Difference between revisions of "ENST00000417262.1"

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(Annotated Information)
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==Annotated Information==
 
==Annotated Information==
 
===Name===
 
===Name===
KDM5BAS1
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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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===Function===
 
===Function===
KDM5B-AS1 expression appears to stimulate KLHL12 gene expression (in HeLa cells). A gene located ~80kb from KDM5B-AS1 on the opposite strand.
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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===
Expressed in HeLa, K562 and GM12878 cells, plus a number of human tissues.
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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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You can also add sub-section(s) at will.
 
You can also add sub-section(s) at will.
 +
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
 
Please input related labs here.
 
Please input related labs here.

Revision as of 09:15, 24 June 2016

Please input one-sentence summary here.

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

Please input conservation information here.

Misc

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Transcriptomic Nomeclature

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Regulation

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Allelic Information and Variation

Please input allelic information and variation information here.

Evolution

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

Labs working on this lncRNA

Please input related labs here.

References

Annotation originally sourced from lncRNAdb..

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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  1. Cite error: Invalid <ref> tag; no text was provided for refs named ref1
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 Cite error: Invalid <ref> tag; no text was provided for refs named ref2