Difference between revisions of "ENST00000553157.1"

From LncRNAWiki
Jump to: navigation, search
(→‎Expression)
 
(2 intermediate revisions by one other user not shown)
Line 1: Line 1:
−
''PCAT6''
+
 
  
 
==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
−
''PCAT6'': prostate cancer associated transcript 6 (non-protein coding)
 
−
 
−
ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
 
  
 
===Characteristics===
 
===Characteristics===
−
 
  
 
===Function===
 
===Function===
−
[[File: ncRNA-a2.jpg|thumb|300px| ncRNA-a2 locus in HeLa cells. <ref name="ref1"/>]]
 
−
 
−
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===
Line 65: Line 32:
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
−
Please input related labs here.
 
  
 
==References==
 
==References==
−
<references>
 
−
<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)
 
−
 
−
<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)
 
−
</references>
 
  
 
{{basic|
 
{{basic|
 
tID = ENST00000553157.1|
 
tID = ENST00000553157.1|
 
source = Gencode19|
 
source = Gencode19|
−
same = lnc-RP11-480I12.4.1-1:2|
+
same = lnc-RP11-480I12.4.1-1:2|ENST00000425295.1|ENST00000417262.1
 
classification = intergenic|
 
classification = intergenic|
 
length = 551 nt|
 
length = 551 nt|

Latest revision as of 11:48, 30 June 2016


Annotated Information

Name

Characteristics

Function

Expression

Conservation

Please input conservation information here.

Misc

Please input misc information here.

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Regulation

Please input regulation information here.

Allelic Information and Variation

Please input allelic information and variation information here.

Evolution

Please input evolution information here.

You can also add sub-section(s) at will.

Labs working on this lncRNA

References

Basic Information

Transcript ID

ENST00000553157.1

Source

Gencode19

Same with

lnc-RP11-480I12.4.1-1:2

Classification

{{{classification}}}

Length

551 nt

Genomic location

chr1+:202780082..202781284

Exon number

2

Exons

202780082..202780498,202781151..202781284

Genome context

Sequence
000001 AGAGGCCGGA CCTGGGCAAC CCCAGCCTGG AGGTGCCGGG GCCGGAGCTC CCAGAGGGCT GGGTGCGAGG CCTAGGCGGG 000080
000081 GTCAGGTTCG GGTTCCTAGG CCATAGCGGA GCTGCAGCCC AGGCGGCCGG AGCGGAACCC AGCCCCGCTC CGAGTGCCAC 000160
000161 GTCTCCAGGA ACCCCCTCCT TACTCTTGGA CAACACTCCG CCCCCGCCCG GGCCTCCGTC CCCCAAACCG CCCTCATTTG 000240
000241 TGCAGCGCCA GATCCTTCGG ACACATCCCT AGGTGTCTCC ATCCTCATTC GGTCCATCCA ACTCCCAGAC CTCACGTCAA 000320
000321 CCGGCTGCAC CCCACTTTCC AGCCTGCGCC CCAGATCTGC AGCCTTCGCC CCTAGATACA CCCGCCTGGT GATGAGGCGC 000400
000401 TCCTCGCGTT CCTTCCGGCA CGTGGCACAC GCTCCACAAA TATTTGTTGA AAGGGAGGGT AAATGGCCTT GAGTTTCTGT 000480
000481 GGCTACCATT GGCTGAGGAT GGAGCTTTGG GCTGGACAAA GAAGAATCTG GTTGACCACA TGAAGCAGGA A
[back to top]
Retrieved from "https://ngdc.cncb.ac.cn/lncrnawiki1/index.php?title=ENST00000553157.1&oldid=1272194"