LINC00163

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LINC00163 encoded on the reverse strand of NLC1 on chromosome 21q22.3 play a role in human narcolepsy.

Contents

Annotated Information

Name

LINC00163: long intergenic non-protein coding RNA 163 (HGNC nomenclature)

"narcolepsy candidate region gene 1A", "narcolepsy candidate-region 1 gene A", NLC1-A, NLC1A[1]

Characteristics

NLC1-A, encoded in NLC1 (a candidate region for susceptibility/resistance to human narcolepsy ), was expressed in human hypothalamus, which also expresses preprohypocretin, 42 a protein important in orchestrating the sleep-wake cycle. NLC1-A includes domains known as integrin β-chain cysteine-rich domain, anaphylatoxin domain, and epidermal growth factor–1 domain signatures. Furthermore, the amino acid sequence of NLC1-A was subjected to secondary structure prediction [1].

It belongs to the category of "Intergenic" in lncRNA classification[1].

Function

The polymorphisms of NLC1-A may be directly involved in resistance to human narcolepsy, indicated by a reporter gene assay that NLC1-A fragments containing the alleles for narcolepsy resistance (D21S0012m [CA]10 allele and rs13046884 g allele) were less transcriptionally active than were those of other alleles[1].

NLC1-A might function as a transporter of certain substances,which has a long loop (residues 78–125) with high hydrophilicity, flexibility, and surface probability that suggests that NLC1-A may be a membrane protein[1].

Diseases

  • human narcolepsy

Expression

NLC1-A and NLC1-C were expressed in human whole brain and hypothalamus. Notably, NLC1-A was also expressed in human spleen, lung, kidney and skeletal muscle[1].

RT-PCR Forward primer Reverse primer
NLC1-A 5'-CTAGGAGGGGAAACTGAGTCC-3' 5'-CAGCACAGTTGGAGACATCACT-3'[1]

Sequence

>gi|299782551|ref|NR_033840.1| Homo sapiens long intergenic non-protein coding RNA 163 (LINC00163), long non-coding RNA

000001 CTCACCCTCG ATGGTGCCCT CGACCTGTCC TCCCTCAGCA GCCTGTGGCA TCCAGACCAG TTCGTGGCCC CTAGGAGGGG 000080
000081 AAACTGAGTC CCAGCCCCAG GGTCCTCCCT CGGCTTCACT GGGTGCCCCA TGGAGGAGAC AGCCAGGGTG TGTCACCTGA 000160
000161 CAGGCTCACC AGAACCAGCA CAGCAGCTGC TGAGTTTTGG CTCCCGGACC CTGGAGCCCC TGCTGCCGAG GCTGGGGATG 000240
000241 GCGGCTCCAG AGGTCATTCC TCCCCCGGAA GACACACGCT GGCCTTGGGC CAGGGGACCC TCAGCGACGG GGTCACCCCA 000320
000321 ATGTTCTGGA GGCTGCGGTT CTGCTTCCTC CTGGGGCTGA GCTGAGCAAG CTCTAGCTCT CGGGCCGAGC GCAAGGAGGG 000400
000401 CAGGAGTGAT GTCTCCAACT GTGCTGAGGT CTGCCCTGGG TGCAAGGGCC CTGTGTTTTC AGCGCTGCCG TGTGGCCCAT 000480
000481 GGATGCCCCA GGCCCCTGGA CAGTTGATGC CTGGGGTCCA CACTCCTGGA CAGGGCTCTG GACAGTTGAT GCCTGGGGTC 000560
000561 CACACTCCTG GACAGGCCCC CGGACAGTTG ATTCCTGGGG TCCACACTCC TGGACAGGGC TCTGGTCAGT TGATGCCTGG 000640
000641 GGTCCACACT CCTGGACAGG GCTCTGGTCA GTTGATGCCT GGGGTCCACA CTCCTGGACA GGCCCCTGGA CAGTTGATGC 000720
000721 CTGGGGTCCA CACTCCTGGA CAGGGCTGAG GAGGTGGTGT CCCCAGACTT GCCCCAGCAC AGCTGTGGGG GGCACCCGGA 000800
000801 CACCCGCCCC GGCCTCAGTC TCCCATCCCA GCTGGCCCTG ACACGGGTGC ATGTGATGCC CTCCTGGTCT TGGCCTCTCA 000880
000881 GACCCAGCTC AGCCACGGCC ATCCAGACCC TTGGGCTCCG GTGTCTTCCC AAAGCTCTGA GAAGCACCCC CTTGGGGCAG 000960
000961 CCAGACCCCT GACCACCCTC CGAACCTCGG CTGGACTCCC TGTGGCCCAG TCCGGAAGGG TTCTCCTCGG AACAGAGGGC 001040
001041 AGATGAGGCA AGAGTCGGTC CGAGTTCTGC CCTCTGGCAC CGGCAGTGCT GTGGAAGGCC CATGGGGCGG CTCAGTGGTC 001120
001121 CCCAGGGACC TCAGCCTTCG GGAAAGTGCA GCAGAGACCT CAAGGCCCCC CACGCTCAGC TAACGTTGCC CTCGCTCATC 001200
001201 CAGAGCACAG CCCGAGCTGC AGGAGGGCCA GGAGGGCAGA TGCTCCACAG CTCGGACAGC ATCCATAAGA CCCGCGTGGA 001280
001281 GAAAATAGCA AAGGCCAGTG TGGAACGGAG AGGACGTGAA CGGCGAGTGC TCGGAGAACA AGCACGCCAG CAGCGAACCC 001360
001361 AGGGGGACCA GCCCGACAGC CAGTGCGCTG AGACACCGGC CAACGGCAAC GCCCCATCCT CACCGCGAAC GCCACTGTGA 001440
001441 CGCGCTGACA GTGGATGCGA ATGCGTGACA CAGACAGCGA GTGCCAGTGT GACCGTCACG GCTGATGCTG AGCACTGCAC 001520
001521 CGACACACCA CAGAATCTGC AGGCCCAGGG CTCAGCTCCT GCTTGCGGGG CGCAGGCCGG CCCCACCGTC CGACGTACAG 001600
001601 ACCAGCATGG GCACCTTAGG CCTCTCCACC CTCCTCTGCC CAGAGCCTGC CACCATCCGT GTTACACAAG AGCCAGGTGC 001680
001681 TGCACAGAGA GGCCACGTGC CTTGCCCCAG GCTGCCAGCT CCAGAGAATG GTCCGGGGAC GCCATGGTCA TCCGGCCCCA 001760
001761 GGACTGCTCC TGACCCTCCT GGGACGGATC CTCCGGGCAG AGAGGGGACG CCGTGGTCAT CCGGCCCCAG GGCTGCTCCT 001840
001841 GACCCTCCTG GGACGGATCC TCCGGGCAGA GAGGGAATGA ATCACATTCC GGATGGTGGC TTCAGGTCAG AAAGCTGTCA 001920
001921 GGTCACCCAG GTGCCATGCG AGCTGCTCCC CGGAGACGGC TTTCGGCCTT GGGTTTATCA CAGCGGCTGT TTTCCGTCTG 002000
002001 CCAAGCCAAG CCTGGCTTTC ATCTCCCCTC GCACAACGGT CTGCTTCCTC AGCCTCTGGG CTTATAGTGG TTTTCTTTTC 002080
002081 TACTGTCTGA AATTGAATGT TTAGTTCATC TATTTTCTAT TCTCTCATTT ATAATAAAAA CATTTCAGAT GAGAA

Labs working on this lncRNA

  • From the Departments of Sleep Disorder Research (Alfresa) (M.K.; T.E.) and Human Genetics (M.K.; H.H.; K.T.), Graduate School of Medicine, University of Tokyo, the Japanese Red Cross Central Blood Center (T.J.), and the Neuropsychiatric Research Institute (Y.H.), Tokyo; and the Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan (G.T.; A.O.; H.I.) [1].

References

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Kawashima M, Tamiya G, Oka A, Hohjoh H, Juji T, Ebisawa T, et al. Genomewide association analysis of human narcolepsy and a new resistance gene[J]. American journal of human genetics. 2006,79(2):252-63.
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