Difference between revisions of "ENST00000553584.1"

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(Expression)
 
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Irm: Imprinted RNA near Meg3/Gtl2.  
 
Irm: Imprinted RNA near Meg3/Gtl2.  
 
MEG8: Maternally expressed gene 8
 
MEG8: Maternally expressed gene 8
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 +
===Disease===
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Prader-Willi/Angelman syndrome
  
 
===Characteristics===
 
===Characteristics===
These overlapping but non-identical transcripts are found in the Dlk1-Dio3 imprinted region ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/17507654 Royo (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/19194500 Hagan (2009)]) and should probably be viewed as different isoforms of the Rian gene. The human and mouse loci are quite similar, whereas the rat loci (Bsr gene) has undergone significant divergence and so has its own entry in the database. Spliced lncRNAs that contain a number of intronic snoRNAs and sometimes miRNAs ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 Cavaill®¶ (2002)], [http://www.ncbi.nlm.nih.gov/pubmed/17507654 Royo (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/19194500 Hagan (2009)]). In human and mouse, transcription of the Meg8 isoform can extend through the snoRNA clusters. Mouse Meg8 is ~4.4kb with over 20 exons. In mouse the ~2.5 kb Irm transcript contains the last 10 exons of Meg8 but has its own transcriptional start site. Mouse Meg8 contains intronic miRNAs not found in Irm [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. RNA sequencing confirms a large number of isoforms with alternative splicing and also retained introns exist at this locus though no evidence was found for Rian overlapping the Meg9/Mirg transcript [http://www.ncbi.nlm.nih.gov/pubmed/20436462 (Guttman (2010))]. It is unclear if the Irm isoform exists in humans.
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These overlapping but non-identical transcripts are found in the Dlk1-Dio3 imprinted region ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/17507654 Royo (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/19194500 Hagan (2009)]) and should probably be viewed as different isoforms of the Rian gene. The human and mouse loci are quite similar, whereas the rat loci (Bsr gene) has undergone significant divergence and so has its own entry in the database. Spliced lncRNAs that contain a number of intronic snoRNAs and sometimes miRNAs ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 Cavaillé (2002)], [http://www.ncbi.nlm.nih.gov/pubmed/17507654 Royo (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/19194500 Hagan (2009)]). In human and mouse, transcription of the Meg8 isoform can extend through the snoRNA clusters. Mouse Meg8 is ~4.4kb with over 20 exons. In mouse the ~2.5 kb Irm transcript contains the last 10 exons of Meg8 but has its own transcriptional start site. Mouse Meg8 contains intronic miRNAs not found in Irm [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. RNA sequencing confirms a large number of isoforms with alternative splicing and also retained introns exist at this locus though no evidence was found for Rian overlapping the Meg9/Mirg transcript [http://www.ncbi.nlm.nih.gov/pubmed/20436462 (Guttman (2010))]. It is unclear if the Irm isoform exists in humans.
  
 
===Function===
 
===Function===
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===Expression===
 
===Expression===
Imprinted: Maternally expressed ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/11337479 Charlier (2001)], ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 (Cavaillé (2002)]). Expressed predominately in brain [http://www.ncbi.nlm.nih.gov/pubmed/11481034 (Hatada (2001))], embryo and muscle [http://www.ncbi.nlm.nih.gov/pubmed/11337479 (Charlier (2001))] with generally weak expression in other tissues [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. Expressed in mouse embryonic stem cells [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))]. In mouse the longer 'Meg8' transcript is also expressed in skin whereas the shorter 3' 'Irm' is not [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. Up-regulated during differentiation of neuronal progenitors to GABAergic neurons in vitro [http://www.ncbi.nlm.nih.gov/pubmed/20137068 (Mercer (2010))]. Localised to the nucleus [http://www.ncbi.nlm.nih.gov/pubmed/11481034 (Hatada (2001))]. Intronic snoRNAs also show brain and embryo imprinted expression ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 (Cavaillé (2002))].
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Imprinted: Maternally expressed ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/11337479 Charlier (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/12045206 Cavaillé (2002)]). Expressed predominately in brain [http://www.ncbi.nlm.nih.gov/pubmed/11481034 (Hatada (2001))], embryo and muscle [http://www.ncbi.nlm.nih.gov/pubmed/11337479 (Charlier (2001))] with generally weak expression in other tissues [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. Expressed in mouse embryonic stem cells [http://www.ncbi.nlm.nih.gov/pubmed/21874018 (Guttman (2011))]. In mouse the longer 'Meg8' transcript is also expressed in skin whereas the shorter 3' 'Irm' is not [http://www.ncbi.nlm.nih.gov/pubmed/19194500 (Hagan (2009))]. Up-regulated during differentiation of neuronal progenitors to GABAergic neurons in vitro [http://www.ncbi.nlm.nih.gov/pubmed/20137068 (Mercer (2010))]. Localised to the nucleus [http://www.ncbi.nlm.nih.gov/pubmed/11481034 (Hatada (2001))]. Intronic snoRNAs also show brain and embryo imprinted expression ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 (Cavaillé (2002))].
  
 
===Conservation===
 
===Conservation===
Bsr and Rian/MEG8/Irm are not highly conserved between species ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 (Cavaillé (2002))]. However, some Rian exons show good homology to Bsr and while many snoRNAs are specific to one species others are homologous ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 Cavaillé (2002)]). Rian gene is present in mammals.
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Bsr and Rian/MEG8/Irm are not highly conserved between species ([http://www.ncbi.nlm.nih.gov/pubmed/12045206 (Cavaillé (2002))]. However, some Rian exons show good homology to Bsr and while many snoRNAs are specific to one species others are homologous ([http://www.ncbi.nlm.nih.gov/pubmed/11481034 Hatada (2001)], [http://www.ncbi.nlm.nih.gov/pubmed/12045206 Cavaillé (2002)]). Rian gene is present in mammals.
  
 
===Misc===
 
===Misc===
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==References==
 
==References==
Please input cited references here.
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[http://www.lncrnadb.org/Rian/ Annotation originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>GGTCTGAAAAATGATATTCATTGTCCTAATGTGTAAATTTCGACAATTTGCAAATTTGTAGATTCTTTAGAATAGAACTAACTCAAGCCCTTCATTCTGCAGCTGAGGCTCACTGCCCCCAGTGGGCAGTGGGTCCAGGGGGTTTCTGAGGACAGGGCATGACCCAGCCCTGCTGCCCCCAAGATGGCACCTGGCTTGGAGGGGTGAGGGGCCCTGTTAGTCTGACTTTGAAGAAGACCAGCCTTCCAGACTCGCTTGGTGCCCTGACAGGAGCCCTGGGCTCCCCCAGTGTTGCCTGGGTCTGACTTTGCCTCAGTGAAAACTGCCTCGAATTCTTTCTTGCACCGATGGGCAGATGGGCAGTGTCGGAGGATCGTGTCATCTGTCCCGTGGCGCTGGTTGGCTTGGTCAAGTCAGTGTTCAAACTATCTCCTGCTCTTTCAAGGGGATCTGGGGCTCTAGAAGATTAGAGGACTTGGAGAGGTTAGTGACTTGCTC</dnaseq>|
 
sequence = <dnaseq>GGTCTGAAAAATGATATTCATTGTCCTAATGTGTAAATTTCGACAATTTGCAAATTTGTAGATTCTTTAGAATAGAACTAACTCAAGCCCTTCATTCTGCAGCTGAGGCTCACTGCCCCCAGTGGGCAGTGGGTCCAGGGGGTTTCTGAGGACAGGGCATGACCCAGCCCTGCTGCCCCCAAGATGGCACCTGGCTTGGAGGGGTGAGGGGCCCTGTTAGTCTGACTTTGAAGAAGACCAGCCTTCCAGACTCGCTTGGTGCCCTGACAGGAGCCCTGGGCTCCCCCAGTGTTGCCTGGGTCTGACTTTGCCTCAGTGAAAACTGCCTCGAATTCTTTCTTGCACCGATGGGCAGATGGGCAGTGTCGGAGGATCGTGTCATCTGTCCCGTGGCGCTGGTTGGCTTGGTCAAGTCAGTGTTCAAACTATCTCCTGCTCTTTCAAGGGGATCTGGGGCTCTAGAAGATTAGAGGACTTGGAGAGGTTAGTGACTTGCTC</dnaseq>|
 
}}
 
}}
[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:lnc-DLK1-6]][[Category:NONHSAG015927]][[Category:ENSG00000258399.2]][[Category:Transcripts]]

Latest revision as of 12:09, 1 July 2016

Please input one-sentence summary here.

Annotated Information

Name

Rian: RNA Imprinted and Accumulated in Nucleus . Irm: Imprinted RNA near Meg3/Gtl2. MEG8: Maternally expressed gene 8

Disease

Prader-Willi/Angelman syndrome

Characteristics

These overlapping but non-identical transcripts are found in the Dlk1-Dio3 imprinted region (Hatada (2001), Royo (2007), Hagan (2009)) and should probably be viewed as different isoforms of the Rian gene. The human and mouse loci are quite similar, whereas the rat loci (Bsr gene) has undergone significant divergence and so has its own entry in the database. Spliced lncRNAs that contain a number of intronic snoRNAs and sometimes miRNAs (Cavaillé (2002), Royo (2007), Hagan (2009)). In human and mouse, transcription of the Meg8 isoform can extend through the snoRNA clusters. Mouse Meg8 is ~4.4kb with over 20 exons. In mouse the ~2.5 kb Irm transcript contains the last 10 exons of Meg8 but has its own transcriptional start site. Mouse Meg8 contains intronic miRNAs not found in Irm (Hagan (2009)). RNA sequencing confirms a large number of isoforms with alternative splicing and also retained introns exist at this locus though no evidence was found for Rian overlapping the Meg9/Mirg transcript (Guttman (2010)). It is unclear if the Irm isoform exists in humans.

Function

LncRNAs contain a number of miRNAs and snoRNAs, little is known about the molecular function of the lncRNAs. Rian transcript(s) bind to the PRC2 chromatin modifying complex in mouse embryonic stem cells (Zhao (2010), Guttman (2011)). Rian was also found to interact with a number of other chromatin binding protein(s)/complexes in mouse embryonic stem cells including PRC1, JARID1B, JARID1C and CBX3, with the general pattern being interaction with repressors of gene expression (Guttman (2011)). Aberrant repression of Rian and other maternally expressed lncRNAs from the DLK1-Dio3 imprinting cluster is present in most induced pluripotent stem cell (iPSC) lines and is responsible for the failure of iPSCs to form viable mice, with embryos dying mid-gestation (Stadtfeld (2010)).

Expression

Imprinted: Maternally expressed (Hatada (2001), Charlier (2001), Cavaillé (2002)). Expressed predominately in brain (Hatada (2001)), embryo and muscle (Charlier (2001)) with generally weak expression in other tissues (Hagan (2009)). Expressed in mouse embryonic stem cells (Guttman (2011)). In mouse the longer 'Meg8' transcript is also expressed in skin whereas the shorter 3' 'Irm' is not (Hagan (2009)). Up-regulated during differentiation of neuronal progenitors to GABAergic neurons in vitro (Mercer (2010)). Localised to the nucleus (Hatada (2001)). Intronic snoRNAs also show brain and embryo imprinted expression ((Cavaillé (2002)).

Conservation

Bsr and Rian/MEG8/Irm are not highly conserved between species ((Cavaillé (2002)). However, some Rian exons show good homology to Bsr and while many snoRNAs are specific to one species others are homologous (Hatada (2001), Cavaillé (2002)). Rian gene is present in mammals.

Misc

Human UCSC browser link below is for Refseq Meg8, however it is clear from known human mRNAs that transcripts from the Meg8 locus can extend much further than the current Refseq annotation.

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Regulation

Please input regulation information here.

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

Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID

ENST00000553584.1

Source

Gencode19

Same with

lnc-DLK1-6:3,NONHSAT039802

Classification

intergenic

Length

498 nt

Genomic location

chr14+:101361107..101373305

Exon number

4

Exons

101361107..101361376,101365294..101365422,101372435..101372500,101373273..101373305

Genome context

Sequence
000001 GGTCTGAAAA ATGATATTCA TTGTCCTAAT GTGTAAATTT CGACAATTTG CAAATTTGTA GATTCTTTAG AATAGAACTA 000080
000081 ACTCAAGCCC TTCATTCTGC AGCTGAGGCT CACTGCCCCC AGTGGGCAGT GGGTCCAGGG GGTTTCTGAG GACAGGGCAT 000160
000161 GACCCAGCCC TGCTGCCCCC AAGATGGCAC CTGGCTTGGA GGGGTGAGGG GCCCTGTTAG TCTGACTTTG AAGAAGACCA 000240
000241 GCCTTCCAGA CTCGCTTGGT GCCCTGACAG GAGCCCTGGG CTCCCCCAGT GTTGCCTGGG TCTGACTTTG CCTCAGTGAA 000320
000321 AACTGCCTCG AATTCTTTCT TGCACCGATG GGCAGATGGG CAGTGTCGGA GGATCGTGTC ATCTGTCCCG TGGCGCTGGT 000400
000401 TGGCTTGGTC AAGTCAGTGT TCAAACTATC TCCTGCTCTT TCAAGGGGAT CTGGGGCTCT AGAAGATTAG AGGACTTGGA 000480
000481 GAGGTTAGTG ACTTGCTC
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