Difference between revisions of "NONHSAT130385"
Chunlei Yu (talk | contribs) |
Chunlei Yu (talk | contribs) (→Expression) |
||
| Line 23: | Line 23: | ||
The primer for qRT-PCR as follows: | The primer for qRT-PCR as follows: | ||
| + | |||
{|class=='wikitable' style="text-align:center" | {|class=='wikitable' style="text-align:center" | ||
|- | |- | ||
| Line 54: | Line 55: | ||
| | CCUGGUUGAGCUGAGGUCUUCAUAG<ref name="ref1" /> | | | CCUGGUUGAGCUGAGGUCUUCAUAG<ref name="ref1" /> | ||
|} | |} | ||
| − | |||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
Revision as of 16:32, 11 April 2015
MIR31HG, located at chromosome 9p21.3,transcribed from 4 exons resulting in a spliced transcript of ~2.2 kb and shows significant roles in breast tumorigenesis.
Contents
Annotated Information
Transcriptomic Nomeclature
MIR31HG: MIR31 host gene(HGNC nomenclature)
LOC554202[1]
Characteristics
The LOC554202 gene which does not contain an open reading frame is located at chromosome 9p21.3. LOC554202 is transcribed from 4 exons resulting in a spliced transcript of ~2.2 kb[1].
Function
Higher expression of Loc554202 in breast cancer tissues was associated with larger tumor size and a more advanced clinical stage, suggesting that the expression of Loc554202 could be used as a diagnostic and prognostic breast cancer marker[1].
Disease
- Breast cancer
Expression
Loc554202 is significantly increased compared with normal control, and associated with advanced pathologic stage and tumor size. Moreover, knockdown of Loc554202 decreased breast cancer cell proliferation, induced apoptosis and inhibits migration/invasion in vitro and impeded tumorigenesis in vivo[1].
LOC554202 is down-regulated in the TNBC cell lines of basal subtype and over-expressed in the luminal counterparts, CpG island methylation plays an important role in silencing of the LOC554202 genes[1].
The primer for qRT-PCR as follows:
| Primer | Forward Primer | Reverse Primer |
|---|---|---|
| GAPDH | 5'-AGAGGCAGGGATGATGTTCTG-3' | 5'-GACTCATGACCACAGTCCATGC-3'[1] |
| Loc554202 | 5'-TCTCTGGTGCTTCCCTCCTT-3' | 5'-GATCTAAGCTTGAGCCCCCA-3'[1] |
The target sequences for the si-LOC554202 included:
| si-RNA | Primer |
|---|---|
| si-Loc554202-1 | GCAGGUAGAGAUGGAUUCCUGGAAA[1] |
| si-LOC554202-2 | GGAGCGCUUUGUGUGAGAAGUUGAA[1] |
| si-LOC554202-3 | CCUGGUUGAGCUGAGGUCUUCAUAG[1] |
Labs working on this lncRNA
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical University, Nanjing, Jiangsu, PR China[1].
- Department of Molecular Cardiology, Cleveland Clinic, Cleveland, OH, USA[2].
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 Shi Y, Lu J, Zhou J, Tan X, He Y, Ding J, et al. Long non-coding RNA Loc554202 regulates proliferation and migration in breast cancer cells[J]. Biochemical and biophysical research communications. 2014,446(2):448-53.
- ↑ Augoff K, McCue B, Plow EF, Sossey-Alaoui K. miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer[J]. Molecular cancer. 2012,11:5.
Basic Information
| Transcript ID |
NONHSAT130385 |
| Source |
NONCODE4.0 |
| Same with |
LOC554202, MIR31HG |
| Classification |
intergenic |
| Length |
2148 nt |
| Genomic location |
chr9-:21454267..21559697 |
| Exon number |
4 |
| Exons |
21454267..21455943,21476898..21477034,21477168..21477291,21559488..21559697 |
| Genome context |
|
| Sequence |
000001 AGGTTCCACG TCCGGCGCCT GGAGAAGGAA GACGCGCGTC CCCGGCCGCG GCGCCGAAGC CGGCTGGGGG ACCGCCTGGT 000080
000081 CCCGGGCCAG AGCTGGGAGG CGGTGTTCCG TGAGCCGCCT GGTCTGGGGT GCGGGGGGCG GGAAGCGGCC CCTTCGTGTG 000160 000161 CGCTTGGGCG AGGCCGGGCG GCGCTTCTGT CCTCCTACTC GGACCCGCAG GTTTCTGGTC CTCATACCGT GTGGTTGAGT 000240 000241 GAAATCAAAA CTTCCACGAT AGCAATGCTG ATTGGACAAA GAATGTGTTG TGGACACAAA ACCAAACTCT GGAGGACAGA 000320 000321 GGATTCATTC CAAGGGTCTG CTTGTATTCA ATGACTGGTC TACGTGGGGG TGTGAAGTCC CCTTACTCCA CCTGTGAAGA 000400 000401 GTCTTCCCAG TTTCAGACCA CCCTCCCAGC CTCCTGTTAT TGGCTAAGGC CATTTTGTGA CTACACTGCA GGTAGAGATG 000480 000481 GATTCCTGGA AATACCTCCT CAAGGCCAGT GTAGAGCCCT CAATCACCCA CTGCCCCCAG CTTCTCCTTC TCCCATCTCC 000560 000561 TGCACCAAGC AGGTCTCCAG GTGTTCCAGC TGCTGATGAC GTAAAGTGTG GAGTTGGTCC AGGAAGGTCA TGTTCCATGC 000640 000641 AGCAGAGGAG CGCTTTGTGT GAGAAGTTGA AGACCTGCTG TAACACATCA TAGAGGAAAG ACATAGCCTG GGCCTTCTGC 000720 000721 AACTGGCTGA CTTCCACCTT CTCCTGGGGG AATCTGAAGT CACTTCTGTC CTTTAGACAC AAGAAGGGAG AGATTCTCCT 000800 000801 CATTTGGCCC AAAAGCACCA AGGTGTTCCT GCCTAGCAGG CCATGGTTCT GAGGCAGGTT ATATCCTAGA GATCCAGAAG 000880 000881 AGCCACAGCT GCACACCTCT AGGGCTGCCA GTAGAGGGAA GAGGAGGGCC ATTGAGAAAT CAGGATGCTT TTGGCCTGGT 000960 000961 TGAGCTGAGG TCTTCATAGA ACCTTGGATC CTAGGTTCTA TGAAGACATT CTATCTATGC ATGGCTTTAA TGGAGCACAA 001040 001041 ATAGTTTTCA TTTTTCTGAG CATTTCTCTA AATTTTTAAT TCCATTTATT GTTTTCATTT ACATGTCTTC TATATCAGCA 001120 001121 TCCACAACCT TTTGGCCACC AGTTTGGTGG AAGATAATTT TTCCACGAAA AATGGGGTCA GGGAGGGAAT GCTTTCAGAG 001200 001201 GCATTAGATT CTCATTAGGA GACCACAACC TAGATCCTTC GCATCTGCAC TTCACAATAG GGTTCCTGCT CTTTTGAGAA 001280 001281 TCCAATGCCA CTGCTGATCT GACAGGAGGC AGAGCTCAGG CGTTAATGCT TGTTGGTTGG CCTGCTTGCC TCCTGCTGTG 001360 001361 CGGCCCTGTT CCTACCAGGC CAGGACCAGT ACCCCGGTCC ATGGATGGGG GTTGAAAAAC CTTGTTCTAT ATGACCTAAA 001440 001441 AGGAGGTCAT CACTCTACAC TCTTGATTTT TGCAATGGAT GTTCAATATT CCCAGTAAAC TTAAGATATA TCAATCCAAA 001520 001521 TGAATATTGA TCAATCAGAT GAGAAACATC TTTGTGCTAC TGTTAGAAGT ATATACTTTT AGCCCAGATC CTAGCCTCCA 001600 001601 GTTTTACCCT CCATTTTGCA TAGGAAATCA GGATCCCTGG GCCCTATGGG TTTCTGTATT CAGTTAGGAA ATTACCTATC 001680 001681 TCTGGAAATT AAACTTTTTA GGACTATCTT TGTTTGATAT TTGATTCACA GAAGACGTTG ATGGTTATTA GTGAAAGAAC 001760 001761 TTCTCTGGTG CTTCCCTCCT TCTAGAATAT ATTCATTCAG GTTCATGTGG TTATGCTTCC CTGGGGGCTC AAGCTTAGAT 001840 001841 CAATGAACAT TGCCTTTTTT GCATTATTTT CTTACTGGAG AAATATAGCA CTCCTCAGGC TGCGCCAATA CCCCTAAAAG 001920 001921 AAATTCTGTT GGTTTGTTTT TTTTTCTTTT TTAAGATGCA TATGGGTGTG GAAATTTTAA TCTTAAAATA ATGTTATTTC 002000 002001 CTCAGCAGTG ATGATTCACA AGGTATTTAT CACATCAAGT CACTCCCTAA ATGCAGGCTC ACCACATCCT GATGACTTTA 002080 002081 GAACTCCTTT TCCAGGGAGG TTCTTGCTTC TTTGTTGCCA AAACAATAAA TCCTTTGTGA CCTTTGTC |
