Difference between revisions of "ENST00000608917.1"

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Please input one-sentence summary here.
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PACER, 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==
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
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Please input transcriptomic nomeclature information here.
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PACER,PTGS2 antisense NFKB1 complex-mediated expression regulator RNA(HGNC nomenclature)
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"p50-associated COX-2 extragenic RNA", PACER, "PTGS2 antisense RNA 1 (head to head)", PTGS2-AS1<ref name="ref1" />
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===Characteristics===
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PACER,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" />.
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===Celluar Localization===
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PACER performs its functions in the nucleus<ref name="ref1" />.
  
 
===Function===
 
===Function===
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Please input function information here.
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PACER 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<ref name="ref1" />.
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PACER directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter<ref name="ref1" />.
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PACER belongs to a novel, unanticipated class of bona-fide transcriptional regulators<ref name="ref1" />.
  
 
===Regulation===
 
===Regulation===
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Please input regulation information here.
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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<ref name="ref1" />.
  
 
===Expression===
 
===Expression===
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Please input expression information here.
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{|class='wikitable' style="text-align:center"
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|-
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===Allelic Information and Variation===
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! | Primers used in RACE|columnspan="3"
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|-
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| |
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===Evolution===
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| | initial
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| | nested
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|-
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You can also add sub-section(s) at will.
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| | 5'RACE
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| | TATGTATGTATGTGCTGCATATAG
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| | ATGTCAGCCTTTCTTAACCTTAC<ref name="ref1" />
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|-
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| | 3'RACE
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| | GTCTTTGCCCGAGCGCTTCCG
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| | CCGCCGTGTCTGGTCTGTACGTC<ref name="ref1" />
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|-
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! | Primers used for RNA quantitation|columnspan="3"
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|-
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| | COX-2 mRNA
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| | TCTGTACTGCGGGTGGAACA
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| | CAATTTGCCTGGTGAATGATTC<ref name="ref1" />
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|-
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| | PACER
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| | TGTAAATAGTTAATGTGAGCTCCACG
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| | GCAAATTCTGGCCATCGC<ref name="ref1" />
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|-
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| | p50 mRNA
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| | TTGCTGGTCCCACATAGTTG
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| | ATGTATGTGAAGGCCCATCC<ref name="ref1" />
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|-
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! | Custom siRNA|columnspan="3"
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|-
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| | siPACER-753
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| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
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| |
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|-
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| | siPACER-870
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| | TGGAAAGAGAGGCGGGAAA<ref name="ref1" />
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|-
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! | shRNA
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|-
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| | PACER ‘870’ shRNA
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| | 5’ - gatcc GGACAAAGGAAGCGGCGAT cttcctgtcaga ATCGCCGCTTCCTTTGTCC tttttg
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| | 3’ -    g CCTGTTTCCTTCGCCGCTA GAAGGACAGTCT TAGCGGCGAAGGAAACAGG aaaaacttaa<ref name="ref1" />
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|}
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
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Please input related labs here.
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Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
  
 
==References==
 
==References==
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Please input cited references here.
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Krawczyk M, Emerson BM. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes[J]. eLife. 2014,3:e01776.
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{{basic|
 
{{basic|
 
tID = ENST00000608917.1|
 
tID = ENST00000608917.1|
 
source = Gencode19|
 
source = Gencode19|
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same = ,|
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same =PACER ,PTGS2-AS1|
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classification = intergenic|
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classification = antisense|
 
length = 825 nt|
 
length = 825 nt|
 
location = chr1+:186649754..186650578|
 
location = chr1+:186649754..186650578|
Line 42: Line 87:
 
sequence = <dnaseq>AATTTGGGAGCAGAGGGGGTAGTCCCCACTCTCCTGTCTGATCCCTCCCTCTCCTCCCCGAGTTCCACCGCCCCAGGCGCACAGGTTTCCGCCAGATGTCTTTTCTTCTTCGCAGTCTTTGCCCGAGCGCTTCCGAGAGCCAGTTCTGGACTGATCGCCTTGGATGGGATACCGGGGGAGGGCAGAAGGACACTTGGCTTCCTCTCCAGGAATCTGAGCGGCCCTGAGGTCCGGGGGCGCAGGGAATCCCCTCTCCCGCCGCCGCCGCCGTGTCTGGTCTGTACGTCTTTAGAGGGTCGAGGAAGTCACGTCGGGACAGACTGGGGCGAGTAAGGTTAAGAAAGGCTGACATGTTTTATGTTTTAGTGACGACGCTTAATAGGCTGTATATCTGCTCTATATGCAGCACATACATACATAGCTTTTTAAAAAACTCTTATTTTGTGGAATGAAATAGCTACCTTCAGTGTACATAGCTGTAATTTATCTTTGTAGCTAAGTTGCTTTCAACAGAAGAAATACTGTTCTCCGTACCTTCACCCCCTCCTTGTTTCTTGGAAAGAGAGGCGGGAAAGGTAAATTCTCCTCATAATACTGGTCCTAAGCAGTTACCCTGTAAATAGTTAATGTGAGCTCCACGGGTCACCAATATAAAGTTTCCTGCCTTCTGATGGACAAAGGAAGCGGCGATGGCCAGAATTTGCAGGGACGCTAAATGTCCAAAACGTATGCCTTAAGGCATTTCTCTCCCTGATGCGTGGATTATTTTGGTTACTAGCCCTTCATAGGAGATACTGGTAAAATAAATTCGAGTTTTAAAGTTCA</dnaseq>|
 
sequence = <dnaseq>AATTTGGGAGCAGAGGGGGTAGTCCCCACTCTCCTGTCTGATCCCTCCCTCTCCTCCCCGAGTTCCACCGCCCCAGGCGCACAGGTTTCCGCCAGATGTCTTTTCTTCTTCGCAGTCTTTGCCCGAGCGCTTCCGAGAGCCAGTTCTGGACTGATCGCCTTGGATGGGATACCGGGGGAGGGCAGAAGGACACTTGGCTTCCTCTCCAGGAATCTGAGCGGCCCTGAGGTCCGGGGGCGCAGGGAATCCCCTCTCCCGCCGCCGCCGCCGTGTCTGGTCTGTACGTCTTTAGAGGGTCGAGGAAGTCACGTCGGGACAGACTGGGGCGAGTAAGGTTAAGAAAGGCTGACATGTTTTATGTTTTAGTGACGACGCTTAATAGGCTGTATATCTGCTCTATATGCAGCACATACATACATAGCTTTTTAAAAAACTCTTATTTTGTGGAATGAAATAGCTACCTTCAGTGTACATAGCTGTAATTTATCTTTGTAGCTAAGTTGCTTTCAACAGAAGAAATACTGTTCTCCGTACCTTCACCCCCTCCTTGTTTCTTGGAAAGAGAGGCGGGAAAGGTAAATTCTCCTCATAATACTGGTCCTAAGCAGTTACCCTGTAAATAGTTAATGTGAGCTCCACGGGTCACCAATATAAAGTTTCCTGCCTTCTGATGGACAAAGGAAGCGGCGATGGCCAGAATTTGCAGGGACGCTAAATGTCCAAAACGTATGCCTTAAGGCATTTCTCTCCCTGATGCGTGGATTATTTTGGTTACTAGCCCTTCATAGGAGATACTGGTAAAATAAATTCGAGTTTTAAAGTTCA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]][[Category:ENSG00000273129.1]][[Category:Transcripts]]
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[[Category:Antisense]][[Category:ENSG00000273129.1]][[Category:Transcripts]]

Revision as of 02:47, 16 April 2015

PACER, 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

Transcriptomic Nomeclature

PACER,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

PACER,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

PACER performs its functions in the nucleus[1].

Function

PACER 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]. PACER directly interacts with the repressive NF-κB subunit p50 to occlude it from the COX-2 promoter[1]. PACER 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|columnspan="3"
initial nested
5'RACE TATGTATGTATGTGCTGCATATAG ATGTCAGCCTTTCTTAACCTTAC[1]
3'RACE GTCTTTGCCCGAGCGCTTCCG CCGCCGTGTCTGGTCTGTACGTC[1]
Primers used for RNA quantitation|columnspan="3"
COX-2 mRNA TCTGTACTGCGGGTGGAACA CAATTTGCCTGGTGAATGATTC[1]
PACER TGTAAATAGTTAATGTGAGCTCCACG GCAAATTCTGGCCATCGC[1]
p50 mRNA TTGCTGGTCCCACATAGTTG ATGTATGTGAAGGCCCATCC[1]
Custom siRNA|columnspan="3"
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

References

Krawczyk M, Emerson BM. p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes[J]. eLife. 2014,3:e01776.

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
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  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 Cite error: Invalid <ref> tag; no text was provided for refs named ref1

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 -
Retrieved from "https://ngdc.cncb.ac.cn/lncrnawiki1/index.php?title=ENST00000608917.1&oldid=1270793"