCGAGATGA GCTTTGATCC AAACCTTCTC CACAACAATG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GACATAATGG GTACCCTAAT GGTACTTCAG CAGCACTGCG TGAAACTGGG GTTATTGAAA AACTGTTAAC CTCTTACGGA TTTATTCAGT GTTCAGAACG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCAAGCTAGA CTTTTCTTCC ACTGTTCACA GTATAATGGC AACCTGCAAG ACTTAAAAGT AGGAGATGAT GTTGAATTTG AAGTATCATC GGACCGACGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACTGGGAAAC CCATTGCTGT TAAACTGGTG AAGATAAAAC AAGAAATCCT CCCTGAAGAA CGAATGAATG GACAAGTTGT GTGCGCTGTT CCTCACAACT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TAGAGAGTAA ATCTCCAGCT GCCCCGGGTC AGAGTCCAAC AGGGAGTGTA TGCTACGAAC GTAATGGGGA AGTGTTTTAT CTGACTTACA CCCCTGAAGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGTCGAAGGG AACGTTCAGC TGGAAACTGG AGATAAAATA AACTTTGTAA TTGATAACAA TAAACATACT GGTGCTGTAA GTGCTCGCAA CATTATGCTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTGAAAAAGA AACAAGCCCG CTGTCAGGGA GTAGTTTGTG CCATGAAGGA GGCATTTGGC TTTATTGAAA GAGGTGATGT TGTAAAAGAG ATATTCTTTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACTATAGTGA ATTTAAGGGT GACTTAGAAA CCTTACAGCC TGGCGATGAT GTGGAATTCA CAATCAAGGA CAGAAATGGT AAAGAAGTTG CAACAGATGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAGACTATTG CCTCAAGGAA CAGTCATTTT TGAAGATATC AGCATTGAAC ATTTTGAAGG AACTGTAACC AAAGTTATCC CAAAAGTACC CAGTAAAAAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CAGAATGACC CATTGCCAGG ACGCATCAAA GTTGACTTTG TGATCCCTAA AGAACTTCCC TTTGGAGACA AAGATACGAA ATCCAAGGTG ACCCTGCTGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGGTGACCA TGTTAGGTTT AATATTTCAA CAGACCGACG TGACAAATTA GAGCGAGCAA CCAATATAGA AGTTCTGTCA AATACATTTC AGTTCACTAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGAAGCCCGA GAAATGGGTG TGATTGCTGC CATGAGAGAT GGTTTTGGTT TCATCAAGTG TGTGGATCGT GATGTTCGTA TGTTCTTCCA CTTCAGTGAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATTCTGGATG GGAACCAGCT CCATATTGCA GATGAAGTAG AGTTTACTGT GGTTCCTGAT ATGCTCTCTG CTCAAAGAAA TCATGCTATT AGGATTAAAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AACTTCCCAA GGGCACGGTT TCATTTCATT CCCATTCAGA TCACCGTTTT CTGGGCACGG TAGAAAAAGA AGCCACTTTT TCCAATCCTA AAACCACTAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCCAAATAAA GGCAAAGAGA AGGAGGCTGA GGATGGCATT ATTGCTTATG ATGACTGTGG GGTGAAACTG ACTATTGCTT TTCAAGCCAA GGATGTGGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGATCTACTT CTCCTCAAAT AGGAGATAAG GTTGAATTTA GTATTAGTGA CAAACAGAGG CCTGGACAGC AGGTTGCAAC TTGTGTGCGA CTTTTAGGTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTAATTCTAA CTCCAAGAGG CTCTTGGGTT ATGTGGCAAC TCTGAAGGAT AATTTTGGAT TTATTGAAAC AGCCAATCAT GATAAGGAAA TCTTTTTCCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTACAGTGAG TTCTCTGGTG ATGTTGATAG CCTGGAACTG GGGGACATGG TCGAGTATAG CTTGTCCAAA GGCAAAGGCA ACAAAGTCAG TGCAGAAAAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTGAACAAAA CACACTCAGT GAATGGCATT ACTGAGGAAG CTGATCCCAC CATTTACTCT GGCAAAGTAA TTCGCCCCCT GAGGAGTGTT GATCCAACAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGACTGAGTA CCAAGGAATG ATTGAGATTG TGGAGGAGGG CGATATGAAA GGTGAGGTCT ATCCATTTGG CATCGTTGGG ATGGCCAACA AAGGGGATTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCTGCAGAAA GGGGAGAGCG TCAAGTTCCA ATTGTGTGTC CTGGGCCAAA ATGCACAAAC TATGGCTTAC AACATCACAC CCCTGCGCAG GGCCACAGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAATGTGTGA AAGATCAGTT TGGCTTCATT AACTATGAAG TAGGAGATAG CAAGAAGCTC TTTTTCCATG TGAAAGAAGT TCAGGATGGC ATTGAGCTAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AGGCAGGAGA TGAGGTGGAG TTCTCAGTGA TTCTTAATCA GCGCACTGGC AAGTGCAGCG CCTGTAATGT TTGGCGAGTC TGTGAGGGCC CCAAGGCTGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGCAGCTCCT CGACCTGATC GGTTGGTCAA TCGCTTGAAG AATATCACTC TGGATGATGC CAGTGCTCCT CGCCTAATGG TTCTTCGTCA GCCAAGGGGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCAGATAACT CAATGGGGTT TGGTGCAGAA AGAAAGATCC GTCAAGCTGG TGTCATTGAC TAACCACATC CACAAAGCAC ACCATTAATC CACTATGATC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAGTTGGGGG GAATCTGGTG AAGGGTTCTG AATATCTCCC TCTTCATCCC TCCCGAAATC TGGAATACTT ATTCTATTGA GCTATTACAC CAGTTTTAAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACCTTCCTCG TGTTATGTTT AAAAAAATAA ATAAATTTAA GAAAACCATT TTAAATAATG CACAGTTGCA GCCTGGAAAA ACTTAAGGTG GCGCCTTATA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GTATCAATTT TAGGAGCTTT ATTTGGTGCA TTTAACGCAA CTGGTAATTG CAGAATCCAC TTTGCCTGTG TAAGTGAAAA ATATAGACTG TTATCTTGTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGCCCTATGA AATTCTGCAC TTTTCATTAT ATACTCTACC TTCATTAATT ACTTCTGGCA AGATGTTCTG CCTTAGCACT CAGTTGCATT CTTTTCCTTT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTCTTCCTGT TCATTATGCT TTAATTCTGA GGACCATATG AGGGTAGAAT ATATTATCTT TTAAAAATTA CAAAAATTTG TATAGGCAAA CCATTTCTTA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AAGTTGATGG CCAAATTTTA AAATGTTATT TTTCATATCA TTTATAATCT TGTCACAATC CACTTAAAGA AGTTTGGTTA TATTTCAGTG AAAATTTTCT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TCCAGAGTAG GTTTTTTTTC GTGGGTTGGG GGGTAACTTT ACTACAATTA GTAAGTATGG TGCAGAATTT CATGCAAATG AGGAGTGCCA GCAGTGTGAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AATTTAAACA TATTTAAACA AAAACAAAAA AAATGAATGC ACAAACTTGC TGCTGCTTAG ATCACTGCAG CTTCTAGGAC CCGGTTTCTT TTACTGATTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAAAACAAAA CAAAAAAAAA TAAAAAAGTT GTGCCTGAAA TGAATCTTGT TTTTTTTTAT AAGTAGCCGC CTGGTTACTG TGTCCTGTAA AATACAGACA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CTTGACCCTT GGTGTAGCTT CTGTTCAACT TTATATCACG GGAATGGATG GGTCTGATTT CTTGGCCCTC TTCTTGAATT GGCCATATAC AGGGTCCCTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCCAGTGGAC TGAAGGCTTT GTCTAAGATG ACAAGGGTCA GCTCAGGGGA TGTGGGGGAG GGCGGTTTTA TCTTCCCCCT TGTCGTTTGA GGTTTTGATC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TCTGGGTAAA GAGGCCGTTT ATCTTTGTAA ACACGAAACA TTTTTGCTTT CTCCAGTTTT CTGTTAATGG CGAAAGAATG GAAGCGAATA AAGTTTTACT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GATTTTTGAG ACACT
^4101      ^4111

Credibility of mRNA sequence:

unknown

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

Homo sapiens

A promoter reported in cDNA corresponding to IRES sequence:
no 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:
no_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 HEK 293T/17 (ATCC CRL-11268)

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

ORF

ORF position:

1

Version: `1`	Last change: `2006-01-15 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
UNR

The description of the protein encoded in this ORF:
upstream of NRAS isoform 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):

467-2863

OPTIONAL: The function of the encoded protein

isoform 1 is encoded by transcript variant 1;
NRAS-related gene; upstream of NRAS;
go_function: DNA binding [goid 0003677] [evidence IEA];
go_function: RNA binding [goid 0003723] [evidence IEA];
go_function: peroxidase activity [goid 0004601] [evidence IEA];
go_process: male gonad development [goid 0008584] [evidence TAS] [pmid 2204029];
go_process: response to oxidative stress [goid 0006979] [evidence IEA];
go_process: regulation of transcription, DNA-dependent [goid 0006355] [evidence IEA]

Remarks:

Presence of a cryptic promoter in human HEK293 cells was ruled out using a cryptic promoter where the
activity observed was 1/15 of the positive control with SV40 promoter (pGL3-basic) and the delta335-355
variant had 1/24 activity of the SV40 based control.

Citations:

Cornelis S., Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R. (2005) UNR translation can be driven by an IRES element that is negatively regulated by polypyrimidine tract binding protein. Nucleic Acids Res. 33(10):3095-3108

IRESs:

IRES:

Version: `2`	Last change: `2007-01-24 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `UNR`

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

36-464

Conclusion:
putative_IRES

How IRES boundaries were determined:
unknown

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

TGCTGCTTAT GGCGGCGCTG GAGAGGGGGC GCTGAGCTGT TGGGTATGAA GTGTAACAGA ACAGACTTTA CCACCTGAAA CTGCTGCTTC AAGTTCAGAT 
^36        ^46        ^56        ^66        ^76        ^86        ^96        ^106       ^116       ^126       

CAGGCAAGGA ACAAACCTCG TAACAACTAA CAAGACCAAA GAAGAGTACA CTTAAGTTGA AGACACAACA CTTGATCTGA AACAAGAAGT TTGTGCCTAC 
^136       ^146       ^156       ^166       ^176       ^186       ^196       ^206       ^216       ^226       

TCAACAGCTT TGAAAGAGCA CTTCCCAACG CTGCTAGTAG TCTTTGTTTT CTTCAGTGCT GTACTGTGAG ATTGCCCGGT ACAGCAGCAG TTGTATTCTT 
^236       ^246       ^256       ^266       ^276       ^286       ^296       ^306       ^316       ^326       

TATTAGCTTG GTAGATCATT TTCTCTCGCT CTTTTTTTTA ATACTAGCAA CTTTCATCCT TTGAAACGTG TGCTGAAAAA GAAGAATCAG CAAATACTAC 
^336       ^346       ^356       ^366       ^376       ^386       ^396       ^406       ^416       ^426       

TGAAAGTGCA ATATTTGAGT ATCACTGCG
^436       ^446       ^456

Remarks:

UNR 5' UTR from nt -431 nt to nt -3.

Citations:

RNA:protein interactions:

The RNA:protein interaction:

Version: `2`	Last change: `2007-01-24 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
PTB bound to UNR IRES in UV cross-linking experiments

The organism where this RNA:protein interaction occurs:

Homo sapiens HEK 293T/17 (ATCC CRL-11268)

Remarks:

Ultraviolet cross-linking analysis and RNA affinity chromatography revealed the binding of polypyrimidine
tract binding protein (PTB) to the UNR IRES, requiring a pyrimidine-rich region (nucleotides 354-374). Whereas
overexpression of PTB in several cell lines inhibited UNR IRES activity and UNR protein expression, depletion
of endogenous PTB using RNAi increased UNR IRES activity. Moreover, a mutant version of the UNR IRES lacking
the PTB binding site was more efficient at directing IRES-mediated translation.

Citations:

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