IRESite_Id:111 summary record describing characteristics of Scamper IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `111`	Version: `2`
Originaly submitted by: Martin Mokrejš	Submission date: `2006-01-12 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2006-04-28 00:00:00`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
21553346

The mRNA/+RNA description:

Canis familiaris scamper mRNA, complete cds.

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

TTAAGATACT TTTTCTAAAA AGATTTATTT CCAGAGTGTT CCCATGTTGG TTTAAAATTC ACTGTTTTCA ACATTTTAGA GCAATACCTC ATCTACTTGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTTTGTGTCT GCTGAAGTCT TCGGTTGCTG CCAGAGGCAG CACTTGACCC TGGGGTTGCA CCTGCAGACC TGAAATGGGT AAAGGCACAA GCATGAGTAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACTATGATTC CAGATACATT TTTTATAAGT ATGAAGACAT TATCCCAAGG CATCACTGTT TAAAGGTTCA GAACTTAAGC AGAAAAAGAA ACCCTTCCTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGTAAGGAA CAAAGGTTCT AATGACATTT CTTCTAATTC CTCTATAATT TCCAGGATTC ATCATATGTT AAAAGTGAGC AGGGTCTCAA GTGAAGGTTT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AATATCACTT TCTATCACTG AGGCACCTGA TCTTAAGATC AGGGATCCTA AGATAGAGAA ACTCTACCTT CCAGTTTTTT ATTTAAATGC ACACATCTAC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTAAATGCAC TCAGTACTCT CCTGAACTCT CATTGTGGCG AGAACTGTTT TCATGGTTAT GAACAATTAC AGAATGCCAC TTTTCCAGTT TGGAGAAATA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TATTCATTTA TATAAACAGG GTCAGGAACA TCAAGAGGCA AGGAGGAGGG GGTGGTGTGA GTGGGAAAGG TGAGATGAAG CAGTGCTTCC TCTCTTAAAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGTACTTCTC TTTTCAAATC CTCAACTGAA GGCCTATTGC TCTCCAGCCA GATCTTTCTT GACCACTGTG GCTTTGAAGT CCTTATCGCT TCCGTTTCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGCTGGCCAT GCTTTCATTT TTCACACACA CATACACACA CAGCTGACCC TTGAACAAGG TGGGGTGTTT GGGGTGCCGA CGCCGACCCC TCCCCCTCCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CATGGTTGAA AATCTGCATA TAACTTTTGA CTCCTCCCAA AATTTAACTA CTAATAGCCT ACTGCTGACC AAAGGCCTTA CCAATAACAT AAACAGTCGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTAACAAGTA TTTTGTATAT TATATGTATC ATACACTGTG TTCTTACAGT AAAGTAAGCT AGAGCAGAAA ATGTTAAGAA AATCGTAAGA CAAGGGCAGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCAGGTGGCT CAGCAGTTTA GCGCCACCTT CAGCCCAGGA CTGATCCTGG AGACCCGGGA TGGAGTCCCA TGTCGGGCTC CCTGCATGGA GCCTGCTTCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCCTCTGCCT GTGTCTCTCT CATGAATAAA TACATAAAAT CTT
^1201      ^1211      ^1221      ^1231      ^1241

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:

Canis familiaris MDCK [NBL-2] (ATCC CCL-34)

A promoter reported in cDNA corresponding to IRES sequence:
yes 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:
not_tested

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:
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:

Canis familiaris MDCK [NBL-2] (ATCC CCL-34)

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:
Scamper

The description of the protein encoded in this ORF:
putative intracellular Ca2+ channel sensitive to sphingosylphosphocholine; type I integral membrane protein

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):

366-698

Remarks:

Promoter confirmed in Scamper 5'-UTR in a promoter-less plasmid. The subsequent experiments used cytosolic
vaccinia virus for production of capped (10% efficiency) and polyadenylated transcripts directly in the
cytoplasm. Integrity of any of the transcripts was not studied. Only monocistronic transcripts were tested in
rabbit reticulocyte lysate.

Citations:

De Pietri Tonelli D., Mihailovich M., Schnurbus R., Pesole G., Grohovaz F., Zacchetti D. (2003) Translational control of Scamper expression via a cell-specific internal ribosome entry site. Nucleic Acids Res. 31(10):2508-2513

IRESs:

IRES:

Version: `4`	Last change: `2007-01-12 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Scamper`

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

1-365

Conclusion:
putative_IRES

How IRES boundaries were determined:
guessed

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

TTAAGATACT TTTTCTAAAA AGATTTATTT CCAGAGTGTT CCCATGTTGG TTTAAAATTC ACTGTTTTCA ACATTTTAGA GCAATACCTC ATCTACTTGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTTTGTGTCT GCTGAAGTCT TCGGTTGCTG CCAGAGGCAG CACTTGACCC TGGGGTTGCA CCTGCAGACC TGAAATGGGT AAAGGCACAA GCATGAGTAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACTATGATTC CAGATACATT TTTTATAAGT ATGAAGACAT TATCCCAAGG CATCACTGTT TAAAGGTTCA GAACTTAAGC AGAAAAAGAA ACCCTTCCTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGTAAGGAA CAAAGGTTCT AATGACATTT CTTCTAATTC CTCTATAATT TCCAGGATTC ATCAT
^301       ^311       ^321       ^331       ^341       ^351       ^361

Citations:

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