Difference between revisions of "PCAT6"

From LncRNAWiki
Jump to: navigation, search
(Created page with "==Annotated Information== ===Approved Symbol=== PCAT6 ===Approved Name=== prostate cancer associated transcript 6 (non-protein coding) ===Previous Symbols=== KDM5B-AS1 ===Syno...")
 
Line 1: Line 1:
 
==Annotated Information==
 
==Annotated Information==
−
===Approved Symbol===
+
===Name===
−
PCAT6
+
''PCAT6'': prostate cancer associated transcript 6 (non-protein coding)
−
===Approved Name===
+
 
−
prostate cancer associated transcript 6 (non-protein coding)
 
−
===Previous Symbols===
 
−
KDM5B-AS1
 
−
===Synonyms===
 
 
ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
 
ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96
−
===Chromosome===
+
 
−
1q32.1
+
===Characteristics===
−
===RefSeq ID===
+
 
−
NR_046325
+
 
−
===OMIM ID===
+
===Function===
−
_
+
[[File: ncRNA-a2.jpg|thumb|300px| ncRNA-a2 locus in HeLa cells. <ref name="ref1"/>]]
−
===Ensembl ID===
+
 
−
ENSG00000228288
+
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" />.
−
===pubmed IDs===
+
 
−
20887892, 23728290
+
===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===
 +
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==
 +
* Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain <ref name="ref1" />
 +
 
 +
 
 +
* Center for Functional Cancer Epigeneitcs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA <ref name="ref2" />
 +
 
 +
==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>
 +
 
 
===Sequence===
 
===Sequence===
 
>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA
 
>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA
 
<dnaseq>GACGCCCCAGAGGCCGGACCTGGGCAACCCCAGCCTGGAGGTGCCGGGGCCGGAGCTCCCAGAGGGCTGGGTGCGAGGCCTAGGCGGGGTCAGGTTCGGGTTCCTAGGCCATAGCGGAGCTGCAGCCCAGGCGGCCGGAGCGGAACCCAGCCCCGCTCCGAGTGCCACGTCTCCAGGAACCCCCTCCTTACTCTTGGACAACACTCCGCCCCCGCCCGGGCCTCCGTCCCCCAAACCGCCCTCATTTGTGCAGCGCCAGATCCTTCGGACACATCCCTAGGTGTCTCCATCCTCATTCGGTCCATCCAACTCCCAGACCTCACGTCAACCGGCTGCACCCCACTTTCCAGCCTGCGCCCCAGATCTGCAGCCTTCGCCCCTAGATACACCCGCCTGGTGATGAGGCGCTCCTCGCGTTCCTTCCGGGCTCCAGGTGTCCGTGAGCCTCCCTTCCGCCCTGGCCTCCGGTCTCTGCCTTGCTCGTGCTTCTACCACCACCCTTCCCCTCCCAACCCGGTGGATCCTCTCGTCTCCCCCAGTCTCCAGTGCACCGGCTTTCCCTCGTCCTCTGCGCAGTCCATCTCAGCTCATCTCTCCAATTCAATGCCATCATCTCTCCTCACCATCTCTCGGTGCCCTGGAATGTTTGCTGTCAGATGTCCCCTGTGAAACCCACAAACGCTTGCGATTTGGCCTCCTTGTTTTATTTTGTGTAGTCCTACAACGTCTTGTTACTACCCCCTATTACAACACTTATAACTCAG</dnaseq>
 
<dnaseq>GACGCCCCAGAGGCCGGACCTGGGCAACCCCAGCCTGGAGGTGCCGGGGCCGGAGCTCCCAGAGGGCTGGGTGCGAGGCCTAGGCGGGGTCAGGTTCGGGTTCCTAGGCCATAGCGGAGCTGCAGCCCAGGCGGCCGGAGCGGAACCCAGCCCCGCTCCGAGTGCCACGTCTCCAGGAACCCCCTCCTTACTCTTGGACAACACTCCGCCCCCGCCCGGGCCTCCGTCCCCCAAACCGCCCTCATTTGTGCAGCGCCAGATCCTTCGGACACATCCCTAGGTGTCTCCATCCTCATTCGGTCCATCCAACTCCCAGACCTCACGTCAACCGGCTGCACCCCACTTTCCAGCCTGCGCCCCAGATCTGCAGCCTTCGCCCCTAGATACACCCGCCTGGTGATGAGGCGCTCCTCGCGTTCCTTCCGGGCTCCAGGTGTCCGTGAGCCTCCCTTCCGCCCTGGCCTCCGGTCTCTGCCTTGCTCGTGCTTCTACCACCACCCTTCCCCTCCCAACCCGGTGGATCCTCTCGTCTCCCCCAGTCTCCAGTGCACCGGCTTTCCCTCGTCCTCTGCGCAGTCCATCTCAGCTCATCTCTCCAATTCAATGCCATCATCTCTCCTCACCATCTCTCGGTGCCCTGGAATGTTTGCTGTCAGATGTCCCCTGTGAAACCCACAAACGCTTGCGATTTGGCCTCCTTGTTTTATTTTGTGTAGTCCTACAACGTCTTGTTACTACCCCCTATTACAACACTTATAACTCAG</dnaseq>

Revision as of 11:46, 30 June 2016

Annotated Information

Name

PCAT6: prostate cancer associated transcript 6 (non-protein coding)

ncRNA-a2, PCAN-R1, KDM5BAS1, onco-lncRNA-96

Characteristics

Function

ncRNA-a2 locus in HeLa cells. [1]

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

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

  • Centre for Genomic Regulation (CRG), UPF, Barcelona, Spain [1]


  • Center for Functional Cancer Epigeneitcs, Dana-Farber Cancer Institute, Boston, Massachusetts, USA [2]

References

  1. ↑ 1.0 1.1 1.2 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. ↑ 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.

Sequence

>gi|375268763|ref|NR_046325.1| Homo sapiens prostate cancer associated transcript 6 (non-protein coding) (PCAT6), transcript variant 1, long non-coding RNA

000001 GACGCCCCAG AGGCCGGACC TGGGCAACCC CAGCCTGGAG GTGCCGGGGC CGGAGCTCCC AGAGGGCTGG GTGCGAGGCC 000080
000081 TAGGCGGGGT CAGGTTCGGG TTCCTAGGCC ATAGCGGAGC TGCAGCCCAG GCGGCCGGAG CGGAACCCAG CCCCGCTCCG 000160
000161 AGTGCCACGT CTCCAGGAAC CCCCTCCTTA CTCTTGGACA ACACTCCGCC CCCGCCCGGG CCTCCGTCCC CCAAACCGCC 000240
000241 CTCATTTGTG CAGCGCCAGA TCCTTCGGAC ACATCCCTAG GTGTCTCCAT CCTCATTCGG TCCATCCAAC TCCCAGACCT 000320
000321 CACGTCAACC GGCTGCACCC CACTTTCCAG CCTGCGCCCC AGATCTGCAG CCTTCGCCCC TAGATACACC CGCCTGGTGA 000400
000401 TGAGGCGCTC CTCGCGTTCC TTCCGGGCTC CAGGTGTCCG TGAGCCTCCC TTCCGCCCTG GCCTCCGGTC TCTGCCTTGC 000480
000481 TCGTGCTTCT ACCACCACCC TTCCCCTCCC AACCCGGTGG ATCCTCTCGT CTCCCCCAGT CTCCAGTGCA CCGGCTTTCC 000560
000561 CTCGTCCTCT GCGCAGTCCA TCTCAGCTCA TCTCTCCAAT TCAATGCCAT CATCTCTCCT CACCATCTCT CGGTGCCCTG 000640
000641 GAATGTTTGC TGTCAGATGT CCCCTGTGAA ACCCACAAAC GCTTGCGATT TGGCCTCCTT GTTTTATTTT GTGTAGTCCT 000720
000721 ACAACGTCTT GTTACTACCC CCTATTACAA CACTTATAAC TCAG
Retrieved from "https://ngdc.cncb.ac.cn/lncrnawiki1/index.php?title=PCAT6&oldid=1272190"