Difference between revisions of "Lnc-EPCAM-1:2"

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==Annotated Information==
 
==Annotated Information==
 +
===Name===
 +
BC200
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 +
===Characteristics===
 +
200 nucleotide ncRNA [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))] exapted from an Alu element [http://www.ncbi.nlm.nih.gov/pubmed/2444875 (Watson (1987))]. Transcribed by RNA polymerase III [http://www.ncbi.nlm.nih.gov/pubmed/8265590 (Martignetti (1993))]. Three structural domains, 5' that shares homology with Alu elements, a central A rich region and a 3' unique region [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))].
 +
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
 
Please input transcriptomic nomeclature information here.
 
Please input transcriptomic nomeclature information here.
  
 
===Function===
 
===Function===
−
Please input function information here.
+
Binds several proteins including the signal recognition particle SRP9/14 heterodimer [http://www.ncbi.nlm.nih.gov/pubmed/9605471 (Kremerskothen (1998))], eukaryotic initiation factor 4A helicase (eIF4A) [http://www.ncbi.nlm.nih.gov/pubmed/18316401 (Lin (2008))] and Poly(A)-binding protein (PABP), binding to PABP requires the central A rich region [http://www.ncbi.nlm.nih.gov/pubmed/12162957 (Muddashetty (2002))].
 +
 
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Inhibits translation in-vitro and in cultured cells similar to BC1.  BC200 binding to eIF4A inhibits it by uncoupling eIF4A ATPase activity from its helicase/ duplex unwinding activity [http://www.ncbi.nlm.nih.gov/pubmed/18316401 (Lin (2008))]. Translational inhibition also involves BC200 binding to to PABP [http://www.ncbi.nlm.nih.gov/pubmed/16154588 (Kondrashov (2005))].  
  
 
===Regulation===
 
===Regulation===
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===Expression===
 
===Expression===
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Please input expression information here.
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Expressed predominantly in different regions of the brain. Also shows low level expression in testis but not in other normal tissues examined ([http://www.ncbi.nlm.nih.gov/pubmed/2444875 Watson (1987)], [http://www.ncbi.nlm.nih.gov/pubmed/7684772 Tiedge (1993)], [http://www.ncbi.nlm.nih.gov/pubmed/11399078 Kuryshev (2001)]). RNA sequencing of 11 human tissues confirmed up-regulation of expression in brain (hypothalamus) and low or no expression elsewhere [http://www.ncbi.nlm.nih.gov/pubmed/20668672 (Castle (2010))].
 +
 
 +
Disregulated in cancer: expressed in a number of human tumours but not in corresponding normal tissue [http://www.ncbi.nlm.nih.gov/pubmed/9422992 (Chen (1998))].
 +
 
 +
Link with aging and Alzheimer disease: BC200 expression decreases with aging but is upregulated in Alzheimer's disease (AD). In AD affected brain regions, expression increased with disease severity. RNA localisation showed intense perikaryal staining, showing build up of RNA in cell body [http://www.ncbi.nlm.nih.gov/pubmed/17553964 (Mus (2007))].
 +
 
 +
Like BC1 ncRNA found in rodents, BC200 also suggested to localise to dendrites [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))].
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
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}}
 
}}
 
[[Category:Intergenic]]
 
[[Category:Intergenic]]
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{{lncrnadb|
 
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tID = lnc-EPCAM-1:2|
 
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ltID = BC200|
 
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ann = <tab class=wikitable sep=tab head=top>
 
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Section Description
 
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ID BC200
 
−
Characteristics 200 nucleotide ncRNA [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))] exapted from an Alu element [http://www.ncbi.nlm.nih.gov/pubmed/2444875 (Watson (1987))]. Transcribed by RNA polymerase III [http://www.ncbi.nlm.nih.gov/pubmed/8265590 (Martignetti (1993))]. Three structural domains, 5' that shares homology with Alu elements, a central A rich region and a 3' unique region [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))].
 
−
Expression Expressed predominantly in different regions of the brain. Also shows low level expression in testis but not in other normal tissues examined ([http://www.ncbi.nlm.nih.gov/pubmed/2444875 Watson (1987)], [http://www.ncbi.nlm.nih.gov/pubmed/7684772 Tiedge (1993)], [http://www.ncbi.nlm.nih.gov/pubmed/11399078 Kuryshev (2001)]). RNA sequencing of 11 human tissues confirmed up-regulation of expression in brain (hypothalamus) and low or no expression elsewhere [http://www.ncbi.nlm.nih.gov/pubmed/20668672 (Castle (2010))]. Disregulated in cancer: expressed in a number of human tumours but not in corresponding normal tissue [http://www.ncbi.nlm.nih.gov/pubmed/9422992 (Chen (1997))]. Link with aging and Alzheimer disease: BC200 expression decreases with aging but is upregulated in Alzheimer's disease (AD). In AD affected brain regions, expression increased with disease severity. RNA localisation showed intense perikaryal staining, showing build up of RNA in cell body [http://www.ncbi.nlm.nih.gov/pubmed/17553964 (Mus (2007))]. Like BC1 ncRNA found in rodents, BC200 also suggested to localise to dendrites [http://www.ncbi.nlm.nih.gov/pubmed/7684772 (Tiedge (1993))]. 
 
−
Function Binds several proteins including the signal recognition particle SRP9/14 heterodimer [http://www.ncbi.nlm.nih.gov/pubmed/9605471 (Kremerskothen (1998))], eukaryotic initiation factor 4A helicase (eIF4A) [http://www.ncbi.nlm.nih.gov/pubmed/18316401 (Lin (2008))] and Poly(A)-binding protein (PABP), binding to PABP requires the central A rich region [http://www.ncbi.nlm.nih.gov/pubmed/12162957 (Muddashetty (2002))]. Inhibits translation in-vitro and in cultured cells similar to BC1.  BC200 binding to eIF4A inhibits it by uncoupling eIF4A ATPase activity from its helicase/ duplex unwinding activity [http://www.ncbi.nlm.nih.gov/pubmed/18316401 (Lin (2008))]. Translational inhibition also involves BC200 binding to to PABP [http://www.ncbi.nlm.nih.gov/pubmed/16154588 (Kondrashov (2005))].
 
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Conservation Anthropoid primates (monkeys, apes and humans) [http://www.ncbi.nlm.nih.gov/pubmed/9847409 (Skryabin (1998))]. BC200, BC1 and G22 likely form a family of independently exapted repetitive elements which have evolved to carry out similar functions in different mammalian species ([http://www.ncbi.nlm.nih.gov/pubmed/12162957 Muddashetty (2002)], [http://www.ncbi.nlm.nih.gov/pubmed/17175535 Khanam (2007)]).
 
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</tab>|
 
−
}}
 

Revision as of 08:12, 8 October 2014

Please input one-sentence summary here.

Annotated Information

Name

BC200

Characteristics

200 nucleotide ncRNA (Tiedge (1993)) exapted from an Alu element (Watson (1987)). Transcribed by RNA polymerase III (Martignetti (1993)). Three structural domains, 5' that shares homology with Alu elements, a central A rich region and a 3' unique region (Tiedge (1993)).

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Function

Binds several proteins including the signal recognition particle SRP9/14 heterodimer (Kremerskothen (1998)), eukaryotic initiation factor 4A helicase (eIF4A) (Lin (2008)) and Poly(A)-binding protein (PABP), binding to PABP requires the central A rich region (Muddashetty (2002)).

Inhibits translation in-vitro and in cultured cells similar to BC1. BC200 binding to eIF4A inhibits it by uncoupling eIF4A ATPase activity from its helicase/ duplex unwinding activity (Lin (2008)). Translational inhibition also involves BC200 binding to to PABP (Kondrashov (2005)).

Regulation

Please input regulation information here.

Expression

Expressed predominantly in different regions of the brain. Also shows low level expression in testis but not in other normal tissues examined (Watson (1987), Tiedge (1993), Kuryshev (2001)). RNA sequencing of 11 human tissues confirmed up-regulation of expression in brain (hypothalamus) and low or no expression elsewhere (Castle (2010)).

Disregulated in cancer: expressed in a number of human tumours but not in corresponding normal tissue (Chen (1998)).

Link with aging and Alzheimer disease: BC200 expression decreases with aging but is upregulated in Alzheimer's disease (AD). In AD affected brain regions, expression increased with disease severity. RNA localisation showed intense perikaryal staining, showing build up of RNA in cell body (Mus (2007)).

Like BC1 ncRNA found in rodents, BC200 also suggested to localise to dendrites (Tiedge (1993)).

Allelic Information and Variation

Please input allelic information and variation information here.

Evolution

Please input evolution information here.

You can also add sub-section(s) at will.

Labs working on this lncRNA

Please input related labs here.

References

Please input cited references here.

Basic Information

Transcript ID

lnc-EPCAM-1:2

Source

LNCipedia2.1

Same with

,

Classification

intergenic

Length

200 nt

Genomic location

chr2+:47562453..47562653

Exon number

1

Exons

47562453..47562653

Genome context

Sequence
000001 GGCCGGGCGC GGTGGCTCAC GCCTGTAATC CCAGCTCTCA GGGAGGCTAA GAGGCGGGAG GATAGCTTGA GCCCAGGAGT 000080
000081 TCGAGACCTG CCTGGGCAAT ATAGCGAGAC CCCGTTCTCC AGAAAAAGGA AAAAAAAAAA CAAAAGACAA AAAAAAAATA 000160
000161 AGCGTAACTT CCCTCAAAGC AACAACCCCC CCCCCCCTTT
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