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 AAGGAAAAAG CCTAATCAAA CAAAAAGATG 004000
004001 CTGCTAGTAA TTCTTACCCT ATTGTGAATC CTATATAAGC AAATTTGTAT CTTTGTTTTT TCCTACATTA GCAGATCTAT 004080
004081 TTGATGTATA TCTCTGAGTG CAGAAAATAT TTTATGGAAA AATCAATATA TGGAATTTCA AATTCAGAAT TGCTGATACA 004160
004161 CACTATTTGG TTTCACAATT TTATCCTAGG AAATAGTATT AGAGATTTCA ATTTCTGGCT TAAATGGTAG AATTAATTAC 004240
004241 TCTTAACTCT TAATTTTACT TCTGAGTTGA GGTCAAGGAA CAGGCAGACA CCTGCAGTTA ACGTCTATAC CTCTCCATGG 004320
004321 CCAAGAGTTT TAATTTTCTC GTCTTCAATT TTGTAGATGT TCATCATTAC TAAATGGATT GATTAGTATT TTATCTCCTC 004400
004401 TCCTTGTCCT TACTTTCCCT CTGGTAAATA TGTTATAAAC AGTGTAAGGC TCCTAAGATA GAGTAGCTGG TAGGACTTAG 004480
004481 AAGAGAAACA AAGGGCACTG ATAACTCACA TAAATGGAAA ATTGGCTCTG GAATAACTGA CAACATATTC AAGTATTTTA 004560
004561 GTGCAGTGTC ACTCTCATTA AGAAGAAGAG AATCAGTAAA TCTATGTGAC TCTAAACATT CTAATGAAAA AAGGAATATT 004640
004641 CTGCCAATTA TCTCACATTT CTAAATATCT GGATATTGGC CATTGTAAAG ACAAAACATA CAGATGATGG ACTTGTCTTT 004720
004721 CCACCTCTCA TTTGCATGGT TTGGAGCATT GTACCTCCAG CCATAGACTC TAAGGCAATT TATATTTGCT TCCTCTTCCC 004800
004801 TCTTGAGAGA AAACGAAAAT CTTATTTTTC CAAGCAATTA AAACTCTTCT GCTTCAGCTA GGATGAAAGA ATTAGGAGTT 004880
004881 CTGTCTCCTT GTATCTAATT GCATGTTTCA TCTTTCTTGT TTTAATGATT GACAGAAAAC TAATAAACTG AGACATCTTT 004960
004961 GAATCCAGGT TGAATGTA
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Internal error

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[XfIkZZBlNTeOZ1LI0sTERwAAAAA] 2019-12-12 11:28:41: Fatal exception of type "TypeError"

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