Difference between revisions of "LINC00165"

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==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
−
LINC00163: long intergenic non-protein coding RNA 163 (HGNC nomenclature)
+
LINC00165: long intergenic non-protein coding RNA 165 (HGNC nomenclature)
  
−
"narcolepsy candidate region gene 1A", "narcolepsy candidate-region 1 gene A", NLC1-A, NLC1A<ref name="ref1" />
+
"narcolepsy candidate-region 1 gene B", NLC1-B<ref name="ref1" />
  
 
===Characteristics===
 
===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-B, encoded in NLC1 (a candidate region for susceptibility/resistance to human narcolepsy ), is on the reverse strand on chromsome 21q22.3 with positions 45238709-45239923<ref name="ref1" />.
−
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 <ref name="ref1" />.
 
  
 
It belongs to the category of "Intergenic" in lncRNA classification<ref name="ref1" />.
 
It belongs to the category of "Intergenic" in lncRNA classification<ref name="ref1" />.
  
 
===Function===
 
===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<ref name="ref1" />.
+
SNP rs13048981 is located 2,602 bp upstream of NLC1-B, which was not expressed in human brain, and its position, 4,164 bp upstream of NLC1-A, suggests that its association with narcolepsy resulted merely from the LD with rs13046884 and D21S0012m. Thus, it is unlikely that NLC1-B is a susceptibility/resistance gene for human narcolepsy<ref name="ref1" />.
−
 
 
−
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<ref name="ref1" />.
 
  
  
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===Expression===
 
===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<ref name="ref1" />.
+
 
  
 
{| class='wikitable' style="text-align:center"
 
{| class='wikitable' style="text-align:center"
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! | Reverse primer
 
! | Reverse primer
 
|-
 
|-
−
| rowspan="1"|NLC1-A
+
| rowspan="1"|NLC1-B
−
| | 5'-CTAGGAGGGGAAACTGAGTCC-3'
+
| | 5'-CCTCACAGCATCCCACATT-3'
−
| | 5'-CAGCACAGTTGGAGACATCACT-3'<ref name="ref1" />
+
| | 5'-TTTCTGGAAACAGCCAGGAG-3'<ref name="ref1" />
 
|}
 
|}
  

Latest revision as of 14:30, 10 April 2015

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

Annotated Information

Name

LINC00165: long intergenic non-protein coding RNA 165 (HGNC nomenclature)

"narcolepsy candidate-region 1 gene B", NLC1-B[1]

Characteristics

NLC1-B, encoded in NLC1 (a candidate region for susceptibility/resistance to human narcolepsy ), is on the reverse strand on chromsome 21q22.3 with positions 45238709-45239923[1].

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

Function

SNP rs13048981 is located 2,602 bp upstream of NLC1-B, which was not expressed in human brain, and its position, 4,164 bp upstream of NLC1-A, suggests that its association with narcolepsy resulted merely from the LD with rs13046884 and D21S0012m. Thus, it is unlikely that NLC1-B is a susceptibility/resistance gene for human narcolepsy[1].


Diseases

  • human narcolepsy

Expression

RT-PCR Forward primer Reverse primer
NLC1-B 5'-CCTCACAGCATCCCACATT-3' 5'-TTTCTGGAAACAGCCAGGAG-3'[1]

Sequence

>gi|22800663|gb|BC009635.1| Homo sapiens chromosome 21 open reading frame 135, mRNA (cDNA clone IMAGE:3891427), with apparent retained intron

000001 GAAGGCCAAT GGCTCCTGGT GTCATTAAAG ACTCTGTTTT TACCTCCTCT GGGCCTCGGG AGACCAGCCT GGCACCAGAG 000080
000081 GAGGGGCTGG CAGAGCCCCA GGCTCCAGTC CACACCCACC GGCCCCAGGT CTGGCCATGG GCTGGGCCCT GGTGTGCAGA 000160
000161 CAGCAGTGGC CACTGCTCCA GGGCCTTTGC ACCAGCCTGC TGCAGGTCCA GGCGGTCATG GGGAGTGGAG CCGCAGCGGC 000240
000241 CTCTTGTTTT CCTTCCCCTC TTGGGAGACG GCTGCTCCTC CTGGCTGTTT CCAGAAAGTG TGTTTGTTAT TTGGCTCCTG 000320
000321 GAAACACCAT CTGATGAAAC AGGCTCTGTT GGGCTGGCCT GCCAGGCGGA GGCTGTGGGC GCCCAGGAGT CTCACCACGA 000400
000401 AGCAGGTGGC AGAGGCCCGA TAGCCCCACC CTGCAGGCCG GGACCTGGCA CCTAAACGGG GAGATGGAAG AACATGGAAA 000480
000481 ATTCCCTAAG AGCAAATTGA TGCTCAGCTT CCGCGGGCAC CAACTTGCTG CGGAATCCTG CTTTGCAGAT CATCGTTCCT 000560
000561 CGAGCATTCG GACGCCTCGG GCCCCAGAAG TTCAAGAACA AGAAAGCTCT GTTTCATGCA GACACGCTCA CGCATGCACA 000640
000641 CATGCTCACA CATGCACTTA TACGTGCACA CACACACACA CACACAACAC ACACACACGC ACACTCACAC AACCATGGCC 000720
000721 ATGTAGCCCC AGTCTCAGCA TCATGTCCTC TATTTAGAAA TATTGGCTAA ACACCTAATA AATAACTAAA CAGAAATGTA 000800
000801 ATCTTTAATA AAGTCTCATA AACCAAAAAA AAAAAAAAA

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 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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