Difference between revisions of "ENST00000425295.1"
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==Annotated Information== | ==Annotated Information== | ||
===Name=== | ===Name=== | ||
| − | KDM5BAS1 | + | ''PCAT6'': prostate cancer associated transcript 6 (non-protein coding) |
| + | |||
| + | ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96 | ||
===Characteristics=== | ===Characteristics=== | ||
| Line 9: | Line 11: | ||
===Function=== | ===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 <ref name="ref1" />. | |
===Expression=== | ===Expression=== | ||
| − | + | PCAN-R1 showed positive correlation between gene expression and SCNA. <ref name="ref2" /> | |
| + | |||
| + | 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. <ref name="ref2" /> | ||
| + | |||
| + | PCAN-R1 and its neighboring PCG KDM5B showed the highest expression in normal testis. <ref name="ref2" /> | ||
| + | |||
| + | {| class='wikitable' style="text-align:center" | ||
| + | |- | ||
| + | ! | Primer | ||
| + | ! | Forward primer | ||
| + | ! | Reverse primer | ||
| + | |- | ||
| + | | rowspan="1"|RT-PCR | ||
| + | | | 5′-CAGGAACCCCCTCCTTACTC-3 | ||
| + | | | 5′-CTAGGGATGTGTCCGAAGGA-3′<ref name="ref2" /> | ||
| + | |- | ||
| + | | rowspan="1"|RACE and northern blot analysis | ||
| + | | | 5′-GACCTGGGCAACCCCAGCCTG-3′ | ||
| + | | | 5′-GATCACTAATACGACTCACTATAGGGCGCGAGGAGCGCCTCATCACC-3′<ref name="ref2" /> | ||
| + | |- | ||
| + | | rowspan="2"|RNA interference | ||
| + | | | siR1-1 | ||
| + | | | 5′-GGTGTCTCCATCCTCATTC-3′<ref name="ref2" /> | ||
| + | |- | ||
| + | | | siR1-2 | ||
| + | | | 5′-CTCCCAGACCTCACGTCAA-3′<ref name="ref2" /> | ||
| + | |} | ||
===Conservation=== | ===Conservation=== | ||
Revision as of 09:22, 24 June 2016
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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
- Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain [1]
- Center for Functional Cancer Epigeneitcs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA [2]
References
- ↑ 1.0 1.1 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 2.7 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 |
ENST00000425295.1 |
| Source |
Gencode19 |
| Same with |
lnc-RP11-480I12.4.1-1:4 |
| Classification |
intergenic |
| Length |
634 nt |
| Genomic location |
chr1+:202780090..202781041 |
| Exon number |
2 |
| Exons |
202780090..202780498,202780817..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 TTCCTTCCGT CTCCAGTGCA CCGGCTTTCC CTCGTCCTCT GCGCAGTCCA TCTCAGCTCA TCTCTCCAAT TCAATGCCAT 000480 000481 CATCTCTCCT CACCATCTCT CGGTGCCCTG GAATGTTTGC TGTCAGATGT CCCCTGTGAA ACCCACAAAC GCTTGCGATT 000560 000561 TGGCCTCCTT GTTTTATTTT GTGTAGTCCT ACAACGTCTT GTTACTACCC CCTATTACAA CACTTATAAC TCAG |
