Difference between revisions of "Lnc-EVX1-9:1"

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==Annotated Information==
 
==Annotated Information==
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===Transcriptomic Nomeclature===
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===Name===
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Please input transcriptomic nomeclature information here.
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''HOXA-AS3'': "HOXA cluster antisense RNA 3 (non-protein coding)"
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HOXA6as
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===Characteristics===
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HOXA6as located between HOXA6-A7, whose tissue-specific expression patterns that in some cases resemble the expression profile of sense transcripts.<ref name="ref2" />
  
 
===Function===
 
===Function===
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HOXA6as may be a regarded as universal reference being applicable for the accurate normalisation of lncRNA expression profiling in various glioma (WHO-Grades II-IV) alone and in combination with brain tissue.<ref name="ref1" />
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===Expression===
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[[File:Stably expressed lncRNAs suitable for studies comparing different glioma entities.jpg|right|thumb|500px|'''Stably expressed lncRNAs suitable for studies comparing different glioma entities.'''<ref name="ref1" />]]
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HOXA6as, which showed stable expression in all investigated brain regions, may be regarded as an universal normaliser suitable for a broad range of lncRNA studies <ref name="ref1" />.
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HOXA6as, like many cases OS-intergenic transcripts, is coexpressed with adjacent coding HOX genes <ref name="ref2" />.
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===Regulation===
 
===Regulation===
 
Please input regulation information here.
 
Please input regulation information here.
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===Expression===
 
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Please input expression information here.
 
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
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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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* Dulbecco Telethon Institute, Naples, Italy. <ref name="ref2" />
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* Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University. <ref name="ref1" />
  
 
==References==
 
==References==
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Please input cited references here.
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<references>
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<ref name="ref1">Kraus TF, Greiner A, Guibourt V, Lisec K, Kretzschmar HA. Identification of Stably Expressed lncRNAs as Valid Endogenous Controls for Profiling of Human Glioma[J]. Journal of Cancer. 2015,6(2):111-9.</ref>(1)
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<ref name="ref2">Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, Orlando V. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster[J]. Rna. 2007,13(2):223-39.</ref>(1)
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</references>
  
 
{{basic|
 
{{basic|
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sequence = <dnaseq>TTCTCTTTTAAGAAGCCAAAGAAACTTTGCTGGTTCTTTCATCCTTTCTTTCTCTCTATTCCTCTTTCTACTCTGTTTCCTCCTTCTTTCTTTCTTTTCCTGCCTCCTTTCCCCTCTCCCTCCACTGTCTTGGGATATGTCTTACCCGCGCAGGAGTTCATCCGCTGCATCCAAGGGTAAACCGGGCTCGTGTACTTCCGGTCGGCGCCTTCGTCATGGAGTGCTTTGCCCTGCCCGCTGCTGCTGTCGGAATTCCACCCACGCACCTATTCCCCCTCCCAGCGCTTCAGACACCTCTCTCATCGAAAAACCGGGCGAAGGGAAGCCGGCAACGAGCGGAGAACTCTGGCTGAATTAACGGTGGCTCCCAGAAGCTCCTGCCCCTCTGACAGCTGTCGCTTGGGCAGCCCGAGAGAAGAATTGTCCTCTTTCCTGGTGCCAGAGGACGCAGGAAATTAGCCAGGTTGCGAGTTGCAAAGCTGCTGCCGCGGCGCCGGGAACGGAGCGCGCCCAATCTCCAGCGGGAGCCGCCAGGCCTGGCCTGGCCTGGCCGGGGCTTCCCTTCGCTCGCCATCTCCGGACAAAGCACAGCCGAGCCCGGCTGGAAGGCAGAGCTCCGAAGCAGGCAGGACGGAGTGGAGCAAAAGAATGCGGCTCTATTCTCGCAAGGGAAATTATAAAAAAGTTCATGTTCACGGTTCTCATCCACATGACCGACAGCGGCCAATGGAAGGGCCGAACAACTCATAAAGTTGTATTGCAAAGTTGTAAATTTTCATAAACAACAACGGATTTATGACCCTTTCCCCATCACTGAGAGGAGGCAGCTCTTACACCGGCGCCATCTTACCACCGAGGCCGCCCCGACTTGGGGCCTCAGGTTTTACAGACCCTTTTGGGCCAGGTTTTACTAAAAGAGCCATAAGAAGCGGGCCCAGCCCAGGCAGGAGACTGGAGACGAGGTCTTGCAGGCGGAACTCAGGATGCTCTGAGCTGCCCGCACAACCCCTGGACCTTCACCCCTCGCCCCTTCCCCGCATCCAGCTGCCCCAGCCCCTGCCCAGGCTGCGTAGCCTAGCGGGGGTCTGCGGTCCTAGCCCCTCCCCGCGCCACCTACTGCAGTGCCGGACCCTGGGGCCCCCTCGCCTGGTCTGCAGGCGGGGTGGGGACCTTAAATCCCATTTCCTAGCCTGGGGCTGGGTTCAGGGCGCATGCGAATCCGGAATCAGCTCTGGGTAATGCCCCTTTCCAAGCCCACTGCTCAGCCTTAGAGGAAAGTGTGGATTTGAAATTTCCTCATGGAATTGATGGAGGTTTTTAGGTAGATTCATAGAATATAACGTATCTACCAAAGATTCCGTTTTCAAGGGATCTAGAAGATGTTAGTGCACACGCAAAAACCAGACAAACGTCTCTACACGGATAAAGGCACATATACAATTATGCACACAGGGAAGGGCATACACTCTATTGTGGGCACAGAATGACATGCAATTATGGACACACAAAAACACATGCACCCAATTATGGACACCAAAATATATACAATTGTGGAATTAGGTAAAAACACACACACAGAAATACATACACAGAAAAATAAGCACATACTCATACAAATACACACATAAAAATACATTAAAAAGATACATGACACCAATACATGGGTACCCAACACTTGGACCATCACAAGGACAGCCACCCCACTTTTGCTTCCCCACTGCCCCCTGCCCTCCAGCCATACTCACCTCCCCTTTCCCAGTCCCCTCTGGATAAGGCAGTCCACATTTTTCTTTGTCACCACGCATCTTTATTTTCGGTTACATAAAACACAGCTGGGCTGGGAAGTGTGCCTTCCCTGAACCCCAGGATGGAGCTGAGCAGGGTACAGGACAACACAGGAGATGAAGGGCATTGCGGAGGGCATTGGACCTCCCCACCCACTACAGTTAACTCAAGACAACATACCATGCTACAAAGTCACCCCATTAACACATCCTTTCCAAGTCAAGACACTGCCTTACAAATGAACTCCAAGACTATAGAAATGATAAAAAAAAATCTTGTTCAAATATACAGTATCTGCTATTATAGGAAACATCAGGGCGTACATATTTAACACAGCTGAACAGTAAGATACAGGAGCCAGAGGAAAGGACAGCGAAGCTGGAAGCATCTCCACAGTCCTGCTAAGCAGAAGCTAACCCACAGATCTGCAGCCAGCTCAGGAACATTCCCCTCCAGAAGTGGGGGTTGATGGGCCTGAGCTGTGGGTGCCAAGCCAGAGAAGGAGGGATTGATTCTAGGGTGCAAGCACTTAGGATGCTTTTTGGAATAAATATATTATTTTTCGATTT</dnaseq>|
 
sequence = <dnaseq>TTCTCTTTTAAGAAGCCAAAGAAACTTTGCTGGTTCTTTCATCCTTTCTTTCTCTCTATTCCTCTTTCTACTCTGTTTCCTCCTTCTTTCTTTCTTTTCCTGCCTCCTTTCCCCTCTCCCTCCACTGTCTTGGGATATGTCTTACCCGCGCAGGAGTTCATCCGCTGCATCCAAGGGTAAACCGGGCTCGTGTACTTCCGGTCGGCGCCTTCGTCATGGAGTGCTTTGCCCTGCCCGCTGCTGCTGTCGGAATTCCACCCACGCACCTATTCCCCCTCCCAGCGCTTCAGACACCTCTCTCATCGAAAAACCGGGCGAAGGGAAGCCGGCAACGAGCGGAGAACTCTGGCTGAATTAACGGTGGCTCCCAGAAGCTCCTGCCCCTCTGACAGCTGTCGCTTGGGCAGCCCGAGAGAAGAATTGTCCTCTTTCCTGGTGCCAGAGGACGCAGGAAATTAGCCAGGTTGCGAGTTGCAAAGCTGCTGCCGCGGCGCCGGGAACGGAGCGCGCCCAATCTCCAGCGGGAGCCGCCAGGCCTGGCCTGGCCTGGCCGGGGCTTCCCTTCGCTCGCCATCTCCGGACAAAGCACAGCCGAGCCCGGCTGGAAGGCAGAGCTCCGAAGCAGGCAGGACGGAGTGGAGCAAAAGAATGCGGCTCTATTCTCGCAAGGGAAATTATAAAAAAGTTCATGTTCACGGTTCTCATCCACATGACCGACAGCGGCCAATGGAAGGGCCGAACAACTCATAAAGTTGTATTGCAAAGTTGTAAATTTTCATAAACAACAACGGATTTATGACCCTTTCCCCATCACTGAGAGGAGGCAGCTCTTACACCGGCGCCATCTTACCACCGAGGCCGCCCCGACTTGGGGCCTCAGGTTTTACAGACCCTTTTGGGCCAGGTTTTACTAAAAGAGCCATAAGAAGCGGGCCCAGCCCAGGCAGGAGACTGGAGACGAGGTCTTGCAGGCGGAACTCAGGATGCTCTGAGCTGCCCGCACAACCCCTGGACCTTCACCCCTCGCCCCTTCCCCGCATCCAGCTGCCCCAGCCCCTGCCCAGGCTGCGTAGCCTAGCGGGGGTCTGCGGTCCTAGCCCCTCCCCGCGCCACCTACTGCAGTGCCGGACCCTGGGGCCCCCTCGCCTGGTCTGCAGGCGGGGTGGGGACCTTAAATCCCATTTCCTAGCCTGGGGCTGGGTTCAGGGCGCATGCGAATCCGGAATCAGCTCTGGGTAATGCCCCTTTCCAAGCCCACTGCTCAGCCTTAGAGGAAAGTGTGGATTTGAAATTTCCTCATGGAATTGATGGAGGTTTTTAGGTAGATTCATAGAATATAACGTATCTACCAAAGATTCCGTTTTCAAGGGATCTAGAAGATGTTAGTGCACACGCAAAAACCAGACAAACGTCTCTACACGGATAAAGGCACATATACAATTATGCACACAGGGAAGGGCATACACTCTATTGTGGGCACAGAATGACATGCAATTATGGACACACAAAAACACATGCACCCAATTATGGACACCAAAATATATACAATTGTGGAATTAGGTAAAAACACACACACAGAAATACATACACAGAAAAATAAGCACATACTCATACAAATACACACATAAAAATACATTAAAAAGATACATGACACCAATACATGGGTACCCAACACTTGGACCATCACAAGGACAGCCACCCCACTTTTGCTTCCCCACTGCCCCCTGCCCTCCAGCCATACTCACCTCCCCTTTCCCAGTCCCCTCTGGATAAGGCAGTCCACATTTTTCTTTGTCACCACGCATCTTTATTTTCGGTTACATAAAACACAGCTGGGCTGGGAAGTGTGCCTTCCCTGAACCCCAGGATGGAGCTGAGCAGGGTACAGGACAACACAGGAGATGAAGGGCATTGCGGAGGGCATTGGACCTCCCCACCCACTACAGTTAACTCAAGACAACATACCATGCTACAAAGTCACCCCATTAACACATCCTTTCCAAGTCAAGACACTGCCTTACAAATGAACTCCAAGACTATAGAAATGATAAAAAAAAATCTTGTTCAAATATACAGTATCTGCTATTATAGGAAACATCAGGGCGTACATATTTAACACAGCTGAACAGTAAGATACAGGAGCCAGAGGAAAGGACAGCGAAGCTGGAAGCATCTCCACAGTCCTGCTAAGCAGAAGCTAACCCACAGATCTGCAGCCAGCTCAGGAACATTCCCCTCCAGAAGTGGGGGTTGATGGGCCTGAGCTGTGGGTGCCAAGCCAGAGAAGGAGGGATTGATTCTAGGGTGCAAGCACTTAGGATGCTTTTTGGAATAAATATATTATTTTTCGATTT</dnaseq>|
 
}}
 
}}
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[[Category:Intergenic]]
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[[Category:Intergenic]][[Category:Transcripts]]
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{{lncrnadb|
 
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tID = lnc-EVX1-9:1|
 
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ltID = HOXA6as|
 
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ann = <tab class=wikitable sep=tab head=top>
 
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Section Description
 
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ID HOXA6as
 
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Characteristics Multiple spliced transcripts between HoxA6 and HOXA7 on the antisense strand, share some splice junctions but have different 5' and 3' ends ([http://www.ncbi.nlm.nih.gov/pubmed/17185360 Sessa (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/17445766 Sasaki (2007)]). Some HOX6as transcripts overlap to one or both HOX protein coding genes ([http://www.ncbi.nlm.nih.gov/pubmed/17185360 Sessa (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/17445766 Sasaki (2007)]).
 
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Expression Expressed in adult lung, kidney, testis, placenta, colon, muscle. Fetal ovary and kidney, similar to HOXA6 and HOXA7 ([http://www.ncbi.nlm.nih.gov/pubmed/17185360 Sessa (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/17445766 Sasaki (2007)]). Expression can be induced by retinoic acid [http://www.ncbi.nlm.nih.gov/pubmed/17185360 (Sessa (2007)]). Shows collinear regulation of expression like HOX PTC genes ([http://www.ncbi.nlm.nih.gov/pubmed/17185360 Sessa (2007)], [http://www.ncbi.nlm.nih.gov/pubmed/17445766 Sasaki (2007)]).
 
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Conservation HOXA6as transcripts contain sequences conserved in mammals and even sequences ultra conserved in vertebrates. Similar mouse transcripts are not known, however, transcripts which run antisense to both HOXA5 and HOXA6, that share an splice junction with HOXA6as and transcribe through the vertebrate conserved element, are present in both species.
 
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Misc Example accessions: AK091933, AK092154.
 
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</tab>|
 
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}}
 

Latest revision as of 13:46, 24 June 2016

Please input one-sentence summary here.

Annotated Information

Name

HOXA-AS3: "HOXA cluster antisense RNA 3 (non-protein coding)"

HOXA6as

Characteristics

HOXA6as located between HOXA6-A7, whose tissue-specific expression patterns that in some cases resemble the expression profile of sense transcripts.[1]

Function

HOXA6as may be a regarded as universal reference being applicable for the accurate normalisation of lncRNA expression profiling in various glioma (WHO-Grades II-IV) alone and in combination with brain tissue.[2]

Expression

Stably expressed lncRNAs suitable for studies comparing different glioma entities.[2]

HOXA6as, which showed stable expression in all investigated brain regions, may be regarded as an universal normaliser suitable for a broad range of lncRNA studies [2].

HOXA6as, like many cases OS-intergenic transcripts, is coexpressed with adjacent coding HOX genes [1].


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

  • Dulbecco Telethon Institute, Naples, Italy. [1]
  • Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University. [2]

References

  1. ↑ 1.0 1.1 1.2 Sessa L, Breiling A, Lavorgna G, Silvestri L, Casari G, Orlando V. Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster[J]. Rna. 2007,13(2):223-39.
  2. ↑ 2.0 2.1 2.2 2.3 Kraus TF, Greiner A, Guibourt V, Lisec K, Kretzschmar HA. Identification of Stably Expressed lncRNAs as Valid Endogenous Controls for Profiling of Human Glioma[J]. Journal of Cancer. 2015,6(2):111-9.

Basic Information

Transcript ID

lnc-EVX1-9:1

Source

LNCipedia2.1

Same with

,

Classification

intergenic

Length

2354 nt

Genomic location

chr7+:27186781..27193904

Exon number

,

Exons

,

Genome context

Sequence
000001 TTCTCTTTTA AGAAGCCAAA GAAACTTTGC TGGTTCTTTC ATCCTTTCTT TCTCTCTATT CCTCTTTCTA CTCTGTTTCC 000080
000081 TCCTTCTTTC TTTCTTTTCC TGCCTCCTTT CCCCTCTCCC TCCACTGTCT TGGGATATGT CTTACCCGCG CAGGAGTTCA 000160
000161 TCCGCTGCAT CCAAGGGTAA ACCGGGCTCG TGTACTTCCG GTCGGCGCCT TCGTCATGGA GTGCTTTGCC CTGCCCGCTG 000240
000241 CTGCTGTCGG AATTCCACCC ACGCACCTAT TCCCCCTCCC AGCGCTTCAG ACACCTCTCT CATCGAAAAA CCGGGCGAAG 000320
000321 GGAAGCCGGC AACGAGCGGA GAACTCTGGC TGAATTAACG GTGGCTCCCA GAAGCTCCTG CCCCTCTGAC AGCTGTCGCT 000400
000401 TGGGCAGCCC GAGAGAAGAA TTGTCCTCTT TCCTGGTGCC AGAGGACGCA GGAAATTAGC CAGGTTGCGA GTTGCAAAGC 000480
000481 TGCTGCCGCG GCGCCGGGAA CGGAGCGCGC CCAATCTCCA GCGGGAGCCG CCAGGCCTGG CCTGGCCTGG CCGGGGCTTC 000560
000561 CCTTCGCTCG CCATCTCCGG ACAAAGCACA GCCGAGCCCG GCTGGAAGGC AGAGCTCCGA AGCAGGCAGG ACGGAGTGGA 000640
000641 GCAAAAGAAT GCGGCTCTAT TCTCGCAAGG GAAATTATAA AAAAGTTCAT GTTCACGGTT CTCATCCACA TGACCGACAG 000720
000721 CGGCCAATGG AAGGGCCGAA CAACTCATAA AGTTGTATTG CAAAGTTGTA AATTTTCATA AACAACAACG GATTTATGAC 000800
000801 CCTTTCCCCA TCACTGAGAG GAGGCAGCTC TTACACCGGC GCCATCTTAC CACCGAGGCC GCCCCGACTT GGGGCCTCAG 000880
000881 GTTTTACAGA CCCTTTTGGG CCAGGTTTTA CTAAAAGAGC CATAAGAAGC GGGCCCAGCC CAGGCAGGAG ACTGGAGACG 000960
000961 AGGTCTTGCA GGCGGAACTC AGGATGCTCT GAGCTGCCCG CACAACCCCT GGACCTTCAC CCCTCGCCCC TTCCCCGCAT 001040
001041 CCAGCTGCCC CAGCCCCTGC CCAGGCTGCG TAGCCTAGCG GGGGTCTGCG GTCCTAGCCC CTCCCCGCGC CACCTACTGC 001120
001121 AGTGCCGGAC CCTGGGGCCC CCTCGCCTGG TCTGCAGGCG GGGTGGGGAC CTTAAATCCC ATTTCCTAGC CTGGGGCTGG 001200
001201 GTTCAGGGCG CATGCGAATC CGGAATCAGC TCTGGGTAAT GCCCCTTTCC AAGCCCACTG CTCAGCCTTA GAGGAAAGTG 001280
001281 TGGATTTGAA ATTTCCTCAT GGAATTGATG GAGGTTTTTA GGTAGATTCA TAGAATATAA CGTATCTACC AAAGATTCCG 001360
001361 TTTTCAAGGG ATCTAGAAGA TGTTAGTGCA CACGCAAAAA CCAGACAAAC GTCTCTACAC GGATAAAGGC ACATATACAA 001440
001441 TTATGCACAC AGGGAAGGGC ATACACTCTA TTGTGGGCAC AGAATGACAT GCAATTATGG ACACACAAAA ACACATGCAC 001520
001521 CCAATTATGG ACACCAAAAT ATATACAATT GTGGAATTAG GTAAAAACAC ACACACAGAA ATACATACAC AGAAAAATAA 001600
001601 GCACATACTC ATACAAATAC ACACATAAAA ATACATTAAA AAGATACATG ACACCAATAC ATGGGTACCC AACACTTGGA 001680
001681 CCATCACAAG GACAGCCACC CCACTTTTGC TTCCCCACTG CCCCCTGCCC TCCAGCCATA CTCACCTCCC CTTTCCCAGT 001760
001761 CCCCTCTGGA TAAGGCAGTC CACATTTTTC TTTGTCACCA CGCATCTTTA TTTTCGGTTA CATAAAACAC AGCTGGGCTG 001840
001841 GGAAGTGTGC CTTCCCTGAA CCCCAGGATG GAGCTGAGCA GGGTACAGGA CAACACAGGA GATGAAGGGC ATTGCGGAGG 001920
001921 GCATTGGACC TCCCCACCCA CTACAGTTAA CTCAAGACAA CATACCATGC TACAAAGTCA CCCCATTAAC ACATCCTTTC 002000
002001 CAAGTCAAGA CACTGCCTTA CAAATGAACT CCAAGACTAT AGAAATGATA AAAAAAAATC TTGTTCAAAT ATACAGTATC 002080
002081 TGCTATTATA GGAAACATCA GGGCGTACAT ATTTAACACA GCTGAACAGT AAGATACAGG AGCCAGAGGA AAGGACAGCG 002160
002161 AAGCTGGAAG CATCTCCACA GTCCTGCTAA GCAGAAGCTA ACCCACAGAT CTGCAGCCAG CTCAGGAACA TTCCCCTCCA 002240
002241 GAAGTGGGGG TTGATGGGCC TGAGCTGTGG GTGCCAAGCC AGAGAAGGAG GGATTGATTC TAGGGTGCAA GCACTTAGGA 002320
002321 TGCTTTTTGG AATAAATATA TTATTTTTCG ATTT
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