Difference between revisions of "ENST00000417262.1"
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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 10: | ||
===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=== | ||
| Line 33: | Line 61: | ||
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.
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
Please input conservation information here.
Misc
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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
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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 |
