Difference between revisions of "NONHSAT128494"
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===Characteristics === | ===Characteristics === | ||
| − | ~300 nucleotide, nonpolyadenylated, RNAP III transcript. | + | ~300 nucleotide, nonpolyadenylated, RNAP III transcript. SINE (short interspersed nucleotide element - AluJb). 21A lacks the Alu-specific intragenic consensus elements needed to promote its pol III transcription such as the blocks A and B, which points to transcription driven by an extragenic type 3 pol III promoter.<ref name="ref1" /> |
| − | |||
| − | SINE (short interspersed nucleotide element - AluJb). 21A lacks the Alu-specific intragenic consensus elements needed to promote its pol III transcription such as the blocks A and B, which points to transcription driven by an extragenic type 3 pol III promoter. | ||
| − | Very low free energy (deltaG) value (deltaG < -100) indicating strong secondary structure. | + | Very low free energy (deltaG) value (deltaG < -100) indicating strong secondary structure.<ref name="ref1" /> |
===Expression=== | ===Expression=== | ||
| − | Nuclear localisation. Detected in tested cultured cells such as HeLa and skin fibroblast cells. | + | Nuclear localisation. Detected in tested cultured cells such as HeLa and skin fibroblast cells.<ref name="ref1" /> |
| − | The level of 21A transcription was very low in three immortalized, fully proliferating cell lines (HeLa, 293T, and LAN5) compared to unproliferating/resting PBL (peripheral blood lymphocyte) cells. Similarly, the 21A RNA level in primary skin fibroblasts was higher than in 293T cells, reinforcing an inverse correlation between endogenous 21A expression and cell proliferation. | + | The level of 21A transcription was very low in three immortalized, fully proliferating cell lines (HeLa, 293T, and LAN5) compared to unproliferating/resting PBL (peripheral blood lymphocyte) cells. Similarly, the 21A RNA level in primary skin fibroblasts was higher than in 293T cells, reinforcing an inverse correlation between endogenous 21A expression and cell proliferation.<ref name="ref1" /> |
===Regulation=== | ===Regulation=== | ||
| Line 19: | Line 17: | ||
===Function === | ===Function === | ||
| − | * | + | * 21A is one of a number of RNAP III-transcribed short ncRNAs that have sequence complementarity to protein-coding genes, possibly acting as as a natural trans-chromosomal antisense RNA. Aligned to the human genome, it shows several homology hits, among which the most highly significant were associated to multiple intronic regions of centromeric protein F gene (CENP-F). In vitro over-expression of 21AS transcripts inhibits CENP-F protein accumulation and decreased levels of CENP-F mRNA, indicating that 21AS regulates CENP-F expression in trans.<ref name="ref1" /> |
| − | * 21A RNAs has a role in the control of the proliferation of human tumor cell lines, possibly via regulation of CENP-F expression. This effect was not observed in a mouse cell line. | + | * 21A RNAs has a role in the control of the proliferation of human tumor cell lines, possibly via regulation of CENP-F expression. This effect was not observed in a mouse cell line.<ref name="ref1" /> |
===Disease=== | ===Disease=== | ||
| Line 30: | Line 28: | ||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
| − | + | * Dipartimento di Oncologia Biologia e Genetica, Università di Genova, Genoa, Italy <ref name="ref1" /> | |
==References== | ==References== | ||
| + | <references> | ||
| + | <ref name="ref1"> Pagano A, Castelnuovo M, Tortelli F, Ferrari R, Dieci G, Cancedda R. New small | ||
| + | nuclear RNA gene-like transcriptional units as sources of regulatory transcripts. | ||
| + | PLoS Genet. 2007 Feb 2;3(2):e1. Epub 2006 Nov 20. | ||
| + | </ref>(1) | ||
| + | </references> | ||
| + | |||
[http://www.lncrnadb.org/21A/ Annotation originally sourced from lncRNAdb]. | [http://www.lncrnadb.org/21A/ Annotation originally sourced from lncRNAdb]. | ||
Latest revision as of 06:43, 27 March 2018
Contents
Annotated Information
Name
21A
Characteristics
~300 nucleotide, nonpolyadenylated, RNAP III transcript. SINE (short interspersed nucleotide element - AluJb). 21A lacks the Alu-specific intragenic consensus elements needed to promote its pol III transcription such as the blocks A and B, which points to transcription driven by an extragenic type 3 pol III promoter.[1]
Very low free energy (deltaG) value (deltaG < -100) indicating strong secondary structure.[1]
Expression
Nuclear localisation. Detected in tested cultured cells such as HeLa and skin fibroblast cells.[1]
The level of 21A transcription was very low in three immortalized, fully proliferating cell lines (HeLa, 293T, and LAN5) compared to unproliferating/resting PBL (peripheral blood lymphocyte) cells. Similarly, the 21A RNA level in primary skin fibroblasts was higher than in 293T cells, reinforcing an inverse correlation between endogenous 21A expression and cell proliferation.[1]
Regulation
Please input regulation information here.
Function
- 21A is one of a number of RNAP III-transcribed short ncRNAs that have sequence complementarity to protein-coding genes, possibly acting as as a natural trans-chromosomal antisense RNA. Aligned to the human genome, it shows several homology hits, among which the most highly significant were associated to multiple intronic regions of centromeric protein F gene (CENP-F). In vitro over-expression of 21AS transcripts inhibits CENP-F protein accumulation and decreased levels of CENP-F mRNA, indicating that 21AS regulates CENP-F expression in trans.[1]
- 21A RNAs has a role in the control of the proliferation of human tumor cell lines, possibly via regulation of CENP-F expression. This effect was not observed in a mouse cell line.[1]
Disease
Please input disease information here.
Evolution
Please input evolution information here.
Labs working on this lncRNA
- Dipartimento di Oncologia Biologia e Genetica, Università di Genova, Genoa, Italy [1]
References
Annotation originally sourced from lncRNAdb.
Basic Information
| Transcript ID |
NONHSAT128494 |
| Source |
NONCODE4.0 |
| Same with |
, |
| Classification |
intergenic |
| Length |
324 nt |
| Genomic location |
chr8-:123704461..123704784 |
| Exon number |
1 |
| Exons |
123704461..123704784 |
| Genome context |
|
| Sequence |
000001 AAATAGTTGA CCAAGTGTGG TGGCTCACGT AGTCCCAGCA CTTTGGGAGG CTGAGGCAGG AGGATCACTT GAGCCCAGGA 000080
000081 ATTTGAGACC AGCTTGGGCA ACATAGTGAG ACCTCATCTC TTAAAAAAAA AAATTAGCTG GGTGTGGTAG TGCACACCTG 000160 000161 TGGTCCCAGC TACTTTAGAG GCTGAGGTAG AGGATTGCTT GAGCCTGGGA AGTTGGGGCT GTAGTGAGCT TTGATTGCAT 000240 000241 CACTGCACTC CAGCCTGGGT GACAGAGCAA GACCCTGTCT CTAAAAAATT AAATAAATAA TAAAAAAATT AAAAAGTAAC 000320 000321 TCCC |
