ENST00000417262.1
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Contents
Annotated Information
Name
PCAT6: prostate cancer associated transcript 6 (non-protein coding) ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
Characteristics
Spliced two exon transcript. Multiple splice variants, ~550- ~750 nt in length, second exon varies. Expressed bidirectionally with KDM5B. In-vitro translation showed no sign of protein product.
Function
With the depletion of ncRNA-a2, the KLHL12, a gene known for its negative regulation of the Wnt-beta catenin pathway, displayed a significant reduction [1].
Expression
PCAN-R1 showed positive correlation between gene expression and SCNA. [2]
PCAN-R1, while one isoform PCAN-R1-A was almost identical to the Ensembl annotated transcript ENST00000425295, the other isoform PCAN-R1-B was a spliced variant of PCAN-R1-A with an intron retention. [2]
PCAN-R1 and its neighboring PCG KDM5B showed the highest expression in normal testis. [2]
| Primer | Forward primer | Reverse primer |
|---|---|---|
| RT-PCR | 5′-CAGGAACCCCCTCCTTACTC-3 | 5′-CTAGGGATGTGTCCGAAGGA-3′[2] |
| RACE and northern blot analysis | 5′-GACCTGGGCAACCCCAGCCTG-3′ | 5′-GATCACTAATACGACTCACTATAGGGCGCGAGGAGCGCCTCATCACC-3′[2] |
| RNA interference | siR1-1 | 5′-GGTGTCTCCATCCTCATTC-3′[2] |
| siR1-2 | 5′-CTCCCAGACCTCACGTCAA-3′[2] |
Conservation
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Misc
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Transcriptomic Nomeclature
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Regulation
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Allelic Information and Variation
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Evolution
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Labs working on this lncRNA
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References
- ↑ Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long noncoding RNAs with enhancer-like function in human cells[J]. Cell. 2010,143(1):46-58.
- ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Du Z, Fei T, Verhaak RG, Su Z, Zhang Y, Brown M, et al. Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer[J]. Nature structural & molecular biology. 2013,20(7):908-13.
Basic Information
| Transcript ID |
ENST00000417262.1 |
| Source |
Gencode19 |
| Same with |
lnc-RP11-480I12.4.1-1:3 |
| Classification |
intergenic |
| Length |
748 nt |
| Genomic location |
chr1+:202780090..202781041 |
| Exon number |
2 |
| Exons |
202780090..202780498,202780703..202781041 |
| Genome context |
|
| Sequence |
000001 GACCTGGGCA ACCCCAGCCT GGAGGTGCCG GGGCCGGAGC TCCCAGAGGG CTGGGTGCGA GGCCTAGGCG GGGTCAGGTT 000080
000081 CGGGTTCCTA GGCCATAGCG GAGCTGCAGC CCAGGCGGCC GGAGCGGAAC CCAGCCCCGC TCCGAGTGCC ACGTCTCCAG 000160 000161 GAACCCCCTC CTTACTCTTG GACAACACTC CGCCCCCGCC CGGGCCTCCG TCCCCCAAAC CGCCCTCATT TGTGCAGCGC 000240 000241 CAGATCCTTC GGACACATCC CTAGGTGTCT CCATCCTCAT TCGGTCCATC CAACTCCCAG ACCTCACGTC AACCGGCTGC 000320 000321 ACCCCACTTT CCAGCCTGCG CCCCAGATCT GCAGCCTTCG CCCCTAGATA CACCCGCCTG GTGATGAGGC GCTCCTCGCG 000400 000401 TTCCTTCCGG GCTCCAGGTG TCCGTGAGCC TCCCTTCCGC CCTGGCCTCC GGTCTCTGCC TTGCTCGTGC TTCTACCACC 000480 000481 ACCCTTCCCC TCCCAACCCG GTGGATCCTC TCGTCTCCCC CAGTCTCCAG TGCACCGGCT TTCCCTCGTC CTCTGCGCAG 000560 000561 TCCATCTCAG CTCATCTCTC CAATTCAATG CCATCATCTC TCCTCACCAT CTCTCGGTGC CCTGGAATGT TTGCTGTCAG 000640 000641 ATGTCCCCTG TGAAACCCAC AAACGCTTGC GATTTGGCCT CCTTGTTTTA TTTTGTGTAG TCCTACAACG TCTTGTTACT 000720 000721 ACCCCCTATT ACAACACTTA TAACTCAG |
