Difference between revisions of "ENST00000556013.2"
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===Characteristics=== | ===Characteristics=== | ||
| − | ''PTCSC3'' consists of 4 exons with a total length of 1152 bp, located on a human chromosome 14q13.3 in a linkage disequilibrium block with a GWAS-derived SNP (rs944289) <ref name="ref1" />. | + | [[File:PTCSC3.jpg|right|thumb|400px|'''''PTCSC3'' structure with promoter region.''' PTCSC3 consists of four exons ORF predicting a 95-amino acid peptide starting in exon 1 and ending in exon 4. The SNP rs944289 is located 3.2 kb upstream of exon 1; rs944289 is located within a C/EBPα and C/EBPβ transcription factor binding site, and the risk allele destroys it (in silico). The full transcript sequence of PTCSC3 (1154 bp) is shown. The ORF is marked in green, and the polyA tail signal sequence (AATAAA) and polyA tail are marked in blue. <ref name="ref1" />]] |
| + | ''PTCSC3'' consists of 4 exons with a total length of 1152 bp, located on a human chromosome 14q13.3 and spanning more than 40 kb of genomic region in a linkage disequilibrium block with a GWAS-derived SNP (rs944289) <ref name="ref1" />. | ||
===Function=== | ===Function=== | ||
Revision as of 05:36, 16 November 2018
PTCSC3, shorted for papillary thyroid carcinoma susceptibility candidate 3, is involved in Papillary thyroid carcinoma.
Contents
Annotated Information
Name
PTCSC3: Papillary thyroid carcinoma susceptibility candidate 3 (HGNC nomenclature)
Characteristics
PTCSC3 consists of 4 exons with a total length of 1152 bp, located on a human chromosome 14q13.3 and spanning more than 40 kb of genomic region in a linkage disequilibrium block with a GWAS-derived SNP (rs944289) [1].
Function
PTCSC3 expression is highly thyroid specific suggests that it is involved in thyroid function [1]. overexpression of PTCSC3 significantly downregulates miR-574-5p expression in thyroid cancer cells that are of papillary, follicular and anaplastic origin [2].
PTCSC3 expression is significantly down-regulated in tumor compared with unaffected thyroid tissue, and the risk allele is associated with significantly stronger suppression of PTCSC3. The restoration of PTCSC3 expression in PTC cell line affects genes involved in thyroid tumorigenesis and inhibits cell growth [1].
rs944289 predisposes to PTC by dysregulating the expression of PTCSC3, which acts as a tumor suppressor[1].
Diseases
- Papillary thyroid carcinoma (PTC) [1]
Regulation
C/EBPα and C/EBPβ regulate the transcriptional activity of the PTCSC3 promoter [1].
Expression
PTCSC3 is almost uniquely expressed in thyroid tissue with very low expression additionally in kidney tissue[1].
The cDNA of PTCSC3 was amplified by PCR,
| Primer | Experiment | Forward | Reverse |
|---|---|---|---|
| PTCSC3 | PCR | 5'-GTACGGTACCCTCCTTCAGACTTCTCAGTACTC-3' | 5'-CGACTCGAGATTGCTACTGTGAGCATAACCTAC-3'[2] |
| PTCSC3 | RT-PCR | 5'-TCAAACTCCAGGGCTTGAAC-3' | 5'-ATTACGGCTGGGTCTACCT-3'[2] |
| PTCSC3 | Quantitative RT-PCR | 5'-TCAAACTCCAGGGCTTGAAC-3' | 5'-ATTACGGCTGGGTCTACCT-3'[2] |
| PTCSC3 | PCR | 5'-gtacggtaccCTCCTTCAGACTTCTCAGTACTC-3' | 5'-tcgactcgagATTGCTACTGTGAGCATAACCTAC-3'[1] |
| rs944289 | PCR | 5'-atcaggtaccGGCAATTGAAGTTCCCAAAA-3' | 5'-atcactcgagGCCTCCAGACTTGGACTGAG-3'[1] |
Labs working on this lncRNA
- Human Cancer Genetics Program, Comprehensive Cancer Center, The Ohio State University, Columbus.[1]
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha 410008, China.[2]
- Department of Geriatrics, Xiangya Second Hospital, Central South University, Changsha 410011, P.R. China.[2]
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Jendrzejewski J, He H, Radomska HS, Li W, Tomsic J, Liyanarachchi S, et al. The polymorphism rs944289 predisposes to papillary thyroid carcinoma through a large intergenic noncoding RNA gene of tumor suppressor type[J]. Proceedings of the National Academy of Sciences of the United States of America. 2012,109(22):8646-51.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 Fan M, Li X, Jiang W, Huang Y, Li J & Wang Z. A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells[J]. Experimental and therapeutic medicine. 2013, 5(4):1143-1146.
Basic Information
| Transcript ID |
ENST00000556013.2 |
| Source |
Gencode19 |
| Same with |
PTCSC3, |
| Classification |
intergenic |
| Length |
571 nt |
| Genomic location |
chr14-:36605314..36645674 |
| Exon number |
4 |
| Exons |
36605314..36605562,36623010..36623100,36631830..36631889,36645504..36645674 |
| Genome context |
|
| Sequence |
000001 GAAAGAGGAA AAAAGTGATC TGGGACCTGT TGTTTTTCTT GCATCCCATT TCTACTCTGC CTGTGAGTGA AGACTGTTGT 000080
000081 GGAAAAGTCA ACTGGAGAGA CCAGGTCAAA GGCCAAGCAG AAGAGGAATT AGGCTTAAGA CTGCACTGAG AGGGAACACT 000160 000161 AGACCATGGT GGCAAAATGG CCGAATAGGA GCAGCTCCAG TCTACAGCTC CCAGGGAGAT TAATGCAAAA GATGGAGTCT 000240 000241 CGACACGTTG CCCAAGCTGT TCTCAAACTC CAGGGCTTGA ACAATCTTCC CACCTTGGCC TCCCAAGGCA CTGGAATTAC 000320 000321 AGAGACAGTG CTCTGCAGGG AGTCTACCAC TGTGATGGTT AATACTGAGT GTCAACTTGA TTGGATTGAA GGATGCAAAG 000400 000401 TATTGTTCCT GGGTGTGTCT GTGAGGGTGT TGCCAAAGGA GATTAACATT TGAGTCAGTG GGCTGGGAAA GGTAGACCCA 000480 000481 GCCGTAATCT AGGTGGGCAC CATCTAATCA GCTGCCAGCA CAGCTAGAAG ATAAAGTAGG CAGAAAAACA TGAAAACATT 000560 000561 AGACTGGCCT A |
