IRESite_Id:438 summary record describing characteristics of Cat-1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `438`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-26 12:56:09`

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: `Cat-1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
33943114

Synonyms of the gene name:

Synonym: Cat1

The mRNA/+RNA description:

Rattus norvegicus cationic amino acid transporter-1 (Cat1) gene, merged from GI:18542255 and GI:33943114.

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

AGCACTGGCC GTGGCCGTGG GGCCCGCGGA GGGCGGCGCG CGGCTGATGA AACCGGCTCG GATTCCGCCC GCGTGCGCCA TCCCCTCAGC TAGCAGGTGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GAGCGGCTTT CTGCCCGCAG TCTCTACACA GCTCAGCATC CTGACGCCTC CTCCCCTTGC AGGGGCGTGA AGCTACTTCA GACTCTGCTG TGACGACTTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCCGCCAGGC ACCGATCCTC CCCGGTGAGA AGGTCCACGA ATCTTACTGC AGACAGATTT GCTCAGCGCG ATGGGCTGCA AAAACCTGTT GAGCCTGGGT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGCAGACGC TGCGCCGGAA AGTGGTGGAC TGCAGCCGGG AGGAGAGCCG GCTGTCCCGC TGCCTCAACA CCTATGATCT GGTAGCTCTT GGGGTGGGCA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCACCTTGGG CGCTGGTGTC TACGTCCTAG CCGGTGCAGT GGCCCGTGAG AATGCTGGTC CTGCCATCGT CATCTCCTTC CTGATCGCTG CTCTTGCCTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGTGCTGGCC GGCCTGTGCT ATGGCGAGTT TGGTGCCCGT GTCCCCAAGA CGGGCTCAGC CTACCTCTAC AGCTATGTGA CAGTGGGGGA GCTCTGGGCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTCATCACTG GCTGGAACCT GATTCTCTCC TACATCATCG GTACATCCAG CGTGGCAAGA GCCTGGAGTG CAACTTTTGA CGAGCTGATA GGCAAACCCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCGGAGAGTT CTCGCGTCAA CACATGGCCC TGAACGCCCC TGGGGTGCTG GCCCAAACCC CGGATATATT TGCTGTGATT ATAATTATCA TCCTGACAGG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACTGTTAACT CTCGGTGTGA AAGAATCAGC CATGGTCAAC AAAATCTTCA CCTGTATCAA TGTCCTGGTC TTGTGCTTCA TCATGGTGTC GGGATTCGTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAAGGCTCCA TTGAGAACTG GCAGCTCACG GAGAATAAAT CCAGTCCTCT CTGTGGGAAC AATGACACAA ACGTGAAATA CGGTGAGGGA GGGTTCATGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCTTTGGATT CTCTGGTGTC CTGTCAGGGG CAGCGACCTG CTTTTATGCC TTCGTGGGCT TTGACTGCAT CGCCACCACA GGGGAAGAAG TCAAGAACCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCAGAAGGCC ATTCCTGTGG GCATTGTGGC GTCCCTCCTC ATTTGCTTCA TAGCTTACTT TGGGGTGTCC GCTGCTCTCA CCCTCATGAT GCCCTACTTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGCCTGGACA CTGACAGCCC ACTGCCTGGC GCCTTCAAGT ACAGGGGCTG GGAAGAAGCT AAGTATGCAG TGGCCGTGGG CTCCCTCTGC GCACTCTCCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCAGTCTCCT AGGTTCCATG TTCCCCATGC CCCGAGTTAT CTATGCCATG GCTGAAGATG GACTACTGTT TAAATTTTTG GCCAAAATCA ACGATAGGAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CAAAACACCA ATAATCGCTA CTGTGACCTC AGGCGCCATC GCTGCTGTGA TGGCCTTCCT CTTTGAACTG AAGGATCTGG TGGACCTCAT GTCCATTGGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTCTCCTGG CTTACTCTTT GGTGGCTGCC TGTGTTTTGG TCTTACGGTA CCAGCCAGAA CAACCTAATC TGGTATACCA GATGGCCAGA ACCACCGATG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGCTAGACCA GGTAGACCAG AATGAGATGG TCAGTGCCAG TGAGTCCCAG ACAGGCTTTT TACCAGCAGC CGAGAAGTTT TCTCTGAAAA CCATACTCTC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACCCAAGAAC ATGGAGCCGT CCAAATTCTC AGGGCTAATT GTGAACATTT CAGCCGGCCT CCTAGCCGTT CTTATCATCA CCGTGTGCAT TGTGGCCGTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTTGGAAGAG AGGCCCTGGC TGAAGGGACG CTGTGGGCAG TCTTTGTAAT GACAGGGTCA GTCCTCCTCT GCATGCTGGT GACGGGCATC ATCTGGAGGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGCCTGAGAG CAAGACCAAG CTCTCGTTTA AGGTACCCTT TGTCCCCGTA CTTCCTGTCT TAAGCATCTT TGTGAACATC TATCTCATGA TGCAACTGGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCAGGGCACG TGGGTCCGGT TCGCAGTGTG GATGCTGATA GGCTTTGCCA TCTACTTTGG CTATGGGGCC TGGCACAGTG AGGAAGCATC CCTGGCTGCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GGCCAGGCAA AGACTCCTGA TAGCAACTTG GACCAGTGCA AATGACCCAC A
^2101      ^2111      ^2121      ^2131      ^2141      ^2151

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

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

Rattus norvegicus Wistar

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:

Rattus norvegicus C6

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

ORF

ORF position:

1

Version: `1`	Last change: `2008-06-26 12:56:09`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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

The description of the protein encoded in this ORF:
cationic amino acid transporter 1 (arginine/lysine)

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):

271-2145

Remarks:

The first 60bp have been added in front of GI:33943114 from GI:18542255. The leftmost 45 nt were not
determined by authors by 5'-RACE as shown in Fernandez et al. (2001), Figure 1A. Additional primer-extension
studies were published in Fernandez et al. (2003) in Figure 2A and have identified transcription start site
'G' residues -254 and -260 nt upstream of initiator ATG. The mRNA sequence used here in IRESite is the one
defined by S1 nuclease protection as shown in Fernandez et al. (2003) in Figure 2B,D (black arrow) and is
longer by 10 or 16 nt then the transcripts mapped by primer-extension (gray arrows).

Citations:

Fernandez J., Yaman I., Mishra R., Merrick W. C., Snider M. D., Lamers W. H., Hatzoglou M. (2001) Internal ribosome entry site-mediated translation of a mammalian mRNA is regulated by amino acid availability. J. Biol. Chem. 276(15):12285-12291

Fernandez J., Yaman I., Merrick W. C., Koromilas A., Wek R. C., Sood R., Hensold J., Hatzoglou M. (2002) Regulation of internal ribosome entry site-mediated translation by eukaryotic initiation factor-2alpha phosphorylation and translation of a small upstream open reading frame. J. Biol. Chem. 277(3):2050-2058

Fernandez J., Lopez A. B., Wang C., Mishra R., Zhou L., Yaman I., Snider M. D., Hatzoglou M. (2003) Transcriptional control of the arginine/lysine transporter, cat-1, by physiological stress. J. Biol. Chem. 278(50):50000-50009

Finley K. D., Kakuda D. K., Barrieux A., Kleeman J., Huynh P. D., MacLeod C. L. (1995) A mammalian arginine/lysine transporter uses multiple promoters. Proc. Natl. Acad. Sci. U. S. A. 92(20):9378-9382

IRESs:

IRES:

Version: `1`	Last change: `2008-06-26 12:56:09`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `Cat-1_224`

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

47-270

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

ATGAAACCGG CTCGGATTCC GCCCGCGTGC GCCATCCCCT CAGCTAGCAG GTGTGAGCGG CTTTCTGCCC GCAGTCTCTA CACAGCTCAG CATCCTGACG 
^47        ^57        ^67        ^77        ^87        ^97        ^107       ^117       ^127       ^137       

CCTCCTCCCC TTGCAGGGGC GTGAAGCTAC TTCAGACTCT GCTGTGACGA CTTGGCCGCC AGGCACCGAT CCTCCCCGGT GAGAAGGTCC ACGAATCTTA 
^147       ^157       ^167       ^177       ^187       ^197       ^207       ^217       ^227       ^237       

CTGCAGACAG ATTTGCTCAG CGCG
^247       ^257       ^267

Remarks:

IRES coordinates located from GI:18542255.

Citations:

Lopez A. B., Wang C., Huang C. C., Yaman I., Li Y., Chakravarty K., Johnson P. F., Chiang C. M., Snider M. D., Wek R. C., Hatzoglou M. (2007) A feedback transcriptional mechanism controls the level of the arginine/lysine transporter cat-1 during amino acid starvation. Biochem. J. 402(1):163-173

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):
107-112

ITAF protein characteristics:

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

ITAF abbreviated name:
PTB

ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)

ITAF description (long):
polypyrimidine-tract binding protein

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:

Rattus norvegicus C6

Remarks:

Predicted secondary structure and the binding regions were shown in Figure 3A.

Citations:

Majumder M, Yaman I, Gaccioli F, Zeenko VV, Wang C, Caprara MG, Venema RC, Komar AA, Snider MD, Hatzoglou M (2009) The hnRNA-binding proteins hnRNP L and PTB are required for efficient translation of the Cat-1 arginine/lysine transporter mRNA during amino acid starvation. Mol. Cell. Biol. 29(10):2899-2912

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):
127-137

ITAF protein characteristics:

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

ITAF abbreviated name:
hnRNP_L

ITAF fullname:
heterogeneous ribonucleoprotein L

ITAF description (long):
heterogeneous ribonucleoprotein L (68 kDa)

3.2.2. 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:

Rattus norvegicus C6

Remarks:

Predicted secondary structure and the binding regions were shown in Figure 3A.

Citations:

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