Difference between revisions of "ENST00000417473.2"

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Please input one-sentence summary here.
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''LINC00570'' (Long Intergenic Non-Protein Coding RNA 570) is a non-coding RNA gene, with a possible role in transcriptional activation of gene expression.
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==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
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LINC00570
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''LINC00570'', Long Intergenic Non-Protein Coding RNA 570 [https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/43717 (HGNC:43717)]
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===Alias===
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Noncoding RNA-Activating 5, ncRNA-a5 [https://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=full_report&list_uids=100874055 (NCBI:100874055)]
  
 
===Characteristics===
 
===Characteristics===
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Multiple 2-4 exon isoforms with variation in splicing and TSSs. Isoforms between 380 nt and 1.3kb. Intergenic between ROCK2 and E2F6. In-vitro translation showed no sign of protein product.
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''LINC00570'' also known as ncRNA-a5 has chromosomal location at 2p25.1. It is adjacent to the ''E2F6'' gene and upstream of ''LINC00570'' is ''ROCK2'' gene. In vitro translation assay confirmed that this ncRNA does not yield any protein product <ref name="ref1" />.
  
 
===Function===
 
===Function===
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LINC00570 expression appears to stimulate ROCK2 gene expression (in HeLa cells).
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Studies have uncovered a new biological function of this ncRNA which is positive regulation of gene expression.''LINC00570'' play a major role in transcriptional activation of its upstream gene ''ROCK2''<ref name="ref1" />.  
  
 
===Expression===
 
===Expression===
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Expressed in HeLa cells.
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Using rapid amplification of 5′ and 3′ complementary DNA ends (5′ and 3′ RACE), PCR and in vitro translation, expression of ncRNA-a5 was confirmed in HeLa cells. Knock-down of ncRNA-a5 did not affect its adjacent E2F6 gene. However, depletion of ncRNA-a5 resulted in a specific reduction in ROCK2 expression levels in HeLa cells, which is located upstream of ncRNA-a5 <ref name="ref1" />.
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===Conservation===
 
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===Misc===
 
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===Transcriptomic Nomeclature===
 
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===Regulation===
 
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===Allelic Information and Variation===
 
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===Evolution===
 
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==Labs working on this lncRNA==
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==Labs working==
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*The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104
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*Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain
  
 
==References==
 
==References==
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<references>
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<ref name="ref1"> Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010, 143(1):46-58.</ref>(1)
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</references>
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>CGGAAGAGTGGGACGTTATGGAACCTTCTCAGCTTATTCAGAGAGGCTTCTTCTTCCTATTTAGTCTCCCTCTGGCTTTCCCTGCTGGGATCTGGGTGGTAGAAGCAGCAGGGGGATCAACGAACAGGCTGAGCGCCAAGAAGCCTGAAGATTCCAGAATCTAGCGGGAAAAGCATTCAGAGTCAGAATGAGCCACTTCCAGCATCGATGGTGTCAGGTCAGGTCCTCTGGGTAGAAGAAATGGAGTCAGTTAGGAGTGCTGGAGACTGAGTAAGAGGTGGCAGCTGAGGCTTACTACCCCAGGAAAGGGATGCCACCAGAGAAGGCAGACAACCAAGATGGCGACTCTCAATTTTTGAGCTCCTAATTTTCTCATGTCAGACATAAGAAAAAAAAATATTTTTTAAAGAAAAAGCTTTAGGTTGCAAAAATCTAGGCCTTTCAACTTTAAAATCCTATTCTTGCAAGCCTTGGAGAATAAAGCTTATGCATAAACAGTAGATTTGGAAACAGAAATATGCCTAATTACCCAGAGCCATTCTTTCAATACGCCAGTGATTGTTTAAAGATTCTATAGGCTGGAGTCAATGGCAGGAGGCGGGTGGGAAAAGAGTCAAGAGGGAGGAGAGAAGAAGCAAGAGGGTTGGGTAGATATTGTCACATGACCCTGAGAGGAGGATTCTGGGTCAAACCCCTAGGGGGTTGTGTGTAATGGAGACTCCAGATCCATTTGGGAATCTGGCTCCAAAGAAGACTTCACCTTGCCTTCTGAGTGGAGCCCTGAAGTGGCAAGACTCATAGAATTCCCCCACGGGTCCACACAAGAGAGAATGAATAGAGAAGGCTGCGTGCTGGCTGGACCAAGGCAGCCTCGGGTGACACCACCACCACCACCGCCGCTGCCGCCATCGCCATCACCACTGCCGCTGCCATCACCGCCACCACCACCACCATCACCACCACCATCACCACATTATGGACAATAGCCCAATGTTTCCTGAGTTCCCTAGAGGGTTGAAAGAGAATAGGACCTAGAGAGATCACATAGTTGGGACAGGCACTCATTAATTTGATCCAATGACAAGAGACCAGATGGGAAGAAGGATGCCTTGAGAGATGTCAGTGTGCACCCATGGATAGAAGCAGCTGGTGACTGGGTACTTGGGAAGCCACATGGACACACACAAAGCTCCTGGAAGACGTTTTCAAGGAGTTGGGCTGTGCTGGGATCCAGAACTGGCTGAAGAAACCATGAGCTGACATAAAATTTCTGCCACCTAGCAGAATGGAGGCTCCATTTGGAAATTAAATTATATACTTAAAAAAACTA</dnaseq>|
 
sequence = <dnaseq>CGGAAGAGTGGGACGTTATGGAACCTTCTCAGCTTATTCAGAGAGGCTTCTTCTTCCTATTTAGTCTCCCTCTGGCTTTCCCTGCTGGGATCTGGGTGGTAGAAGCAGCAGGGGGATCAACGAACAGGCTGAGCGCCAAGAAGCCTGAAGATTCCAGAATCTAGCGGGAAAAGCATTCAGAGTCAGAATGAGCCACTTCCAGCATCGATGGTGTCAGGTCAGGTCCTCTGGGTAGAAGAAATGGAGTCAGTTAGGAGTGCTGGAGACTGAGTAAGAGGTGGCAGCTGAGGCTTACTACCCCAGGAAAGGGATGCCACCAGAGAAGGCAGACAACCAAGATGGCGACTCTCAATTTTTGAGCTCCTAATTTTCTCATGTCAGACATAAGAAAAAAAAATATTTTTTAAAGAAAAAGCTTTAGGTTGCAAAAATCTAGGCCTTTCAACTTTAAAATCCTATTCTTGCAAGCCTTGGAGAATAAAGCTTATGCATAAACAGTAGATTTGGAAACAGAAATATGCCTAATTACCCAGAGCCATTCTTTCAATACGCCAGTGATTGTTTAAAGATTCTATAGGCTGGAGTCAATGGCAGGAGGCGGGTGGGAAAAGAGTCAAGAGGGAGGAGAGAAGAAGCAAGAGGGTTGGGTAGATATTGTCACATGACCCTGAGAGGAGGATTCTGGGTCAAACCCCTAGGGGGTTGTGTGTAATGGAGACTCCAGATCCATTTGGGAATCTGGCTCCAAAGAAGACTTCACCTTGCCTTCTGAGTGGAGCCCTGAAGTGGCAAGACTCATAGAATTCCCCCACGGGTCCACACAAGAGAGAATGAATAGAGAAGGCTGCGTGCTGGCTGGACCAAGGCAGCCTCGGGTGACACCACCACCACCACCGCCGCTGCCGCCATCGCCATCACCACTGCCGCTGCCATCACCGCCACCACCACCACCATCACCACCACCATCACCACATTATGGACAATAGCCCAATGTTTCCTGAGTTCCCTAGAGGGTTGAAAGAGAATAGGACCTAGAGAGATCACATAGTTGGGACAGGCACTCATTAATTTGATCCAATGACAAGAGACCAGATGGGAAGAAGGATGCCTTGAGAGATGTCAGTGTGCACCCATGGATAGAAGCAGCTGGTGACTGGGTACTTGGGAAGCCACATGGACACACACAAAGCTCCTGGAAGACGTTTTCAAGGAGTTGGGCTGTGCTGGGATCCAGAACTGGCTGAAGAAACCATGAGCTGACATAAAATTTCTGCCACCTAGCAGAATGGAGGCTCCATTTGGAAATTAAATTATATACTTAAAAAAACTA</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:lnc-GREB1-4]][[Category:NONHSAG027008]][[Category:Transcripts]]

Latest revision as of 07:14, 15 November 2018

LINC00570 (Long Intergenic Non-Protein Coding RNA 570) is a non-coding RNA gene, with a possible role in transcriptional activation of gene expression.

Annotated Information

Name

LINC00570, Long Intergenic Non-Protein Coding RNA 570 (HGNC:43717)

Alias

Noncoding RNA-Activating 5, ncRNA-a5 (NCBI:100874055)

Characteristics

LINC00570 also known as ncRNA-a5 has chromosomal location at 2p25.1. It is adjacent to the E2F6 gene and upstream of LINC00570 is ROCK2 gene. In vitro translation assay confirmed that this ncRNA does not yield any protein product [1].

Function

Studies have uncovered a new biological function of this ncRNA which is positive regulation of gene expression.LINC00570 play a major role in transcriptional activation of its upstream gene ROCK2[1].

Expression

Using rapid amplification of 5′ and 3′ complementary DNA ends (5′ and 3′ RACE), PCR and in vitro translation, expression of ncRNA-a5 was confirmed in HeLa cells. Knock-down of ncRNA-a5 did not affect its adjacent E2F6 gene. However, depletion of ncRNA-a5 resulted in a specific reduction in ROCK2 expression levels in HeLa cells, which is located upstream of ncRNA-a5 [1].

Labs working

  • The Wistar Institute, 3601 Spruce Street, Philadelphia, PA 19104
  • Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain

References

  1. ↑ 1.0 1.1 1.2 Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010, 143(1):46-58.

Basic Information

Transcript ID

ENST00000417473.2

Source

Gencode19

Same with

lnc-GREB1-4:1,NONHSAT069164

Classification

intergenic

Length

1330 nt

Genomic location

chr2+:11534107..11543203

Exon number

3

Exons

11534107..11534297,11540498..11540583,11542151..11543203

Genome context

Sequence
000001 CGGAAGAGTG GGACGTTATG GAACCTTCTC AGCTTATTCA GAGAGGCTTC TTCTTCCTAT TTAGTCTCCC TCTGGCTTTC 000080
000081 CCTGCTGGGA TCTGGGTGGT AGAAGCAGCA GGGGGATCAA CGAACAGGCT GAGCGCCAAG AAGCCTGAAG ATTCCAGAAT 000160
000161 CTAGCGGGAA AAGCATTCAG AGTCAGAATG AGCCACTTCC AGCATCGATG GTGTCAGGTC AGGTCCTCTG GGTAGAAGAA 000240
000241 ATGGAGTCAG TTAGGAGTGC TGGAGACTGA GTAAGAGGTG GCAGCTGAGG CTTACTACCC CAGGAAAGGG ATGCCACCAG 000320
000321 AGAAGGCAGA CAACCAAGAT GGCGACTCTC AATTTTTGAG CTCCTAATTT TCTCATGTCA GACATAAGAA AAAAAAATAT 000400
000401 TTTTTAAAGA AAAAGCTTTA GGTTGCAAAA ATCTAGGCCT TTCAACTTTA AAATCCTATT CTTGCAAGCC TTGGAGAATA 000480
000481 AAGCTTATGC ATAAACAGTA GATTTGGAAA CAGAAATATG CCTAATTACC CAGAGCCATT CTTTCAATAC GCCAGTGATT 000560
000561 GTTTAAAGAT TCTATAGGCT GGAGTCAATG GCAGGAGGCG GGTGGGAAAA GAGTCAAGAG GGAGGAGAGA AGAAGCAAGA 000640
000641 GGGTTGGGTA GATATTGTCA CATGACCCTG AGAGGAGGAT TCTGGGTCAA ACCCCTAGGG GGTTGTGTGT AATGGAGACT 000720
000721 CCAGATCCAT TTGGGAATCT GGCTCCAAAG AAGACTTCAC CTTGCCTTCT GAGTGGAGCC CTGAAGTGGC AAGACTCATA 000800
000801 GAATTCCCCC ACGGGTCCAC ACAAGAGAGA ATGAATAGAG AAGGCTGCGT GCTGGCTGGA CCAAGGCAGC CTCGGGTGAC 000880
000881 ACCACCACCA CCACCGCCGC TGCCGCCATC GCCATCACCA CTGCCGCTGC CATCACCGCC ACCACCACCA CCATCACCAC 000960
000961 CACCATCACC ACATTATGGA CAATAGCCCA ATGTTTCCTG AGTTCCCTAG AGGGTTGAAA GAGAATAGGA CCTAGAGAGA 001040
001041 TCACATAGTT GGGACAGGCA CTCATTAATT TGATCCAATG ACAAGAGACC AGATGGGAAG AAGGATGCCT TGAGAGATGT 001120
001121 CAGTGTGCAC CCATGGATAG AAGCAGCTGG TGACTGGGTA CTTGGGAAGC CACATGGACA CACACAAAGC TCCTGGAAGA 001200
001201 CGTTTTCAAG GAGTTGGGCT GTGCTGGGAT CCAGAACTGG CTGAAGAAAC CATGAGCTGA CATAAAATTT CTGCCACCTA 001280
001281 GCAGAATGGA GGCTCCATTT GGAAATTAAA TTATATACTT AAAAAAACTA
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