Difference between revisions of "ENST00000511918.1"
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''SCAL1'', "smoke and cancer associated lncRNA 1"<ref name="ref1" /> | ''SCAL1'', "smoke and cancer associated lncRNA 1"<ref name="ref1" /> | ||
| + | [[File:SCAL1 expression in CL1-0and CL1-5 cells and in nonsmokers and smokers.jpg|right|thumb|400px|'''SCAL1 expression in CL1-0and CL1-5 cells and in nonsmokers and smokers. '''<ref name="ref1" />]] | ||
===Characteristics=== | ===Characteristics=== | ||
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''LUCAT1'', a novel long noncoding RNA (lncRNA), which is located in chromosome 5 and encompass four exons and three introns, is induced by cigarette smoke extract (CSE) both in vitro and in vivo and is elevated in numerous lung cancer cell lines<ref name="ref1" />. | ''LUCAT1'', a novel long noncoding RNA (lncRNA), which is located in chromosome 5 and encompass four exons and three introns, is induced by cigarette smoke extract (CSE) both in vitro and in vivo and is elevated in numerous lung cancer cell lines<ref name="ref1" />. | ||
| − | + | [[File:SCAL1 siRNA knockdown potentiates smoke-induced toxicity in HBE1 cells.jpg|right|thumb|400px|'''SCAL1 siRNA knockdown potentiates smoke-induced toxicity in HBE1 cells.'''<ref name="ref1" />]] | |
===Function=== | ===Function=== | ||
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''LUCAT1'' may be a novel key downstream mediator of NRF2 in regulating the genes responsible for oxidative stress protection, which indicated that LUCAT1 plays a protective role in suppressing smoke-induced toxicity in airway epithelial cells. | ''LUCAT1'' may be a novel key downstream mediator of NRF2 in regulating the genes responsible for oxidative stress protection, which indicated that LUCAT1 plays a protective role in suppressing smoke-induced toxicity in airway epithelial cells. | ||
Revision as of 05:48, 30 June 2016
LUCAT1,a smoke and cancer–associated lncRNA, which regulated by NRF2,is induced by smoke and up-regulated in airways of smokers in many lung cancer cell lines and plays a functional role in mediating protection against cigarette smoke–induced toxicity.
Contents
Annotated Information
Name
LUCAT1: lung cancer associated transcript 1 (non-protein coding)(HGNC nomenclature)
SCAL1, "smoke and cancer associated lncRNA 1"[1]
SCAL1 expression in CL1-0and CL1-5 cells and in nonsmokers and smokers. [1]
Characteristics
LUCAT1, a novel long noncoding RNA (lncRNA), which is located in chromosome 5 and encompass four exons and three introns, is induced by cigarette smoke extract (CSE) both in vitro and in vivo and is elevated in numerous lung cancer cell lines[1].
SCAL1 siRNA knockdown potentiates smoke-induced toxicity in HBE1 cells.[1]
Function
LUCAT1 may be a novel key downstream mediator of NRF2 in regulating the genes responsible for oxidative stress protection, which indicated that LUCAT1 plays a protective role in suppressing smoke-induced toxicity in airway epithelial cells.
Regulation
The expression of SCAL1 is regulated transcriptionally by nuclear factor erythroid 2-related factor (NRF2)[1].
Disease
Lung cancer
Expression
Its expression is NRF2-dependent[1].
| siRNA | primer |
|---|---|
| human NRF2 | GTAAGAAGCCAGATGTTAAdtdt[1] |
| KEAP1 | GGGCGTGGCTGTCCTCAATdtdt[1] |
| SCAL1-1 | CCCACAAAUAGGAAGAAAAdtdt[1] |
| SCAL1-2 | CAUUUCAGUCACUAAAUAAdtdt[1] |
| RT-PCR | Forward Primer | Reverse Primer |
|---|---|---|
| SCAL1 | 5'-ACCAGCTGTCCCTCAGTGTTCT-3' | 5'-AGGCCTTTATCCTCGGGTTGCCT-3'[1] |
| NRF2 | 5'-ATTGAGCAAGTTTGGGAGGA-3' | 5'-AAGACACTGTAACTCAGGAATGGA-3'[1] |
| β-actin | 5'-GCGGGAAATCGTGCGTGACATT-3' | 5'-GATGGAGTTGAAGGTAGTTTCGTG-3'[1] |
Labs working on this lncRNA
- Center for Comparative Respiratory Biology and Medicine, Genome and Biomedical Science Facility, and Division of Pulmonary and Critical Care Medicine, School of Medicine, University of California at Davis, Davis, CA 95616, USA.[1]
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Thai P, Statt S, Chen CH, Liang E, Campbell C, Wu R. Characterization of a novel long noncoding RNA, SCAL1, induced by cigarette smoke and elevated in lung cancer cell lines[J]. American journal of respiratory cell and molecular biology. 2013,49(2):204-11.
Basic Information
| Transcript ID |
ENST00000511918.1 |
| Source |
Gencode19 |
| Same with |
lnc-ARRDC3-1:5,LUCAT1,SCAL1 |
| Classification |
intergenic |
| Length |
828 nt |
| Genomic location |
chr5-:90598846..90610200 |
| Exon number |
5 |
| Exons |
90598846..90598978,90599690..90599788,90608895..90609046,90609455..90609594,90609897..90610200 |
| Genome context |
|
| Sequence |
000001 CAATGCCCAG ACCTCCAGAA ACCATGTGTC AAGCTCGGAT TGCCTTAGAC AGGTGCAATT TAAGAACAGC TTTCATCCTC 000080
000081 TTTTCTCTCA TATTGTCACA CTATGTGTTC TGACTTCTGG CTCCTTTCCT CACAAGAAGC TCACCCAGCT GGAACTCTTA 000160 000161 TGGGACCTTG GCACCAGAGA CCACAAATTC CTCTTTGAAG TTTTCTAACA GCAACAATGG TATTTCTGAC TTGGCTTTCT 000240 000241 TGTATTTCTC TCACGTTAAC AAAATTGGTT CAGCATCTAC CATGGGCTAC ATGCTGAGCT ACAGAGTTTC GCTCTGTCGC 000320 000321 CCAGGCTGGA GTGCAGTGGC GCGCGATCTC GGTTCACTGC AAGCTCCACC TCCCGGGTTC ACGCCATTCT CCTGCCTCAG 000400 000401 CCTCCTGAGT AGCTGGGACT ACAGGCGCCC GCCACCACAC CCAGGAATCC AACTTGCTGT TTGCTATCAC ATGTGCTATA 000480 000481 CATGCTGTTG ATGAAACTGC TAAAGGGGCT GAATGTGACT GACGTCTTTG GAAGGATGAG ACTTAGCGTG CCTGTACAGT 000560 000561 TGTGTCCAAA TGCTGTCCTC ATCTCCCAAT GAAAAGGAAC AAAACCCATC AGAAGATGTC AGAAGATAAG GATTTTTGTC 000640 000641 CTGATGCTAC ACTTACCAGC TGTCCCTCAG TGTTCTACTT CTTAAAAAAA GAGAGATGGA TAAACAGAGG CAACCCGAGG 000720 000721 ATAAAGGCCT TGCTCAGTGT CACACATTTC AGTCACTAAA TAAGACACAA TGGATGCCAG TATTCTCATC CCCTCACAAA 000800 000801 TAAAGAGCCT TCAAGCTCTT GCAGTCAA |
Predicted Small Protein
| Name | ENST00000511918.1_smProtein_281:490 |
| Length | 70 |
| Molecular weight | 7712.9769 |
| Aromaticity | 0.130434782609 |
| Instability index | 56.4536231884 |
| Isoelectric point | 8.63775634766 |
| Runs | 9 |
| Runs residual | 0.0088965418281 |
| Runs probability | 0.0445347308093 |
| Amino acid sequence | MGYMLSYRVSLCRPGWSAVARDLGSLQAPPPGFTPFSCLSLLSSWDYRRPPPHPGIQLAV CYHMCYTCC |
| Secondary structure | LLEEEEEEEELLLLLHHHHHHHHLLLLLLLLLLLLHHHHLLLLLLLLLLLLLLLLEEEEE EEEEEEEEL |
| PRMN | - |
| PiMo | - |
