Difference between revisions of "NONHSAT080206"
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==Annotated Information==
===Transcriptomic Nomeclature===
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[[Category:Intergenic]] | [[Category:Intergenic]] | ||
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+ | {{lncrnadb| | ||
+ | tID = NONHSAT080206| | ||
+ | ltID = Zfas1| | ||
+ | ann = <tab class=wikitable sep=tab head=top> | ||
+ | Section Description | ||
+ | ID Zfas1 | ||
+ | Characteristics Expressed from a bi-directional promoter with the protein-coding gene Znfx1. Zfas1 5°Ø is antisense to 5°Ø of Znfx1. Spliced, polyadenylated. SnoRNA host gene, contains 3 intronic C/D box snoRNAs. Human orthologue is alternatively spliced. | ||
+ | Expression Highly expressed and differentially expressed during mammary development. Strongly down-regulated during lactation compared to pregnancy and then up-regulated again during involution. Znfx1 coding gene,in contrast, was more lowly expressed and was not differentially expressed during mammary gland development. Expressed in the epithelial cells of the mammary gland ducts and alveoli. Zfas1 is widely expressed in mouse tissues including brain, liver, lung, kidney, spleen, heart and embryo, showing higher expression than Znfx1. Zfas1 extremely stable with a half life of >32 hrs in N2A (neuroblastoma) cells. Compared to a half life of 50 minutes for Znfx1. The increased stability of Zfas1 may explain why its expression level is much higher than Znfx1. However, in mouse 3T3 and embryonic stem cells Zfas1 stability was much lower with a half-life of 1.7 hr and 63 min respectively, while the human ZFAS1 had a half-life of 3 hr in B-cells ([http://www.ncbi.nlm.nih.gov/pubmed/19561200 Friedel (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/19001483 Sharova (2009)], [http://www.ncbi.nlm.nih.gov/pubmed/22406755 Clark (2012)]). These results suggest there is significant regulation of Zfas1 stability both within and between species [http://www.ncbi.nlm.nih.gov/pubmed/22406755 (Clark (2012))]. Localised to both the nucleus and the cytoplasm. Human ZFAS1 expression is reduced in ductal carinoma compared to normal tissue. | ||
+ | Function Zfas1 appears to have a role in mammary gland proliferation and differentiation. - Zfas1 knockdown in a HC11 cell culture model of mammary differentiation showed increased differentiation and a probable increase in proliferation. Knockdown had little effect on intronic snoRNA expression suggesting the Zfas1 host transcript is functional. - Zfas1 knockdown appears to affect Znfx1 expression. | ||
+ | Conservation Syntenic transcription observed in multiple mammals. Low conservation of Zfas1 sequence between human and mouse compared to snoRNAs, but Zfas1 has potential secondary structural similarities. | ||
+ | Name Zinc finger antisense 1 | ||
+ | </tab>| | ||
+ | }} |
Revision as of 12:13, 6 October 2014
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Contents
Annotated Information
Transcriptomic Nomeclature
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Function
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Regulation
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Expression
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Allelic Information and Variation
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Evolution
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You can also add sub-section(s) at will.
Labs working on this lncRNA
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References
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Basic Information
Transcript ID |
NONHSAT080206 |
Source |
NONCODE4.0 |
Same with |
, |
Classification |
intergenic |
Length |
1020 nt |
Genomic location |
chr20+:47894715..47905797 |
Exon number |
5 |
Exons |
47894715..47895253,47895641..47895745,47897022..47897107,47897440..47897501,47905582..47905797 |
Genome context |
|
Sequence |
000001 CGGGGGCCCA GGGTGGAGAG CACGAGGGCC TGGCCCAGGC ACGGCCGGCG CCTCCGCCCT CGAGGAGGGC GTCACCTCAG 000080
000081 CTCCCCCCGG CGGCGGAGCC GGCGGGCTCA GGCGGGCGCG GCTGAGGGGA GCGGACCGCG GGGGGCGGGA GATGACTGCG 000160 000161 CCCAAGGCCT TTGCGGGCCT CAGCCGGCCC CAGAGGAAGG GGAACCCGTC GAGCGGTTTG GTGCGTGTGA AGCGCGACAT 000240 000241 GGCGAGGAAG CGGACAAGCC CGGGTGGCCC GGCGTGTAGA GGGAAGGGGG CGGGGCTAGA CGCGGCCTGG ACAACTACTA 000320 000321 GAGCGCCTCG GGCTGTGCTG CTCGAGACTA CATTTCCCAG AGCGACGCGC GCGGAGCGGG CGGGAAAGAG AGCGTTTCGG 000400 000401 GTCCAGTGCG CAGGTGCGAA AGCCATCTTT GGTTATATAA GGGAGGTTCA GGAAGCCATT CGTTCTTTCG CGTCTGCGGT 000480 000481 GCCCGGAGTG TGGTACTTCT CCTAGTTGCA GTCAGGCTTC ATACGCTATT GTCCTGCCCG TTAGAGCAGC CAGCGGGTAC 000560 000561 AGAATGGATT TTGGAAGAGG GAGTCACCAC TGGACCTCCA AGGAAGCCAC GTGCAGACAT CTACAACCTT CGATCTCCTG 000640 000641 ACGAGTTTAT TGTTGGCCAA AACCAGGCTT TGATTGAACC AGGATGAATG CGGGTGTTGG AAGTAGAATA TATATATACA 000720 000721 TATAAAATTG GTTGGGAGCC ACGTGTACCA GTGTGTGTTG ATCTTGGCTT GATTCAGTCT GCCTTGTAAC AGAAACTGGC 000800 000801 GATGGAATAT GAGAGGAGCC CTCTGGAAAG AAAAGGACAG ACCCTGTGCT TTCATGAAAG TGAAGATCTG GCTGAACCAG 000880 000881 TTCCACAAGG TTACTGTATA CATAGCCTGA GTTTAAAAGG CTGTGCCCAC TTCAAGAATG TCATTGTTAG ACTTTGAAAT 000960 000961 TTCTAACTGC CTACCTGCAT AAAGAAAATA AAATCTTTTA AATCAAAAAA AAAAAAAAAA |
Annotation (From lncRNAdb)
Section | Description |
---|---|
ID | Zfas1 |
Characteristics | Expressed from a bi-directional promoter with the protein-coding gene Znfx1. Zfas1 5°Ø is antisense to 5°Ø of Znfx1. Spliced, polyadenylated. SnoRNA host gene, contains 3 intronic C/D box snoRNAs. Human orthologue is alternatively spliced. |
Expression | Highly expressed and differentially expressed during mammary development. Strongly down-regulated during lactation compared to pregnancy and then up-regulated again during involution. Znfx1 coding gene,in contrast, was more lowly expressed and was not differentially expressed during mammary gland development. Expressed in the epithelial cells of the mammary gland ducts and alveoli. Zfas1 is widely expressed in mouse tissues including brain, liver, lung, kidney, spleen, heart and embryo, showing higher expression than Znfx1. Zfas1 extremely stable with a half life of >32 hrs in N2A (neuroblastoma) cells. Compared to a half life of 50 minutes for Znfx1. The increased stability of Zfas1 may explain why its expression level is much higher than Znfx1. However, in mouse 3T3 and embryonic stem cells Zfas1 stability was much lower with a half-life of 1.7 hr and 63 min respectively, while the human ZFAS1 had a half-life of 3 hr in B-cells (Friedel (2009), Sharova (2009), Clark (2012)). These results suggest there is significant regulation of Zfas1 stability both within and between species (Clark (2012)). Localised to both the nucleus and the cytoplasm. Human ZFAS1 expression is reduced in ductal carinoma compared to normal tissue. |
Function | Zfas1 appears to have a role in mammary gland proliferation and differentiation. - Zfas1 knockdown in a HC11 cell culture model of mammary differentiation showed increased differentiation and a probable increase in proliferation. Knockdown had little effect on intronic snoRNA expression suggesting the Zfas1 host transcript is functional. - Zfas1 knockdown appears to affect Znfx1 expression. |
Conservation | Syntenic transcription observed in multiple mammals. Low conservation of Zfas1 sequence between human and mouse compared to snoRNAs, but Zfas1 has potential secondary structural similarities. |
Name | Zinc finger antisense 1 |