Difference between revisions of "ENST00000417262.1"

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==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
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''PCAT6'': prostate cancer associated transcript 6 (non-protein coding)
 
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ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
 
  
 
===Characteristics===
 
===Characteristics===
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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===
 
===Function===
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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" />.
 
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===Expression===
 
===Expression===
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PCAN-R1 showed positive correlation between gene expression and SCNA. <ref name="ref2" />
 
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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" />
 
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PCAN-R1 and its neighboring PCG KDM5B showed the highest expression in normal testis. <ref name="ref2" />
 
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{| class='wikitable' style="text-align:center"
 
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|-
 
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! | Primer
 
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! | Forward primer
 
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! | Reverse primer
 
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|-
 
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| rowspan="1"|RT-PCR
 
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| | 5′-CAGGAACCCCCTCCTTACTC-3
 
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| | 5′-CTAGGGATGTGTCCGAAGGA-3′<ref name="ref2" />
 
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|-
 
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| rowspan="1"|RACE and northern blot analysis
 
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| | 5′-GACCTGGGCAACCCCAGCCTG-3′
 
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| |  5′-GATCACTAATACGACTCACTATAGGGCGCGAGGAGCGCCTCATCACC-3′<ref name="ref2" />
 
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|-
 
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| rowspan="2"|RNA interference
 
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| | siR1-1
 
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| | 5′-GGTGTCTCCATCCTCATTC-3′<ref name="ref2" />
 
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|-
 
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| | siR1-2
 
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| | 5′-CTCCCAGACCTCACGTCAA-3′<ref name="ref2" />
 
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|}
 
  
 
===Conservation===
 
===Conservation===
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==References==
 
==References==
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<references>
 
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<ref name="ref1">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.</ref>(1)
 
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<ref name="ref2">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.</ref>(2)
 
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</references>
 
  
 
{{basic|
 
{{basic|

Latest revision as of 11:49, 30 June 2016

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Annotated Information

Name

Characteristics

Function

Expression

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

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
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