Lnc-PDZD8-3:1

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Annotated Information

Name

Emx2os: Emx2 opposite strand transcript.

Characteristics

5 kb. Spliced, bi-directional to Emx2, with a 271 nucleotide head-to-head antisense overlap. Riboprobe Northern blot indicates the existence of three additional Emx2os splicing isoforms differentially detected in the murine urogenital system, with sizes of 6.0, 2,3 and 1,8 kb, which are supported by cDNA evidence (Noonan (2003)).

Function

EMX2OS is suggested to regulate EMX2 expression (Noonan (2003)), which may involve distinct regulatory mechanisms in different cell types (Spigoni (2010)). In vitro knock-down experiments indicate that Emx2os contributes to post-transcriptional down-regulation of its sense partner in cortical precursors and their neuronal progenies, possibly by a Dicer1-dependent process (Spigoni (2010)). However, ectopic expression of a 5' fragment (OS1-179+) of Emx2os in neural precursors of the rhombo-spinal tract stimulates expression of Emx2, indicating a complex regulatory mechanism, perhaps at transcriptional level. In addition, Emx2 knock-out results in a strong reduction of Emx2os transcript levels, indicating a possible reciprocal regulatory loop (Spigoni (2010)).

Expression

EMX2 and EMX2OS and their murine orthologs have similar profiles and extensively coincident cellular expression patterns in the endometrium. Expressed in the uterus, abundant in normal postmenopausal endometrium, reduced in premenopausal endometrium (Noonan (2003)). Emx2os is expressed in the developing mouse CNS. Examination of expression at E10.5, E12.5, E14.5 and E18.5 showed, similar to Emx2, that its levels reduce progressively from E10.5 to E18.5. At E12.5, it is detected in a number of CNS structures also expressing Emx2 mRNA, such as the pallium and basal ganglia, mammillary recess of the hypothalamus, optic tectum, olfactory placode and otic vesicle. Emx2os is found in the developing telencephalon in periventricular proliferative layers and the cortical plate (Spigoni (2010)). However, the sense/antisense pair may also show mutually exclusive patterns, such as within the cortex. Emx2os is detected in periventricular precursors that also express Emx2, but peaks in newly born post-mitotic neurons, which do not express Emx2, whereas Emx2 is expressed Cajal-Retzius neurons lying in the marginal zone, which do not express the antisense RNA (Spigoni (2010)). In human brain, expression has been detected in normal nucleus accumbens (Michelhaugh (2010)).

Conservation

Association of Emx2os and Emx2 is conserved between mouse and humans, but no sequence conservation was found (Noonan (2003)).

Misc

EMX2OS lies in the minimal interval with allelic loss in endometrial tumors and is a candidate endometrial cancer tumor suppressor (Noonan (2003)).

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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References

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Basic Information

Transcript ID

lnc-PDZD8-3:1

Source

LNCipedia2.1

Same with

NONHSAT016525

Classification

intergenic

Length

7282 nt

Genomic location

chr10-:119243804..119304579

Exon number

4

Exons

119243804..119250422,119251532..119251620,119303817..119303887,119304077..119304579

Genome context

Sequence
000001 GTGCTTGGCT ACAGCCGCTG CTGCCTCTCG CGAACTGGGC TCCGGGGCTC CCGGCTCCCG AGAACTAGAA GAGAAACGCG 000080
000081 AGCGAAGGGA TCGAAACCCG GGGGGTTACC GACTTGCAGA CACCGCCAGG ACAGTCTGTA ACGCAGGAAG ATCCCAGCGG 000160
000161 CTCCGGGTCT GGTGAGGGGA CCATAAGCAT GACTGATAGC GAATGAGGAA GGGCAGCCCT AAACTTTTCA AGCAAAGCCT 000240
000241 CAGAGTTTTG GGTTCACTCA TTAGCATAGG AAATCGATTC ACCGAAAACC CAAACAAAGA AAAACAAGCC GACAGTCCAG 000320
000321 GCAGGATGCA GGCAAATCCA GTTCGGGATT AAGGGTAAAA GGCTTTTTGG GTTTTTTTTC CTTTGGTTTG ATTTTTTAAA 000400
000401 ATATGGGGAG GGGGGTGACA TCTACCCGAT TCTAGGCTCC GGCAGGAACG CAATGGGTTA ATGAATGGAC AAGCCGCGGA 000480
000481 GTATTGATCG GCTGCCGCCG GAGAAAGAAA GAAAAACAAA AACCAGACCG AACCTGCCTT CCCGCTGTGG CTGCTCGGCG 000560
000561 CCCCAATTAA GCAGGGTCAT CTCAGGCTGG CTGCATGCCT CAGCTGAAGA TCCCAGCTCC TGTCAATGCC ACCTCTCTGC 000640
000641 TTGACTGTCT CCTTCCAGAT TCGAGCAGGT ATGAGCTGGG AAGAATGAAG GCAGGGCATG CCCGTGTGCC AGCTCTGCAC 000720
000721 AGCTGGATAG CTGAGGAAAG ATGTGGAGGA GAAGCCGGGG ATTGTGTGGA AGTCTAAGGG TGTTGTTTGC CCTTTGGGTT 000800
000801 CCAGAAGATG CATGCCAGGA CCCTGGGTGG CACTGCCAGG AAGCAACAGA GAGGAGATAA AACTCACAGC AGACAGACTT 000880
000881 GCCTTAACAA CAACTCCCTT GAATTAAAAC ACGCTTTTCA AGAAAACAAA TTATCAGTTC GATCAGCAAA CAGCAGAGAA 000960
000961 GTTTCTCTCA TAATGGCAAA GAAGGGCCGG GTTGCTGACC AGTGAAAGAG CTTCAGAAAA GGAGAGGGGA GATGAGATGG 001040
001041 CCAGAAGGAG CAAGAGCACC GTACATCCCT GGACAACCTC ATTCTAATGG GTCAGGGGCT GGGACGTGCA TTTTGGAGTG 001120
001121 CAGGAGAAGT GGCAACTCAC AAATGCTAGA TTTTCTTCTA GAGATGACCA AGCTGTAGTT CTTAAAGCAG TGGCACTAGG 001200
001201 GCAGAAAACT CTCACACTTT GATGTGCACA CACAGCCCCT GGGGATCTTG TTGACATGTA GATTCTGATT CCGTAAGTCG 001280
001281 GGCTGAGATT CTGCATTTCC AACAAGCTCC TAGATGAGGT CCATTTTGCT GGTCCATGAA ACACACTTAG AATAAGTAGC 001360
001361 AAGGTATAGG AGGATACTGA CTTTGCTCAG TGATGCTTGG GCTTCCGTCC AAACTAAAAT AAAACAAAAG CAGACATAAA 001440
001441 TGGCCCAATT CAACAGCCTG AGAAGTTTGG TGATAATGAC CCAAGCCCTG GCCTGGTGAC CAAGTGGCTG CTCAGAGAGC 001520
001521 TCTATCTCCA AACTCCTTCC CTTCCTGCCT CCCCTCCAAG AGTGAGTAAT GTGCCAGAGT TCATTGGGGT CTGCTGTCCC 001600
001601 CAGGGAAAGG TGGCCCAGTT GCCAAGTGCA AGTGTATAGA ACGGCTTACC TGTGCAAAGC TATCAGCCCT GGACCTATGG 001680
001681 GCCTAGAAAC ATTACTTGCC ACTCACTCAC TCACTATCAT TCATTCATTT CTGCAACAAA CACTTCCTGA GCATATGCTA 001760
001761 TACACCAGGC CCTGAGCTCA GCTCTGGGGA TACAGGATGA ATGGCAGATT GTGCCATCAG GAAGCCGACT GCACAGTCAG 001840
001841 CCCGCTGGAG CACATATGAA AAACAATACG GATGTTTTGA TTTATTATCA TATTGATCAT TATGATGGTA GCGTATACTT 001920
001921 TTGGAAGGCT TGCCATACAT TAGGCATTGT GCTAAGCACA TTATATGGTT AATCTCATCA ATCTTCACAA CCTATGTGGC 002000
002001 AGGTACTATT ATTAAACCCA CTTCAAAGAG GAGGGAACTG AACCTCAGAG AGGGTAAGTG ACTTGCACAA GGACACAAGC 002080
002081 TAGTGAGGAG AGGAACTGAG AGGAATGGCC AGACAGGCCA TCAGCCTCTG TCCCCACATG CTGGGTCTGA GTGTCTGACG 002160
002161 GTGGACACAT TCCCTTCCTG GAGGGAGAGC TCCTAGGGAG CTGATGGCAG CACTGAGTCT GGAATGTGAT GGGAGTGCAT 002240
002241 TAGATGACGT GGGTGATCTG ATGAGTACAG AGGCGTCACA CTGCAATGAC TTCATGCACA TATCTCCCCT TGAATGCACA 002320
002321 GAGATTCAGC AGAGGCCAGG AGCTCAAGTT TCTGGCCCAG TGTCCCCCTC TTCCCCTGGG GAAAGCCAGG GACACACTGC 002400
002401 CTGGCTTTGC TACACCTTTC TAGGCAAAGG CAGTATGCTC TCCCTCTCCT TGGCCTCCCT GGCTGTCCAC ACATCCACAC 002480
002481 CCACTCACAC ACACATGCAC ATGATCATAC ACATTACACA AGCCCACATG CCCACAGACA TGCTCACACT CACACTCACA 002560
002561 TGCATACACT GCCATACACA ACACACATAC ATACATTCAC ACACACTTGC ACACACACAC ACACACACAG TTCTGATGGC 002640
002641 CAATCTTTTG GGGCTATGTT GACACTGTGA AGCAGGTGAA ACAAAGTCTT TGCCACTCCC TGCTTTGGGC CTATTATGTT 002720
002721 TGTTTTATAG TTTAACTCTC AAAAGACAAC TTTATTTTCC AAAATTATTC AGGTTCCCAG CCAGGTGCAG TGGCTCACAC 002800
002801 CTGTAATCCC AGTACTTTGG GAGGCCAAGG CGGGCAGATC ACCTGAGGTC AGGAGTTTGA GACCAGCTTG GCCAACATGG 002880
002881 TGAAACCCAG TCTCTACTAA AAATACAAAA ATTAGCCAGA CATGGTGGCA CACACATGTA ATCCCAGCTA TTCGGGAGGC 002960
002961 TGAGGCAGGA GAATCGCTTG AACCCGGGAG GCGGAGGTTG CAGTGGGCCA AGATCGTGCC ACTGCACTCC AGCCTGGGCA 003040
003041 ACAGAGCAAG ACTCCATCTC AAAAAACAAA AACAAAATCA TTCAGGTTCT GTAGGGGACC CTCACTGTGT CCTGGATTCC 003120
003121 ATTCCACTTT TAAAGTCCCA AACAGCTTGT ATGGCCACTT CCCTTGACAC CCAAACCAGA TAGGAGTCTT AAATGACACA 003200
003201 GAGTATTGAT GGTTTCTTTA AAAGGAAATC CACTCTCAAT GGGAAGCTGG ATAACTTCGC ATCCAGATTT CATCCATCTT 003280
003281 GGGCTTTGGT GGCTGCTGTT TGTTTTTGTG CAGGAGAATC TCTCCCAGCC AACGTCGATT TCACTAACAC AGTGGTTAAC 003360
003361 CTTTGCTCTC TACTCCTGCA TCAATCTTCC GCCTACCGCA TGTTGAGCCA TGCTGCTTTC TGGCATTCCT TTTGGATTTT 003440
003441 CAGTTTACTA CCCAACTACC AGTCCTAATA ACATCAGATA AAAGGGCTTC CGCTGTGCTG CACTTGTTTT CAAAAACTAT 003520
003521 AAATGCCATC GACCCAGAGT TAAGTCCAGC CTCAGAGAGA CAGAATATAA ATACCCAAGT GGCCCTGGGC CACTGAGTTC 003600
003601 CTCAGACATT ATGTGCTATG GGAGTTCCAG AAAGGGGGAT TGCCTGGTTT TGAGTGCAGA AGGCTTCCTG GAGGAGGCGA 003680
003681 GATTTCTGAT GGGCCTCTGT TATGAGCTAA ATTGAGTCCA CCCCAAAATT CAGATGTTCA AATCCTAACC TGTAGTACCT 003760
003761 AAGCATGTGG CCTTATTTGG AAGCAGAAGC ATAACAGAGG TAATTCGTTA AGATGAGGTC ACAGTGGAAG AGGGTGGACC 003840
003841 CCAATCTGAT ACAACTCGTG TCCTTATAAA AAGCAGAAAT TTGAAGACAG ACACACAAGA AGATGAAGGC AGAGACCTGG 003920
003921 CTGATGCGGC TATAAGCCAA GGAACGCCAA AGATTGCCAG CAAAGCACCA GCAGCCAGGG AGAGGCCTCG AACAAATTCT 004000
004001 CCCTCCCAGC AAAAAGGAGG AAGGAAGGAA CCTCCAAAAG AAGCAGGCCA GGCACAGTGG CTCACGCCTG TAATCCCAGT 004080
004081 ACTTTGGGAG GTTAAGGCAG GCGGATCACC TGAGATCAAG AGTTCAAGAC CAGCCTGGCC AACATGGTGA AACCTCATCT 004160
004161 CTACAGAAAA ATACAAAAAT TAGTCAGGTG TAGTGGCGTG CACCTGTAGT CCCAGTTACT CGGGAGGCTG AGGCAAGAGA 004240
004241 ATCGCTTGAA CCTGGGAGGT GGAGGTTGCA GTGAGCCAAG ATCGTGCCAT TGCACTCCAG CCTGGGTGAC AGAGCGAGAC 004320
004321 TCCATCTCAG AAAAACAAAA AAGAACCCTA CTGACACCTG GATTTCAGAC TTCCAGCCTC CAGAACTGTG AGATGTTACA 004400
004401 TTTCTGTCAT TTAAACACCC AGTTTGTAGT ACTTTGTTGC AACAGCTCTA GTGAGCTAAT ACAGCCTTGT AGGACAGGTA 004480
004481 GGAATTTGTA ATGCACAGAG AAAGCCAACT GGCCACAGTT GTTGAAAATA ATAGAATCGA AGCGCCCCTA TCACTACCAC 004560
004561 CCCAGGCCAT CACTTTCAAA GCTGTTCAAA ATGATGCAGC CGCGTGAGAA GGCCGGAAGG CCAGGGCGGG AGATGGGCTC 004640
004641 CAGGTGGGCC CAGGCTGCCT GCAGAACCAG CTTGCCTCAC TGCCTGGTTG CCAAGGAGCA CCTGTGGCTA GGAGGAGATG 004720
004721 CCCAGGAAGA AAATTTGGCC ACATCCCTGC CTGCCTCCCT GGCAATGGGT GATGCTCTCT GCCAGCTGGC CCAGCTCCCC 004800
004801 CACCACATAC CTGGCTAGGA GTCAGTAGGA AAACAGTGTG TGTTTGTAGG GCTCTGCACT GAAGGGCATT AGATCCATGC 004880
004881 AAAGGCTAAT AAATTAGAGA TAAGTGGGAT TTGTAGATTT GCTGGAGGTT AGAGCTGCAG GGTCTGGCAT CAGCTCTGGG 004960
004961 TCTTTTCCAT GGCCCCAGGC TGGCTCAGGT GTGAGCTGAA GAGGCAAAAC TGTCTGTTTA GGTTGCATTG GGTTCCCCTG 005040
005041 AAAGATCTGT TGAAGTCCTA ACCTCGGGTA CCTCTGTTTG TGCTATTTGC AAACAGGCTC TTTGCAGATG TAATCAAGGA 005120
005121 AAGATGAGGC AACGCTGATT TAGTCAGGCC TTAATCCAGT GACTGGTGTC TTCATAAGAC AAGGAAATCT GGACACAGAC 005200
005201 ACACAAAGAG GAAAAAGCCA AAGACACAGA GACACATGTA CACAGGGAGA ACTCCATGGG ACAACGCAGG CACAGATCGG 005280
005281 AGTGACGCGG CTGCAAGCCA AGGAGCGCCA AGATTGCCAG CAACCCCCTG GGGCTGCAAG AGGTGAGAAG GAGCCTTCGG 005360
005361 AGGGAACATG CACTGCTGAT TCCTTGATTC CAGATTTCTG ACCTCCAGAA GCATGGGAGA ACAGATTTCC CTTGTTTGAA 005440
005441 GGCACCCAGT CTGTGGTCCT TCATCATGGC AGCCCTCAGG AATGGATACA GGCCCTTCCC TGCCTGCCTG GTGGAGCAGC 005520
005521 CTCCAAGGGG AGCCTTTGCT AGCAGGAAGA GGCATCGCAT GGAGCTCAGA CCCGCCTCAG AGGAACTTCT CTCAGCCTCC 005600
005601 TCTCTCCGCA CACCCGACCA AGGTGTGAAA TCCCTCCCCT TTACCTCTGC CACTTGCAGG TGGCAGGATG CTGGAGCTGT 005680
005681 CCCTGCCTCT TTGTAAAGTG AGGGAAGGGC AGCCCTCTCT GCTCTTTTTT TTTTTTTTTT TGAGACAGAG TCTCACTCTG 005760
005761 TCTCCCAGGC TGGAGTGCAA TAGCACGATC TCGGCTCACT GCAACCTCCG CCTCCCAGGT TCAAGCGATT CTCCTGCCTC 005840
005841 AACCTCCTGA GTAGCTGGAA TTACAGGTGC CTGCCACCAC GCCCAGCTAA TTTTGTATTG TTAGTAGAGC CAGGGTTTCA 005920
005921 CCATGTCGGC CAGGCTAGTC TCAAACTCCT GACCTCAGGT GATCCACCTG CCTCGGCCTC CCAAAGTGCT GCGATTACAG 006000
006001 ACATGAGCCA CCACGCCCGG CCTGCTCCAC TTCTAAGGCT TCTTGTGACA ATGTAAGAGA AAGGAGATGA CAGAGCTTTG 006080
006081 CAACGGGAGG AGGGCTATGT GTTCTGGTGA CCAATTCACT GTCTTGTGTC GGGACAGGAA GAAGCCCTTC ATACGGGCAG 006160
006161 CAGGCTGGGA GCCAGGGAGG AGGAAAGATC ACGATCCACT CCCTGGTACA TGGCCCTTCT GCACCCCGCA GTCTCCTTCC 006240
006241 AGGTGCCACA ACGAGAAGGC ACACATCCTT GGCACAGCAC TTGAGGCTTT TCACCACTGG CTGCACTCAC CCCTCCAGAC 006320
006321 TCACTGCCTT GCACCAACCC TTTTCCGCCC ACCCCACTCT ATGCTGTCCA CAGCCTCCAC CCCAGCCACC TGATTCTGCA 006400
006401 GGCCAATGTC ACATTCTTCC AGTCCAGGTT CTATTCTGGC ATTTCTTGTC ATTATTTTGC TGAGAATGTG TCTCTCTTGA 006480
006481 CTTTGAACTT ATTGAGAGCA GGAATCATGA CTCAGCCATA TATCCCAGCA CTTGGCCCAG GGCCTGTCGT TTCCAGGGTA 006560
006561 GGTGGTCTAG GCTGATTGAA GGAATGGCAT TTAGTCTTTA AAATGAAAGC ATGTTGCCTA GCTTGGTTAT TTTTGAACTC 006640
006641 TATAATCAAG GACTACGTTT ACCTGAATAG CCTCTGCAGA ACACCAATTC CGTAAGGTGC TTCACACACA CACACCAATT 006720
006721 CTATCATTTA ATACATTTTG GAAAGGCTAC ATACTACTAC AGCCTCTTTT ACAGATTAGC AATGTCCATG AGCGCACTAA 006800
006801 AGGTTGAGAC ATTCTGCAGT GAAGAAGCCT ATTTCATTTT GTTTAACCAA GTATTTCTCA AATTTATTTG ATCATATGTG 006880
006881 GCAGAAAATG CTGTGTCTGG CATTCTTCAT TTCCCTCTTC CTCCTTTAAC ATGGAACCCC T