ENST00000416928.2

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HAGLR, which is induced by RA and regulated via PI3K/Akt pathway, controls genes involved in RA signaling, angiogenesis and inflammation.

Annotated Information

Name

HAGLR:HOXD antisense growth-associated long non-coding RNA(HGNC nomenclature)

Mdgt[1]

"HOXD cluster antisense RNA 1", "HOXD cluster antisense RNA 1 (non-protein coding)", HOXD-AS1[2]

LncBook ID: HSALNT0043560

Function

Significantly overrepresented pathways identified from genes regulated by HOXD-AS1[2]

HOXD-AS1 is evolutionary conserved among hominids and has all bona fide features of a gene. HOXD-AS1 is a subject to morphogenic regulation, is activated by PI3K/Akt pathway and itself is involved in control of RA-induced cell differentiation. Knock-down experiments revealed that HOXD-AS1 controls expression levels of clinically significant protein-coding genes involved in angiogenesis and inflammation, the hallmarks of metastatic cancer[2].

Regulation

HOXD-AS1 is regulated by PI3K/Akt pathway[2].

Diseases

neuroblastoma[2]

Expression

Mdgt is highly expressed in testes, and more moderately in brain, kidney, colon and skeletal muscles[1].

Tissue expression pattern of HOXD-AS1 correlates with HOXD1 and HOXD3 transcripts[2]

HOXD-AS1 is expressed in multiple tissues with the highest levels of expression in kidney, colon and testes and the lowest in liver, heart, pancreas and stomach. In general, HOXD-AS1 demonstrated highly correlated expression with its neighboring protein coding genes HOXD1 and HOXD3, thus implying that they are subject to the common regulatory mechanism[2].

Evolution

Evolutionary analysis of HOXD-AS1 transcript[2]

More than 96% of this gene sequence is evolutionary conserved among hominids (H. sapiens, P. paniscus, P. troglodytes and P. abelii). At the same time, only 12% to 52% of HOXD-AS1sequence is shared with other primates (M. mulatta, N. leucogenys, C. jacchus and O. garnettii), comparable to 11% of dog (C. lupus) and 8-12% of ungulates (E. caballus, S. scrofa and B. taurus). Thus, a gap between HOXD-AS1 genomic sequence in apes and other monkeys is apparent[2].

Cellular Localization

HOXD-AS1 is evenly distributed between nucleus and cytoplasm[2].

Labs working on this lncRNA

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, United States[1].

Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Matrix, 138671 Singapore[2].

References

  1. 1.0 1.1 1.2 Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development[J]. eLife. 2013,2:e01749.
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 Yarmishyn AA, Batagov AO, Tan JZ, Sundaram GM, Sampath P, Kuznetsov VA, et al. HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome[J]. BMC genomics. 2014,15 Suppl 9:S7.

Basic Information

Transcript ID

ENST00000416928.2

Source

Gencode19

Same with

lnc-AC009336.1-2:6,HAGLR,Mdgt,HOXD-AS1

Classification

intergenic

Length

4235 nt

Genomic location

chr2-:177037923..177043012

Exon number

3

Exons

177037923..177041420,177042060..177042222,177042439..177043012

Genome context

Sequence
000001 CGGCCGCCAG CCGGTAGGGT GATTAACTCA CCGTCTGTCT TTGCAAAAGT GTTCCAGGTG GATCAGGAGC GCCAGCCCAC 000080
000081 CCCGCCCGCA GCCTGGCCGC TCGCTGAGGC GCGGAGAGCG CGGAACGAGC GCGCGCATCA CGTGGCGGCG CGGACGTTTG 000160
000161 TGCCGCGCGC CCGCCAGACC GCCCAGGAGG CGGCGGCTAT TGTTCCCCGC AGGGGCCCGG GGCGCCCTGA AACGGGGTCC 000240
000241 ACGTCAGCCC GCTCCCGAGC GTGTCCTCAG GTCTAAGGAC GGGTGGGGCT TCCTTTGTGT GTTCTCTGGA AGGGGCTGGG 000320
000321 ATGGCGTCGT TGCTGCCCCA AGGGGTAACC GAGGGGGATT GAGGGAAGAT GGTACCAGCT CCCTAGAGCT CAGCTCACCA 000400
000401 GACCTACTCT TCCGCTCGAC CCTTGCAGAG GAGGTGGGGA CGGATATGGT ATTTGTAGGG CAGCGCTGTG AACAATGGAG 000480
000481 CCATCAAAAA GGCCTTCTCC CAGCCTCCTC ACCAACCACG GACATTCCTG GCCCAACAAG ACCTCCTGGC CAGGTTTTGA 000560
000561 GCCCTGCTTC CCAGATCTGG GGACCCTTCA CCTGCCTCTA CTACTGCAAA TGATTGGATA TTCGTCTGAC TTGGCTCTTC 000640
000641 CCTAATGTGT GGAACTAATT TTGTTCACTC TGTTTCATGC TGGACCTGGC CTGAAAATGG GCCCTTATAT TGTCTTTGCA 000720
000721 CTTTCCAACT TGCCAAGTTT CTGAAAGAAG GACCAAAGTA ATGCCAAGAA CTCCCAGATG AAGAGGACCT TCCTTAGACC 000800
000801 TATAACAGAT TCACTACTTG ACTTCAGAGG GAAGTTTCAG CTAATTCTCA GGAAAAGGTC AAAACAGGCC TGTGACTGTC 000880
000881 CCTTGAATAC TGAAGGTATA AACAAGCTTC TGGCTCCTCC AGGTCAAGCA GAGGAACACT TTTATTAGAA TGAAGGGTTA 000960
000961 CTTCTTTGTT ATTCAAACAC ACACCCACAC ACATCCTCTG TAGTCTCCCT AATGAAAAAC CTCAACAGAT GGAGAGCCTG 001040
001041 AGCTCCCAAG TCCGCAGGCT GAGAAGATGC ACTTCACTCA AGGGCCAGTG GGCTGGTACA GACTAGGGAA GAGAAAAGGG 001120
001121 ACAAAGGCTG CTAGTATAGG TAATCACTAT CTTTTAATAC TCCTAACACA TAGAAATTCG AAAAATCTTG TTCAGCAATG 001200
001201 TTAGCAGCCT GTGAGCCTCG GAAACTAATT TGGCTGATGT GTCTCTGATA GGGAGCTTGG GGCTGCACCA AGGGGAAACA 001280
001281 TTCTCCTCCT GTATTCTCTC CTCTCTCTCG TTTGAAAGCC TGTACAAAGA AATGGTACAA ATGGATGGTT AACTTAATGA 001360
001361 TTCCATCAGA GGCAGATTTT TCTCTGTCAG GTCCCTGGAT AAGGTGGAGG TCTGAAAGCC AGGAGACAGA ATATGTACTT 001440
001441 AATCGCCCTT TCTGACCTGC TTACCAGTGA CCAGGACTAC TCTCCAGGCC TTTCTTCTGC CACTTCCCCA TTCTTCCTGG 001520
001521 CTAGTTCAGT TGGGTCTCAG CACTTCAACT CCTGGCTGGA TCCTGAGTTT TTCTTGGTTG CAGGGAAAGC TCTCACTGTC 001600
001601 TGCATCTCCT TCCCCACCCC CACCTCCCGT TTTGCAGCTG GCCATTCTGG CTGCCTCACA GCTATCCTGC CTTAATTCAT 001680
001681 ATTTGATTGC CTGGACAGAA CCACCTAGAA TGTCCAGACG ACTGCCACCC CTCAGCCATG GGCCTGAGAT CCTGCCCTGA 001760
001761 CCCCTTTCTT CAGACCCCAG GAGGACCCAC AATCTCCCTG ATCCCCACCT TCCCCAAAGT AGTCTCTAGG AAAAAAGCAG 001840
001841 AGCTGGCTAA GGCCTGAGAC AGAGCCATTT CTTCCCCTTG GGCAAACGAG GTAGACCCTC CCAGAGACCA ATGCCGGAGA 001920
001921 GGCCCGGATC CGAGCTCCCT TTATATGGCC TCCCCCATCA CGGATCCCGT GGGAAAACCT GACACACAAT GGCGCGGCTG 002000
002001 CTCCGGGCAC CCTCAACCCA GCGCCCTGCG GCAAGGCCTG GAGCAGCCTG GTGGTCTTGG TGCGCTCCCT TTGCCCTCCC 002080
002081 CGCAACCCTC TGCGAGCACT CGTCCCAGGA GAGAGACCCT GGCTAGGGTG GAGGTTGCCT CCCGCAAAGG GCGCTGTTGC 002160
002161 TGGGGCCTCC CCTCCCCCAT TCTCTTGTTT TTCTGCTTCT GAGACTCGGG AGGGAGGCGG CAGGCGCCTC CGCAGCCGAT 002240
002241 AGAGCAGCTA TTGTGACCTT CCCTTGCAGA GCGGGAACCC AGCCGAGTGT GTACCGCCGG CGGTGGCGGG GGAGGAGGCG 002320
002321 ACTGTGTGTG CAAACCTCAG TCGGAGAGGG GGTGGCGCTG GGAAATAAAG GTTTGCAACC TCAGGCAGTT GGGCCCTTCA 002400
002401 GAGGGCGTTT GGTTGTGTTT AGACTCGGTT GCTTTCTAAC ACTAATTGCA GGCTCAAAAG GAGCGGAATT TATTGCGAAG 002480
002481 GCCAAGGCGG CTTGTTTATA ATTTATGAAG TTTTAAATGG CTGTGCCGCG GGCCCCAACT TTCTCCTGGG CTGGCAGCCG 002560
002561 CGCGGAAACG CGCCCTCCCC CGGCTCGCCG CCCACCCCCA CCCACGCCCC TCAGATGAGT CTCACGCCAA TGGCAGGAAC 002640
002641 AGATCCGAGC TATTAGAAGT CTCGGGAACC TCCAGAGATG ACAGAAGGTG GCAGATTTGG TCCAAGCCCT CACCCCACTC 002720
002721 GAGAGGAGGG CGTCGGGGAA AGCTGTGGCT GCCTGGAGAG GGAGCCCCTG ATCCCACACT TCCTTGGAGC CTGAGTGTGA 002800
002801 GAGGAAGCTA ATGTCAGCCG GGCTAGACAC CGTTTAAAGT CTAATCCATG AAACCCTAAG CCGCAAATGA CACTTGGGGC 002880
002881 TTTGCAGACA CCCGCAGACT CAGCAGATAC TCCTGCGGTA ACACACTGTG CTGGAAAACG CCTGGAGCCA TGACACATTA 002960
002961 CGTATTTTTA TTATTATTTA TGGTAGGAAG AGGAGATGAG GGAAAATCGG GCTGAATCTA AGCAGCCTGA CAATTCAGCT 003040
003041 AGTTAATATT TAGCCAGTTA AGAAAGGTGG TTGTAATCCC TGCAAGGCAG TGAGCTCTCC TTTGATTTCT CTAATAGCTT 003120
003121 AAAAAATAAT TTCTTACAAG ACAATTAGAA ATTCTGCCTA TGGATGCAAA TTTCATAGAA AACAATGTTA AGCCTTGAAA 003200
003201 GTGGGTAAAA TGTGCCTTCG ATTGAAGTCA TTTATTCTGT TGATACACTT CTACAACATA TATATTTTAA ACCTGCTCAG 003280
003281 ATAAAGTGAA ATTTAGCAAA AGGATATCCC CTCCCACCCC CAAATCTAAC ATGCCATTTT AAAAACAGCA CAAAGGAACA 003360
003361 AGGAAACTAA ATATTATTTT GAGCCATCAT TACTTAGTGA AATACAAACA TCCAAATAGA AACGATTGTT GTTCCACCAG 003440
003441 AAGATTAGAA GTTAAATTAT TTCCACACAA TAGGAATTTC ACTTCGTGTC ATCGGGGATG TAGTAGGAGT TGCATTATTT 003520
003521 GTCAAACCAA ATAGAGATGC GTGGGCTGAC TTTGCTGAAA TACAAAAGAA TTGAACCTTA TCTGAAGGCG TTTTCTAAGT 003600
003601 GGCCCCTCCC ATAGAAGCCG GGAAGTTGTC CACCCCTAGC AGAAGCCACA TTAATATTTA CAAAATGGTT ATAAATCCTT 003680
003681 GAAGACATTT TTGCCCATTT TGTATAAGAA ACAGGAGTAA ACAAGGTGTT TATACTTGTT ATGTTTCATT AATGAAATAT 003760
003761 TATTACTTTA CATCTTGGGG AATGTTTGTT TTCTTTAGAA ATGAACTAAT GATCACTACA AAGGAAGAAT TCATGACAGC 003840
003841 ATTTCCTAGA GAAAAAGCTT AGGTACGCGT CTCCAAATGA TGGTTTCTTT TTCTACACCT TAGCTTTTTC ATAGCTCAAT 003920
003921 TCTTCTTACA ACTTCTCTTG TGTTTTTTCT TTGATTGTCA GTTTTCTTTC AAAGTTTATT TTTTGTTACT TAATGCAGAA 004000
004001 AAGTGAGCTC TGGTCTCCCC AGTGTAAAAG TCGATTGTGT CTAGAAAGAA GGCAGTAAAA ACAGCAAAGC AGGCGCTGCT 004080
004081 TTCAAAAAGC CCTGCCCAAA TCATCCCGCC CAGAACCTTC TTAGGTTTGC ATCCTCATTT CCCCCTCCCC TAATTTCAAT 004160
004161 AGCTGGAAAG TAATCAAGTA TCCCGAGAAC CAATTTATGC ACTAGACTCC AAATAAATAA AATATTTTTT TCAAA
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Internal error - LncRNAWiki

Internal error

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[XetwOWYveWuFn0BZF4E7UAAAAAY] 2019-12-07 09:26:19: Fatal exception of type "TypeError"

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