Difference between revisions of "ENST00000513868.2"
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===Regulation=== | ===Regulation=== | ||
The E-boxes region in the PVT-1 proximal promoter is important for PVT-1 transcriptional regulation by Myc proteins<ref name="ref1" />. | The E-boxes region in the PVT-1 proximal promoter is important for PVT-1 transcriptional regulation by Myc proteins<ref name="ref1" />. | ||
| + | [[File: PVT-1.jpg|right|thumb|400px|'''PVT-1 transactivation by c-Myc''' <ref name="ref1" />.]] | ||
===Expression=== | ===Expression=== | ||
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===Evolution=== | ===Evolution=== | ||
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A computer-assisted alignment of the human PVT-1 promoter nucleotidesequence with the homologous mouse and rat sequences,indicates the existence of a significant evolutionary conservation both at the nucleotide level and in the spacing ofthe E-boxes relative to the transcriptional start site. | A computer-assisted alignment of the human PVT-1 promoter nucleotidesequence with the homologous mouse and rat sequences,indicates the existence of a significant evolutionary conservation both at the nucleotide level and in the spacing ofthe E-boxes relative to the transcriptional start site. | ||
Revision as of 05:47, 30 June 2016
PVT1,1716 bp long intergenic non-coding RNA in 8q24, which was regulated by Myc proteins,may function with c-Myc and N-Myc genes.
Contents
Annotated Information
Name
PVT1:Pvt1 oncogene (non-protein coding)(HGNC nomenclature)
LINC00079, "long intergenic non-protein coding RNA 79", NCRNA00079, "non-protein coding RNA 79"[1]
Characteristics
PVT-1 gene is located on chromosome 8 telomeric to the c-Myc gene and it is frequently involved in the translocations occurring in variant Burkitt's lymphomas and murine plasmacytomas[1].
PVT-1 gene contains two non canonical Myc-binding sites (E-box CACGCG) in the promoter region proximal to the transcriptional start site (−155/−95) the consensus and the surrounding sequences are conserved in the homologous mouse and rat genes[1].
Function
PVT-1 is a downstream target of both c-Myc and N-Myc genes[1].
The E-boxes region in the PVT-1 proximal promoter is important for PVT-1 transcriptional regulation by Myc proteins and reveal a novel cross-talk between PVT-1 and N-Myc in neuroblastoma cells[1].
Regulation
The E-boxes region in the PVT-1 proximal promoter is important for PVT-1 transcriptional regulation by Myc proteins[1].
Expression
| Primer | Forward | Reverse |
|---|---|---|
| PVT-1 | CAT GGT TCC ACC AGC GTT ATT C | TCC TTG CGG AAA GGA TGT TGG[1] |
| c- Myc | CAG CAG AGC GAG CTG CAG CC | CTG TCT TTG CGC GCA GCC TG[1] |
| N-Myc | CAG CAG AGC GAG CTG CAG CC | CTG TCT TTG CGC GCA GCC TG[1] |
| GAPDH | TGA CAT CAA GAA GGT GGT GA | TCC ACC ACC CTG TTG CTG TA[1] |
Evolution
A computer-assisted alignment of the human PVT-1 promoter nucleotidesequence with the homologous mouse and rat sequences,indicates the existence of a significant evolutionary conservation both at the nucleotide level and in the spacing ofthe E-boxes relative to the transcriptional start site.
Labs working on this lncRNA
- Dipartimento di Oncologia Sperimentale e Applicazioni Cliniche, Università di Palermo, Palermo, Italy[1].
References
Basic Information
| Transcript ID |
ENST00000513868.2 |
| Source |
Gencode19 |
| Same with |
lnc-MYC-2:14,NONHSAT129063,PVT1,LINC00079 |
| Classification |
intergenic |
| Length |
1699 nt |
| Genomic location |
chr8+:128902874..129113499 |
| Exon number |
8 |
| Exons |
128902874..128903244,128951754..128951922,128996150..128996450,129001408..129001537,129082406..129082518,129108764..129108900,129111616..129111819,129113226..129113499 |
| Genome context |
|
| Sequence |
000001 CTCAAGATGG CTGTGCCTGT CAGCTGCATG GAGCTTCGTT CAAGTATTTT CTGAGCCTGA TGGATTTACA GTGATCTTCA 000080
000081 GTGGTCTGGG GAATAACGCT GGTGGAACCA TGCACTGGAA TGACACACGC CCGGCACATT TCAGGATACT AAAAGTGGTT 000160 000161 TTAAGGGAGG CTGTGGCTGA ATGCCTCATG GATTCTTACA GCTTGGATGT CCATGGGGGA CGAAGGACTG CAGCTGGCTG 000240 000241 AGAGGGTTGA GATCTCTGTT TACTTAGATC TCTGCCAACT TCCTTTGGGT CTCCCTATGG AATGTAAGAC CCCGACTCTT 000320 000321 CCTGGTGAAG CATCTGATGC ACGTTCCATC CGGCGCTCAG CTGGGCTTGA GCTGACCATA CTCCCTGGAG CCTTCTCCCG 000400 000401 AGGTGCGCGG GTGACCTTGG CACATACAGC CATCATGATG GTACTTTAAG TGGAGGCTGA ATCATCTCCC CTTTGAGCTG 000480 000481 CTTGGCACGT GGCTCCCTTG GTGTTCCCCT TTTACTGCCA GGACACTGAG ATTTGGAGAG AGTCTCACTC TGTGGTCCAG 000560 000561 GCTGAAGTAC AGTGGCATGA TCCCAGGTCA CTGCAACCCC CACCTCCCGG GTTCAAGTGA TCCTCCTGCC TCAGCCTCCC 000640 000641 GAGTAGCTGG TATTACAGGC GTGTGCCACA AAGCCTGGCT AAGTTTTGTA TTTTTAGTAG AGACGGGGTT TCACCATGTT 000720 000721 GGCCAGGTTG GTCTCGAACT CCTGACCTCA AGTGATCCAC TCACTTTGGC CTTTCAACGT GCTGGGATTA CAGGCGAGAG 000800 000801 TCACCGCACC CGGACGACTC TGACATTTTT GAAGAGTCCA GAATCCTGTT ACACCTGGGA TTTAGGCACT TTCAATCTGA 000880 000881 AAAAATACAT ATCCTTTCAG CACTCTGGAC GGACTTGAGA ACTGTCCTTA CGTGACCTAA AGCTGGAGTA TTTTGAGATT 000960 000961 GGAGAATTAA GAGCCAGTCT TGGTGCTCTG TGTTCACCTG GTTCATCTGA GGAGCTGCAT CTACCCTGCC CATGCCATAG 001040 001041 ATCCTGCCCT GTTTGCTTCT CCTGTTGCTG CTAGTGGACA TGAGAAGGAC AGAATAACGG GCTCCCAGAT TCACAAGCCC 001120 001121 CACCAAGAGG ATCACCCCAG GAACGCTTGG AGGCTGAGGA GTTCACTGAG GCTACTGCAT CTTGAGACTC AGGATGAAGA 001200 001201 CCCAGCTTGG GGCTGTCAAA GAGGCCTGAA GAGGCAGAAC ACCCCAGAGG AGCCTGGGGC CACCACCCAG CATCACTGTG 001280 001281 GGAAAACGGC AGCAGGAAAT GTCCTCTCGC CTGCGTGCTC CACCTCGGTC CACGCCTTCC CTCCTTCTGG AAGCCTTGCC 001360 001361 TGACCACTGG CCTGCCCCTT CTATGGGAAT CACTACTGAC CTTGCAGCTT ATTATAGACT TATATGTTTT TTGCATGTCT 001440 001441 GACACCCATG ACTCCACCTG GACCTTATGG CTCCACCCAG AAGCAATTCA GCCCAACAGG AGGACAGCTT CAACCCATTA 001520 001521 CGATTTCATC TCTGCCCCAA CCACTCAGCA GCAAGCACCT GTTACCTGTC CACCCCCACC CCTTCCCCCA AACTGCCTTT 001600 001601 GAAAAATCCC TAACCTATGA GCTTTGAATA AGATGAGTAC GAACTTCATC GCCCACGTGG CGTGGCCGGC CTCGTGTCTA 001680 001681 TTAAATTCTT TTTCTACTA |
Predicted Small Protein
| Name | ENST00000513868.2_smProtein_206:448 |
| Length | 81 |
| Molecular weight | 8571.0033 |
| Aromaticity | 0.025 |
| Instability index | 49.55375 |
| Isoelectric point | 5.18756103516 |
| Runs | 12 |
| Runs residual | 0.0111842105263 |
| Runs probability | 0.0499838073367 |
| Amino acid sequence | MSMGDEGLQLAERVEISVYLDLCQLPLGLPMECKTPTLPGEASDARSIRRSAGLELTILP GAFSRGARVTLAHTAIMMVL |
| Secondary structure | LLLLHHHHLHHHHEEEEEEELLLLLLLLLLLLLLLLLLLLLLLLHHHHHHHLLLEEEELL LLLLLLLLHHHHHHHHHHHL |
| PRMN | - |
| PiMo | - |
