Difference between revisions of "ENST00000608917.1"
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| − | PACERR, a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA) is expressed in the upstream region of COX-2 and functions to directly sequester the repressive NF-κB p50 subunit from the COX-2 promoter. | + | ''PACERR'', a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA) is expressed in the upstream region of COX-2 and functions to directly sequester the repressive NF-κB p50 subunit from the COX-2 promoter. |
==Annotated Information== | ==Annotated Information== | ||
===Name=== | ===Name=== | ||
| − | + | ''PACERR'',PTGS2 antisense NFKB1 complex-mediated expression regulator RNA(HGNC nomenclature) | |
"p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1<ref name="ref1" /> | "p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1<ref name="ref1" /> | ||
===Characteristics=== | ===Characteristics=== | ||
| − | PACERR,homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, with 793 bp, was located in the upstream region of the human COX-2 gene<ref name="ref1" />. | + | ''PACERR'',homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, with 793 bp, was located in the upstream region of the human COX-2 gene<ref name="ref1" />. |
===Celluar Localization=== | ===Celluar Localization=== | ||
Revision as of 14:03, 26 June 2016
PACERR, a nuclear antisense long non-coding RNA PACER (P50-Associated COX-2 Extragenic RNA) is expressed in the upstream region of COX-2 and functions to directly sequester the repressive NF-κB p50 subunit from the COX-2 promoter.
Contents
Annotated Information
Name
PACERR,PTGS2 antisense NFKB1 complex-mediated expression regulator RNA(HGNC nomenclature)
"p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1[1]
Characteristics
PACERR,homo sapiens PTGS2 antisense NFKB1 complex-mediated expression regulator RNA, with 793 bp, was located in the upstream region of the human COX-2 gene[1].
Celluar Localization
PACERR performs its functions in the nucleus[1].
Function
PACERR facilitates assembly of RNA Polymerase II pre-initiation complexes, through recruitment of the histone acetyltransferase p300 to catalyze histone acetylation at the COX-2 locus upon stimulus-induction[1]. PACERR directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter[1]. PACERR belongs to a novel, unanticipated class of bona-fide transcriptional regulators[1].
Regulation
CTCF regulates the COX-2 locus by establishing and maintaining an open chromatin domain demarcated by two CTCF/cohesin complexes that is characterized by decreased H4K20 trimethylation, increased H3K4 di- and tri- methylation and increased histone acetylation[1].
Expression
| Primers used in RACE | ||
|---|---|---|
| initial | nested | |
| 5'RACE | TATGTATGTATGTGCTGCATATAG | ATGTCAGCCTTTCTTAACCTTAC[1] |
| 3'RACE | GTCTTTGCCCGAGCGCTTCCG | CCGCCGTGTCTGGTCTGTACGTC[1] |
| Primers used for RNA quantitation | ||
| COX-2 mRNA | TCTGTACTGCGGGTGGAACA | CAATTTGCCTGGTGAATGATTC[1] |
| PACER | TGTAAATAGTTAATGTGAGCTCCACG | GCAAATTCTGGCCATCGC[1] |
| p50 mRNA | TTGCTGGTCCCACATAGTTG | ATGTATGTGAAGGCCCATCC[1] |
| Custom siRNA | ||
| siPACER-753 | TGGAAAGAGAGGCGGGAAA[1] | |
| siPACER-870 | TGGAAAGAGAGGCGGGAAA[1] | |
| shRNA | ||
| PACER ‘870’ shRNA | 5’ - gatcc GGACAAAGGAAGCGGCGAT cttcctgtcaga ATCGCCGCTTCCTTTGTCC tttttg | 3’ - g CCTGTTTCCTTCGCCGCTA GAAGGACAGTCT TAGCGGCGAAGGAAACAGG aaaaacttaa[1] |
Labs working on this lncRNA
Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States[1]
References
Basic Information
| Transcript ID |
ENST00000608917.1 |
| Source |
Gencode19 |
| Same with |
PACER ,PTGS2-AS1 |
| Classification |
antisense |
| Length |
825 nt |
| Genomic location |
chr1+:186649754..186650578 |
| Exon number |
1 |
| Exons |
186649754..186650578 |
| Genome context |
|
| Sequence |
000001 AATTTGGGAG CAGAGGGGGT AGTCCCCACT CTCCTGTCTG ATCCCTCCCT CTCCTCCCCG AGTTCCACCG CCCCAGGCGC 000080
000081 ACAGGTTTCC GCCAGATGTC TTTTCTTCTT CGCAGTCTTT GCCCGAGCGC TTCCGAGAGC CAGTTCTGGA CTGATCGCCT 000160 000161 TGGATGGGAT ACCGGGGGAG GGCAGAAGGA CACTTGGCTT CCTCTCCAGG AATCTGAGCG GCCCTGAGGT CCGGGGGCGC 000240 000241 AGGGAATCCC CTCTCCCGCC GCCGCCGCCG TGTCTGGTCT GTACGTCTTT AGAGGGTCGA GGAAGTCACG TCGGGACAGA 000320 000321 CTGGGGCGAG TAAGGTTAAG AAAGGCTGAC ATGTTTTATG TTTTAGTGAC GACGCTTAAT AGGCTGTATA TCTGCTCTAT 000400 000401 ATGCAGCACA TACATACATA GCTTTTTAAA AAACTCTTAT TTTGTGGAAT GAAATAGCTA CCTTCAGTGT ACATAGCTGT 000480 000481 AATTTATCTT TGTAGCTAAG TTGCTTTCAA CAGAAGAAAT ACTGTTCTCC GTACCTTCAC CCCCTCCTTG TTTCTTGGAA 000560 000561 AGAGAGGCGG GAAAGGTAAA TTCTCCTCAT AATACTGGTC CTAAGCAGTT ACCCTGTAAA TAGTTAATGT GAGCTCCACG 000640 000641 GGTCACCAAT ATAAAGTTTC CTGCCTTCTG ATGGACAAAG GAAGCGGCGA TGGCCAGAAT TTGCAGGGAC GCTAAATGTC 000720 000721 CAAAACGTAT GCCTTAAGGC ATTTCTCTCC CTGATGCGTG GATTATTTTG GTTACTAGCC CTTCATAGGA GATACTGGTA 000800 000801 AAATAAATTC GAGTTTTAAA GTTCA |
Predicted Small Protein
| Name | ENST00000608917.1_smProtein_95:226 |
| Length | 44 |
| Molecular weight | 4914.4025 |
| Aromaticity | 0.116279069767 |
| Instability index | 79.0720930233 |
| Isoelectric point | 4.59381103516 |
| Runs | 5 |
| Runs residual | 0.0410243010191 |
| Runs probability | 0.0137078254725 |
| Amino acid sequence | MSFLLRSLCPSASESQFWTDRLGWDTGGGQKDTWLPLQESERP |
| Secondary structure | LLEEELLLLLLLLLLLLHHHHLLLLLLLLLLLLLLLLLLLLLL |
| PRMN | - |
| PiMo | - |
