LINC00271

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LINC00271, Long Intergenic Non-Protein Coding RNA 271, identified as a candidate gene in schizophrenia and also has suppressive role in many cancer types.

Annotation

Name

LINC00271

Alias

C6orf217; NCRNA00271 (NCBI:100131814)

Chromosome 6 Open Reading Frame 217 (HGNC:32526)

Non-Protein Coding RNA 271 (HGNC:32526)

Characteristics

Genomic location of C6orf217 and orientation with respect to adjacent AHI1 gene. (a) The purple and green arrows indicate AHI1 and C6orf217 orientation, respectively. Gene structure of AHI1 and C6orf217 are depicted in purple and green vertical lines respectively, indicating exon positions. Yellow circles and their connecting arrows point to the location of significant SNPs (after Bonferroni correction). Grey lines indicate the positions of all SNPs genotyped in this genomic region.(b) Haploview representation of SNPs and their LD (linkage disequilibrium) structure.[1]

C6orf217 is a primate specific gene located on chromosome 6q23 adjacent to AHI1 gene (Abelson Helper Integration Site 1) [2].The two genes appear in opposite orientations and their regulatory upstream regions overlap, which might affect their expression. It consists of 10 exons and has several alternatively splice isoforms but does not seem to encode a functional protein. [1].

Function

C6orf217 encodes a small protein with no known motif and may well function as a regulatory gene either at its mRNA or protein level [1]. In silico studies show that it may function as a regulatory RNA gene, and may be a regulator of an adjacent AHI1 gene or of other genes. Its Suppressive role is observed in many common cancer types including BRCA, LUAD, KIRP and HNSCC [2].

Expression

C6orf217 is expressed in brain, eye, kidney, testis, tongue, pancreas and lung during development as well as in the adult [1]. In a combined group of schizophrenia and bipolar disorder patients, there was increased expression of C6orf217 [2]. Also its expression was significantly downregulated in PTC (papillary thyroid cancer) compared with the level in the adjacent normal tissues [3].

Experiment Forward primer Reverse primer
qRT-PCR 5'-GCTATTGGTGGGAGGCTTCAG- 3' 5'-TGGGCTGGACTTAATGACTTGC- 3'[3]

Disease

  • bipolar disorder [2]
  • breast cancer [4]
  • head and neck cancers [4]
  • papillary thyroid cancer [3]
  • schizophrenia, SNPs within this gene is associated with susceptibility to schizophrenia [1]
  • type 2 diabetes [4]
  • virus infections [4]

Labs Working

  • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
  • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
  • Department of Psychology, Hebrew University and Sara Herzog Memorial Hospital, Jerusalem, Israel
  • Regional Mental Health Center, Taibe, Israel
  • Dr Kemal Hospital, Bethlehem, Palestinian Authority, Palestine
  • Department of Psychiatry, University of Bonn, Germany
  • Department of Biology, University of Milan, Milan, Italy
  • Dépt de Génétique Médicale, CHUV-UNIL, Lausanne, Switzerland
  • Biological Psychiatry Laboratory, Department of Psychiatry, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
  • Psychiatry Research Unit, Faculty of Health Sciences, Ben Gurion University of the Negev and Mental Health Center, Beer Sheva, Israel
  • Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
  • Department of Head and Neck Surgery, Fudan University Shanghai
  • Cancer Center, Shanghai, People’s Republic of China
  • Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
  • Institute of Biomedical Science, Shanghai Medical College, Fudan University, Shanghai, People’s Republic of China
  • Department of Biological Sciences, Charles E. Schmidt College of Science, Florida Atlantic University, USA

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Amann-Zalcenstein D, Avidan N, Kanyas K, Ebstein RP, Kohn Y, Hamdan A et al. AHI1, a pivotal neurodevelopmental gene, and C6orf217 are associated with susceptibility to schizophrenia[J]. European journal of human genetics . 2006,14:1111-1119.
  2. ↑ 2.0 2.1 2.2 2.3 Slonimsky A, Levy I, Kohn Y, Rigbi A, Ben-Asher E, Lancet D et al. Lymphoblast and brain expression of AHI1 and the novel primate-specific gene, C6orf217, in schizophrenia and bipolar disorder[J]. Schizophrenia Research. 2010, 120(1):159-166.
  3. ↑ 3.0 3.1 3.2 Ma B, Liao T, Wen D, Dong C, Zhou L, Yang S et al. Long intergenic non-coding RNA 271 is predictive of a poorer prognosis of papillary thyroid cancer[J]. Scientific Reports. 2016, 6:36973.
  4. ↑ 4.0 4.1 4.2 4.3 Delgado A P, Brandao P, Narayanan R. Diabetes associated genes from the dark matter of the human proteome[J]. MOJ proteomics & bioinform, 2014, 1(4): 00020.

Sequence

>gi|100131814|ref|NR_152845.1| Homo sapiens long intergenic non-protein coding RNA 271 (LINC00271), transcript variant 5, long non-coding RNA

000001 ATGGCGACCG ATGCGTCCCG CGCTCTAGGC GAAGACCGCG GCCCCGTCCC CGCGCCTCCA CCGCCTTCTT CCAGGAGGAG 000080
000081 GGGCCGTGCG GCGCCTGCCC GGGGGCCCTC AGGCCGCAGG CGGGCGCGAG CTTCAGGGAA CTTAGGGGGC TCCCGCCTCC 000160
000161 CCGGCCACGC GAGCGGGAAC AGTCTCCTCC ACTCGGAGCG CCACTCATCA TGCCTTACCT GGATGATGCA GAAGTCCCTG 000240
000241 GAAACAGAAG GTCTCACCCT TCTTTATCTT TCTCATGGCT TTCCAAGGCT CTTTATCATG TTACTTTCCT GCTCAGAATT 000320
000321 CTTTAATGAC TTGCCTCAAT GACCAGATAC ATGTGATCTA CAGTCAGCCT TCCAGCCTCA TCATTCCTCT TCCATTTCCT 000400
000401 CCCCAGAAAC ACTGTACTTT ATGAAGCTCC TCCAAGACAT TATAGATCCA GACTCCTGTG CCTGACCACT GCCCATGGCC 000480
000481 AACTCTCTGC TGATGACTGG ACTTGACTAC ACAAGTTGTT GGCCATCTTA AAACCACTCA AAGTTGACGG TCTCCTCTCC 000560
000561 TGCCTCCTGC GGCTTCCATT ACCATGGCAG AGACTGTGGT GTCTGAGGTG GTGTAGCGTA CTGAAGCAAG GCTGTCTTGA 000640
000641 AGAAGAGGAG ACAACTCACA ATTCTACCAC CTTTGTTGAC CTCTTCTTCC CCCCAACTTA TTGCTGTAGA GGCTACCTGA 000720
000721 GCTCATTGTC CCTGGAGATG GACCAAATAG AAGAATAAGC AGTGCCTGTG TGGTGAGCTT CAAGAGGCAT CTGTTCTCTG 000800
000801 GGGAGTGGGT GGGTGGTAAA GCAAAGACGG GAGATGTGTA TATTAGCTAT CCATTACTGT ATAATTAATT ATACACAAAA 000880
000881 CTAAACTATA CACTAAACTA AAACTTCACA GCTTAAAACA GGAAATATGT ATTATCTCAC ACAATTTCTG AGAGTCAGGA 000960
000961 ATCTGAAAAT GGCTTAGCTA GTTTGGTTCT GGCTCAGGGT GACCTATGGA GTTGCAGCCA AGATGTCATC TGGGACTACT 001040
001041 ATCATTGGAA GGCTCAGCTG GGGCTGGAGG CTACACTTCC AAGATGGCTC ACTTATAGGG CTATTGGTGG GAGGCTTCAG 001120
001121 TTCCTCTCCA CATGAAACTT TCCTCATGCC ATGGAACTGG CTTCCCTCAG AGTGAAAGAC CCAAGAGAGA GACTAAGACA 001200
001201 GAAGCTGCAA TGTTTTTATG ACCTAGTCTT GGAAGTGACT TACTGTCATT TCTACTGTAT TTTATTCATT AGAAGCAAGT 001280
001281 CATTAAGTCC AGCCCACATT CAAAGTAAGA GGATTTAAGC TGAACCTCTT GAAAAAATGG TATCAAAGTA TTTACGGACA 001360
001361 TTTTAAAAAC TACCACAATA CATATAGGTG AACTTCACAA GGTGTAGACA TGGGCTGAGA CAGAATATTG GATAATATCT 001440
001441 CATTCTGCAA ACAGCAGCCT CATCTGTAAT AAAATCCCAG CATTCAGAAA TTATCACGAT CAAGTAGGAA AAGGGCTTGT 001520
001521 TGGAAAAAAC TTATCAAAGA TGTTACTTCA TTTATCCATT TATTCTGAGC CATAGCATAA TAGCGACAAA TTGTGTGTCC 001600
001601 TGTGTAATTT GGATACCTCT GCTCAATAAT AGCTGAACAG ATTTTATCCT ATTTTTAGAA TAGTTAATAT ATACACATGG 001680
001681 CACAAAATTT AAAAGGTATA AAAGTTTCTG GTTCAAAAAT AAGATTCCCT CATTTTCTTT TTTTCTGATT CTTTGAATGC 001760
001761 AATTCGATTT ACTGATTTCT CATGTAGCCT TAGAAAGTAT TCTATGTACT TACAAACATA TATGTACACA TATTTTTTCT 001840
001841 TTCCCACAAA TAAAATACTG TATGCATTGT TTTA
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