Lnc-DLX5-3:1

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Annotated Information

Name

Evf2

Characteristics

~3.8 kb. Antisense to Dlx6 genes in the Dlx5/6 cluster. Evf1 and 2 are isoforms with alternative promoters expressed from ultraconserved enhancers. Different Evf-1 and Evf-2 transcripts result from alternative transcription initiation, alternative splicing of exon 3, and alternative polyadenylation. Therefore, Evf-1 and Evf-2 cDNA sequences have unique 5' and 3' ends, and share a 2561bp region of identity (Feng (2006), Kohtz (2004)).

A large (7.5-kb) non-polyadenylated form recognized by both Evf-1 and Evf-2 Northern blot probes is present in the total RNA fraction and absent from the poly(A) containing fraction. The Evf-2-specific probe also identifies a smaller (500-bp) transcript (Feng (2006)).

Function

Evf-2 ncRNA and Dlx-2 proten display an intranuclear colocalization (Feng (2006)). The ultraconserved region* of Evf-2 binds and co-operates with Dlx-2 in vivo to increase the transcriptional activity of the Dlx-5/6 enhancer in a target and homeodomain-specific manner (Feng (2006)). *The Evf-2 5' region is both necessary and sufficient for activity. Evf2 recruitment of DLX2 and MECP2 controls the expression of targets Dlx5, Dlx6 and Gad1 through trans and cis-acting mechanisms in developing ventral forebrain. Evf2 function is also required for proper gene regulation and formation of hippocampal GABA-dependent neuronal circuitry in mouse adult brain (Bond (2009)).

Expression

Nuclear localisation (Feng (2006), Sone (2007)).

Similar expression pattern to Dlx6 and Dlx5 mRNAs. Developmentally regulated, expressed in the ventral forebrain. Detected in immature neurons as they exit the ventricular zone (Feng (2006)).

Ectopic expression of Sonic hedgehog (Shh) induces the expression of Evf-2, Evf-1, Dlx-2, Dlx-5, and Dlx-6 in the dorsal telencephalon in vivo (mouse embryos) (Feng (2006)).

Up-regulated in vitro during differentiation of neuronal progenitors to GABAergic neurons and during mouse embryonic stem cells differentiation (Dinger (2008)) (Mercer (2010)). Also found co-expressed in the first and second branchial arches of E10.5 mouse embryos (Jeong (2008)).

Brain expression of Evf2 and Evf1 is dependent on Dlx1/2 function. Expression of Evf2 and Evf1 is also greatly reduced in Dlx5/6, and Dlx5 or Dlx6, knock-out mutants, indicating that they may be their direct or indirect regulatory targets (Kohtz (2004), Jeong (2008)). Evf1 and Evf2 were more down-regulated in Dlx5-/- than in Dlx6-/- mutants (Jeong (2008)).

Conservation

Evf-2 is transcribed from (and contains in its first exon) a vertebrate ultraconserved element. Analysis of transcripts by isolation from a cDNA library (rat), RT®CPCR (zebrafish and chicken), or expressed sequence tag (EST) databases (human and mouse) showed that transcription of the ultraconserved element associated with Evf-2 (enhancer ei) is conserved in vertebrates (Feng (2006)). Evf-1 and Evf-2 exhibit a high degree (86%®C93%) of conservation between rat and mouse sequences in their 5' and 3' regions, and a compilation of transcripts found in human, rat, mouse, zebrafish, and chicken shows that only transcription from exon 2 is conserved (Feng (2006)).

Misc

Evf-2 is proposed to belong to a class of transcription regulating, ultraconserved ncRNAs (trucRNAs), and may be part of a broader Dlx gene/antisense RNA regulatory network (Feng (2006), Dinger (2008)).

Transcriptomic Nomeclature

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Regulation

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Allelic Information and Variation

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Evolution

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References

Annotation originally sourced from lncRNAdb.

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Basic Information

Transcript ID	lnc-DLX5-3:1
Source	LNCipedia2.1
Same with	,
Classification	intergenic
Length	4978 nt
Genomic location	chr7-:96594837..96643377
Exon number	,
Exons	,
Genome context
Sequence	000001 ATTTCACACC TGGATGTGCT CACTCAACCA AGAATATAGA GAAAGAGCTT CTGCCCTGAG ACTCAGAAAA ATATTCTCCT 000080 000081 GTGCTTTGGT TCAGTATAGA TTTCTAAACC CTGATCATTG CTTAAGAGAT ATTCACTGAG GACAGAGTCT TGCTCTATTG 000160 000161 CCCAGGCTGC AACTGGTGTG ATCTCGGCTC ACTACAACCT CTGCCTCCTG GGTTCAAGCG ATTCTCCTGC CTCAAGCTCC 000240 000241 CAAGTAGCTG GGATTACAAG CATGCACCAC CATGCCTGGC TAATTTTTGT ATTTTTAGTG GAGACGGGGT TTCGCCACAT 000320 000321 TGGCCAGGGT GGTCTTGAAC TCCTGACCTC AAGTGATCCA CCTGCCTTGG CCTCCCAAAG TGCTGGGATT ATAAGCATGA 000400 000401 GCCACTGCAC CCAGCCTTAT ACTGAACTTT CAATGGGTTC AATTCCACTA GGAGCATAAA GGCCACTGCA TATGAGTTGT 000480 000481 GGAAAGAAGA GATTAGAAGA AGGAAGAACT TGAGATGAGT TCCTCCCTTC AACATTCTGT CTCCTCCTAC CTAGCATCTT 000560 000561 CTTTCTTTTA GTCTTTCTAG AATGTCCATC TGTTTTTGGC CATTGCGGAG AGAGAAGCTG AGCTTTAAAG GAGTAGGAGC 000640 000641 TTCAAAGGCG TAGGAGCTTC AAAATTCTTG TTTCTTCATG TTTGATCACC CTTCTAAACC TGTCTTCTGT TCCTTCTGCT 000720 000721 ATTCTTTTTT CTTAGAGCAT AGGAAAGGGG AGCTTTTAAA TTAATACTTA AAGCATGGAA AAAAAGAACT TGAGAAGAAA 000800 000801 GTAAAACAAG GGAGATGAGG CTAGTAAAGT AAGGAAAATG AAGAGGAAGA GGAGGAAGGG TTAGCTTCTA AATTCCAAGT 000880 000881 CAAATTGATA TGGAACAGGC AAGCCGCTTG TCTTACTTAA ACTTCAGAAA AGGATCTGCT GAAACTTGAT AGAAATGGAA 000960 000961 AGGGAAATCC TTGGGGTGGG GAACCTCCAA ACATTAGTAA TGATATTGAA CAACTCAAAG TATTGAGGAA ATCTGCAGGC 001040 001041 TACATGCCTG AAGATTACCC ATGCAGATAG ACCAAAAGGA TTAGAATTAT CTGTTGATAT TAGTAATATT TATTGACATC 001120 001121 TAGCTAGTAT TGGTAATTTT AAGTTTTAGA TTAATTTCTT TGGTAATAGC TATGATATAT TTTATAGACA AGAATTATAT 001200 001201 CTATAGGCTT GCTATCATAG GCTCTTTTAA TCAGCATTAA TTTAGTCTAC TGATTTTTAG CACATTTGAA TCATTCACTT 001280 001281 ATGCTAGGTA ACTCATTGCA AAATAAAAAG ATGATTCCTG TATGTATGGC AGCTATACAT TAAGGAGGAG TCTACCAGAA 001360 001361 TATGAAAAAG TCAGCTGACC TAAATATTGC TGAGACAAAG GAAAACCCAC TCCCTTGGAG GAGCATGACC TTTTCCTGTA 001440 001441 ATTCTTCCCA CTGCTGTTGT TGAGCTCCTT GGATCCTGGC TCCTGGACAC CATCATCAAG AAGACTTTAT GGATGGGCTG 001520 001521 TCCACCCACT GAGAGAAGAG GAGCATCAGC TACAGTTTCT CTCTAGATTG CCTTCTTCAT TTTGAGTAAT GACTGTCAGC 001600 001601 AGGGTCAGAT TAAACACAAA ACAACTGGAC AATTGCTTGG AGGACTAAAC TATAAGGGCA CTAACATGTC AATAGTAGGC 001680 001681 TAACACATCC ATGGAAAATA TATTTACCAG CTCTTCTCTC AGGGAGGATT CTGTGTGGGG TTGGAAGTAA TGATTTGTTA 001760 001761 AATTCCTTAG GGGTAGAAAG TAGGGCATAA TCAGAATATA GAGGAATATG CTGTTTGACT TCAGGGTTTC TGTTTTTCTT 001840 001841 ACTAGGATAT ATAAAACAGG GACTCTAGCT AGATTGTTTA TGACCACAGA GGGTAGGCTG AGTGCTCCCA TGATCTTCCT 001920 001921 GCTTGGTTCT TGCCCATACA GAGGTCAGCC TTTCCTCTAA TAAAGATTGA ACAAGTAGTG GTCTGAGGGA GACACCAATT 002000 002001 CATTACCCTA CATGTCTCTT CTCTGCACTC CAGGGCTTTG ATAATAAAGA CACTGGCAGA CTATCTATCT TCCATTTCTA 002080 002081 TAATGTGAGC CCTTAGGGAG TCTTCGTTCA CTTGGGGGTG AGGGTCATTG CTCACAGAGT AGTTCAAGTC AAATGGAACT 002160 002161 TGAACTCTTT GCCTATGGGC CTGGTGGTCA GACTCTGTGT TGAGTTCATT AGATTATTGG AGACACAAGG TAGAGCTGGA 002240 002241 TGCTTCAAAA ATATTTGGCT AAAGGATGAC ATTGCTGGTT ATTTGTAGAT AAAGCCATGA TGGAACCTGC TTGGAATCAT 002320 002321 GAAATATGGA ACTGGTGGTC ATGTTTAAAA ATACAACTAA TAGTTAAGTA CCTACTGGAC ACTGTAGAGA CTTAGGGGCT 002400 002401 AGACAGACAT GGTTCCTGCC CCCTTGGAGC TTACACTGTA GCTTCCCCTT AGGTATGAAG AACAGTGGCT ACAACTAACA 002480 002481 AATGGCCACA AAGATATAAT TGAGCCAGTG TTCCAATTAT TAGGGTAATT CCTATTTCCT TAATCATTCC TATTGACCAT 002560 002561 GTTCTATAAG CCTGCATTCT ATAAATGGCG TATGACCATG GGCTGTTTCC CCCCAGCAAG TTGTACAAAG TTCTGTGGTA 002640 002641 CCAGGGAAAG GGCTTAAGGT TAGCAGGGCC TCTGCGGAAG GACATATGAA GTGACTTGGG TTAGGAAACA GGAAGGGATA 002720 002721 GGATTCAAGA ACAGCTATTG CTTCTGTTCT ATATAGGAAA CTGCAGCGTG AAAAATGCTG GGCTGGGAAT TTTGAGACCT 002800 002801 GGGTTTTAGT TTGTGTTCTA ATACTAACAA GCTATGTGAC TGTGGGTAAG TCATTTCACA TTCCATTTGG ATGCCTCTTG 002880 002881 AGTGACTCCA GGCCTCTCCA GCTCTAAAAC ATTAAGATCA GGCCCTACGC TACAGCTGGC CAGTGTGTAA TTCTTCTGTT 002960 002961 TCTATGCTGT TAGGTCAAAT AGATCTTCAA TAGTTACTTG ATTGTTATTA CTTTTTTCTG AAGTGGGTGT TTTATCAATG 003040 003041 TTTTAGGATA CAGTGAGTCT GCTTCTCCCC TTTGGAGTTA GGAAGGTTGT AGGAATATAC ACTGTAGAGC ATATGGGAGC 003120 003121 TTTATCCCCT CCTTTTTTCC CCGCTACCTT TCTCCCTCTC CTTCCCTTCA TCACATTTCT ATTGAGCATA TGCCATTGCC 003200 003201 GTGTACCAGG TGTGTGCTAG GTTTGGAGAT ACAAGGTAAA CCTGAGACTT TCCCAGTCTC CAGGAGACAA AACCCTAATT 003280 003281 TCTTTCATCT GCTGTCTTTC TCTTTGGAAA GAATCAACGA TATCCCAGGG GAATGTGCCC ATGTCCCAGG GTAACCAACT 003360 003361 ACAGACAGAT GCCCCATTCT ACTCAAGCAA CTTTTAGAGT GCCTTGAGAT ACACATCAGA TAATTATGCA GGGCCAGGCA 003440 003441 TGGTGCTGCA CACTTGTAAT CACAGCACTT TGGGAGGCCG AGGCAGCAGA TTGCTTGAGC CCAGGAATTC AAGTGTAGCC 003520 003521 TAGGGAACAT GGCAAAACCC CAGCTCTACA AAAAAATACA CAAATTAGCT GCGTGTGGTG GCCTATGACA GGAGGCTGAG 003600 003601 ATGGGAGGAT TGCTTGAGCC TGTGAGGTCG AGGCTGCAGT GAGCCGAGAT CATGCCATTA CTCCAGCCTG GGTGACATAG 003680 003681 GGAGACCCTG TCTTGAAAAA AAAAAAAAAA AGATAATTAT TCAGCCCTAG AGTCATTGTG AAAAGATCTA TCTTCAGATA 003760 003761 TAAGGAAGAA ACAATCTTTT ATTTCTTAGG ATAAATCTGT AGAAGGACCT CCAGACAGTG AAGGCCACTG ACTACTTTAT 003840 003841 ACTCTGTAAG CCATCCCTCC CTGGTAGGAA GGACTATTTC CAATCTTACA GAGTACCTCT CAGCAAATAG ACGTTTTCAC 003920 003921 ATATACTGTG ATTCATACAT CCCTATGGCT GGTGACCTCT TTAAAAAGGA A