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

Revision as of 13:42, 24 June 2016

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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

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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

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Allelic Information and Variation

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Evolution

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Labs working on this lncRNA

Center for Neuropathology and Prion Research (ZNP), Ludwig-Maximilians-University. ^[2]

References

↑ ^1.0 ^1.1 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.
↑ ^2.0 ^2.1 ^2.2 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 GATGAAGGG

[ref2-1] 1.0 ^1.1 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.

[ref1-2] 2.0 ^2.1 ^2.2 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.

[1]

[2]

@@ Line 19: / Line 19: @@
 HOXA6as, like many cases OS-intergenic transcripts, is coexpressed with adjacent coding HOX genes <ref name="ref2" />.
-===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.