Difference between revisions of "NONHSAT134764"

From LncRNAWiki
Jump to: navigation, search
(→‎References)
 
(13 intermediate revisions by 5 users not shown)
Line 2: Line 2:
  
 
==Annotated Information==
 
==Annotated Information==
 +
===Name===
 +
Approved symbol: NRON
 +
 +
Approved name: non-coding repressor of NFAT
 +
 +
HGNC ID: HGNC:37079
 +
 +
Previous names: non-protein coding RNA, repressor of NFAT
 +
 +
Alias symbols: NCRNA00194
 +
 +
Alias names: noncoding repressor of NFAT; non-protein coding RNA 194
 +
 +
RefSeq ID: NR_045006
 +
 +
LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0289382 HSALNT0289382]
 +
 +
===Characteristics===
 +
noncoding repressor of NFAT (NRON). ~2.7 kb. Composed of three exons, which can be alternatively spliced to yield transcripts ranging in size from 0.8 to 3.7 kb, is a cytoplasmic lncRNA<ref name="ref1" />.
 +
 +
===Disease===
 +
AIDS
 +
 +
===Function===
 +
Identified in a shRNA knock down screening for conserved long noncoding RNAs that modulate the activity of nuclear factor of activated T cells (NFAT). Knockdown of human or mouse NRON sequences in human embryonic kidney (HEK) 293 cells or mouse 3T3 and Jurkat cell lines resulted in significantly increased NFAT activity. Knockdown of NRON increases NFAT transcription factor activity by specifically affecting NFAT nuclear trafficking. This effect is observed on the activity of multiple NFAT family members (NFATc1, NFATc2, NFATc3, and NFATc4). Using an RNA-protein affinity purification strategy with part of NRON sequence, 11 proteins were reported to putatively bind NRON. These included: calmodulin-binding protein (IQGAP1), a nuclear transport factor (KPNB1), the structural subunit of a phosphatase (PPP2R1A), a component of the proteasome (PSMD11) and an RNA helicase (DDX3X); as well as three members of the importin-beta superfamily, factors which mediate the nucleocytoplasmic transport of cargoes such as NFAT. Direct interaction was demonstrated with importin-beta 1 (KPNB1). In summary, having a repressive effect on NFAT signaling, NRON is proposed to regulate NFAT's subcellular localization as an RNA component of a protein complex that acts to represses NFAT activity. It has presumed implications in immune response and developmental processes regulated by NFAT.
 +
 +
NRON acts as a scaffold to maintain the structure of a ribonucleoprotein complex which can retain the transcription factor NFAT in the cytoplasm, meaning that NRON plays a significant role in the immune response<ref name="ref1" />.
 +
 +
===Expression===
 +
Expressed in relatively low levels. Present in mouse embryos and enriched in cells derived from human and mouse placenta, muscle, and lymphoid tissues such as the spleen, thymus and lymph nodes, with differential expression of isoforms.
 +
 +
NRON expression level is much lower in CRSsNP patients compared to both the control group and CRSwNP group, Previously reported highly expressed in human immune cells including macrophages, dendritic cells, and neutrophils.<ref name="ref1" />
 +
 +
===Conservation===
 +
NRON contains blocks of sequence which are highly conserved back to chicken. In particular, it contains two large regions of 300 to 400 bases regions of near-perfect sequence conservation between rodents and primates.
 +
 
===Transcriptomic Nomeclature===
 
===Transcriptomic Nomeclature===
 
Please input transcriptomic nomeclature information here.
 
Please input transcriptomic nomeclature information here.
−
 
−
===Function===
 
−
Please input function information here.
 
  
 
===Regulation===
 
===Regulation===
 
Please input regulation information here.
 
Please input regulation information here.
−
 
−
===Expression===
 
−
Please input expression information here.
 
  
 
===Allelic Information and Variation===
 
===Allelic Information and Variation===
Line 23: Line 53:
  
 
==Labs working on this lncRNA==
 
==Labs working on this lncRNA==
−
Please input related labs here.
+
* Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, 83 Fenyang Road, Xuhui District, Shanghai, 200031 People's Republic of China.
 +
* Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China.
  
 
==References==
 
==References==
−
Please input cited references here.
+
<references>
 +
<ref name="ref1"> Ma Y, Zheng C and Shi L. The kinase LRRK2 is differently expressed in chronic rhinosinusitis with and without nasal polyps[J]. Clin Transl Allergy, 2018, 8: 8.
 +
</ref>(1)
 +
</references>
 +
 
 +
 
 +
[http://www.lncrnadb.org/NRON/ Annotation originally sourced from lncRNAdb.]
  
 
{{basic|
 
{{basic|
Line 42: Line 79:
 
sequence = <dnaseq>cacatctctaatgtaaacaacccagcaagggaagtagtaccctatatgtgggggaaaagtggttcagagaggttaagtaactcacccaaagtcacacagctgaagaaaatggctgggctaggatgtgcgttcatgctctttccaccatgccatgttgctttactgagatgacacagggcacaaagtaagtgcaaacacagacctgttcattttccattcaggaagcccatttgccacgaccaatgcaactccaacctaccaggctgactgtagaatgggttttcctcatgggcaacacatacacacatgcatgcatgcgcgtgcatgcgtgcacacacacacacacacacacacacacacacaaaaccaaatcactgtgcattggacaaggggaaaaaaaagctgccactggaagatgaaggaaatcacaattccaaactccccaagttcctaaatgcataaagtacgtgcagcttgacggcatatggcaaatcaattactagtttaaatcttaaaacaaaaacatggcaagtgtggtgcagaaataatcaagaacaacggttaggtttagattacagtgggccactagagttttgaatacaattaatcatcattccaggcaatgggaagccatattgacacttattcctaatttgaatatttaattagggtgaagttcttcatcaaattatcgcagaactgggagaaagcctggaagacttacacaattactatcttaaccccttcccagctgctcacctgtgaacacagccattctagtcccagctccgcaggggaggttgcctgtgcccagtctctgatgctgtggggtgctggaggggtgctggtgactggagttgcaactgcagcaggcgggagccacgtggtggcaaaggaaaggtctaaggggatgccctgctcatgcttaggctaagttctgcattgaaccctggacacagacagaaagccagcatgcatgggtgctcactgggcaccagggtggtgctttctgtgtccccccccaatttaattctcatgacaaatcctgcaaaggaggcatttctatccccatttcacagaggaagaaacaggctcagagagtgataaaactcactcaaagtaacaccgcctgtgagtggtgtaaagaaggcccaagggacacacacacacacacacacacacacacacacacacacacacacacagagttactcaccaaaagtgatgacaaagagaacacgcaaaggcccacaaaaatgttttcaaggctgtattttggatcatctgcaccgtgtggctaaatcaaaggaaaaccaaaacccaggcctcttcaatcagcattctaaaatttaactcttgggttcaaaatgcattactgagcccccccccacaatggaagtcacgatgccgttgtggccaggggctcagcagaatggtggaggtgggggcagcaaagctcaaggaacagtcccacaaggccgatttgaggcaaggtgacaaggtggccatccaaaccccgcagagtaggactcgagaaggtgggcgctgcgggacaggtgtccttggggaggggaatgtttgcaacaggacaaaaaaatgtgaactctttcttctttcaagatggccaaggctcaatgatagcatttagaactatacatcagcttggtgattacgttccttaatgtacgcctttgctatctgaaaagacttttactaacatttcatagatactatgtgattctacgtgaccaaaaacaacacattttgccacataatctccccgaaggactcaggacacggccaagggctgagtgcacacatgggactggaccacggtaggtccagagacctttctgcttccagcctccaccgagaagccgaaaaggagggacatcctgatagtttcaggttagccatctctccttaaaagcctgtgacgggttcacttaccctcttgtggaaaaggctccatttgcagtggccactttcagcaggaagtggatcgccaggcagaaggagggagccgccccagccccctgcctgggcccactgcaggcacagaccccggatccggatccatcaggcctgcgtggggggagcgaatggcatcgggaactttgaaactttcctttgtatattacattaatccatataagaaaatctcttttaatgaggagtgatgtagttacaaactctccagagccataattagagcaaactaattgaagttgtgttttgacacactttccaaattcacgggtgccggatgacatattcacaacactgctgccgcacaaccatggcgacggcaaaatcattaggctaataacgcttatttgcattcttatcatgccggcagctcgcccttaaatactgtttccactactgctcctttactgtaagtttccaccgaaagatattaacagtaattattagtactttagtggaattttaatgttaaagaataacaatgtgcattaacatacattgaatggcaattctttttcttaaccacccatcggaaggtttgggggttcttccttggccctctccccagagctcaagggtaaccagatgcgatttcagcttcatttacaattcagggtccacacccagtgggatctgaagtcaggtttctgaaccattctgctccaaaagtttgatgagaaaaatctttctttcttttttttaagtacaataaaatgaaatagttaaggagaaattttttcc</dnaseq>|
 
sequence = <dnaseq>cacatctctaatgtaaacaacccagcaagggaagtagtaccctatatgtgggggaaaagtggttcagagaggttaagtaactcacccaaagtcacacagctgaagaaaatggctgggctaggatgtgcgttcatgctctttccaccatgccatgttgctttactgagatgacacagggcacaaagtaagtgcaaacacagacctgttcattttccattcaggaagcccatttgccacgaccaatgcaactccaacctaccaggctgactgtagaatgggttttcctcatgggcaacacatacacacatgcatgcatgcgcgtgcatgcgtgcacacacacacacacacacacacacacacacaaaaccaaatcactgtgcattggacaaggggaaaaaaaagctgccactggaagatgaaggaaatcacaattccaaactccccaagttcctaaatgcataaagtacgtgcagcttgacggcatatggcaaatcaattactagtttaaatcttaaaacaaaaacatggcaagtgtggtgcagaaataatcaagaacaacggttaggtttagattacagtgggccactagagttttgaatacaattaatcatcattccaggcaatgggaagccatattgacacttattcctaatttgaatatttaattagggtgaagttcttcatcaaattatcgcagaactgggagaaagcctggaagacttacacaattactatcttaaccccttcccagctgctcacctgtgaacacagccattctagtcccagctccgcaggggaggttgcctgtgcccagtctctgatgctgtggggtgctggaggggtgctggtgactggagttgcaactgcagcaggcgggagccacgtggtggcaaaggaaaggtctaaggggatgccctgctcatgcttaggctaagttctgcattgaaccctggacacagacagaaagccagcatgcatgggtgctcactgggcaccagggtggtgctttctgtgtccccccccaatttaattctcatgacaaatcctgcaaaggaggcatttctatccccatttcacagaggaagaaacaggctcagagagtgataaaactcactcaaagtaacaccgcctgtgagtggtgtaaagaaggcccaagggacacacacacacacacacacacacacacacacacacacacacacacagagttactcaccaaaagtgatgacaaagagaacacgcaaaggcccacaaaaatgttttcaaggctgtattttggatcatctgcaccgtgtggctaaatcaaaggaaaaccaaaacccaggcctcttcaatcagcattctaaaatttaactcttgggttcaaaatgcattactgagcccccccccacaatggaagtcacgatgccgttgtggccaggggctcagcagaatggtggaggtgggggcagcaaagctcaaggaacagtcccacaaggccgatttgaggcaaggtgacaaggtggccatccaaaccccgcagagtaggactcgagaaggtgggcgctgcgggacaggtgtccttggggaggggaatgtttgcaacaggacaaaaaaatgtgaactctttcttctttcaagatggccaaggctcaatgatagcatttagaactatacatcagcttggtgattacgttccttaatgtacgcctttgctatctgaaaagacttttactaacatttcatagatactatgtgattctacgtgaccaaaaacaacacattttgccacataatctccccgaaggactcaggacacggccaagggctgagtgcacacatgggactggaccacggtaggtccagagacctttctgcttccagcctccaccgagaagccgaaaaggagggacatcctgatagtttcaggttagccatctctccttaaaagcctgtgacgggttcacttaccctcttgtggaaaaggctccatttgcagtggccactttcagcaggaagtggatcgccaggcagaaggagggagccgccccagccccctgcctgggcccactgcaggcacagaccccggatccggatccatcaggcctgcgtggggggagcgaatggcatcgggaactttgaaactttcctttgtatattacattaatccatataagaaaatctcttttaatgaggagtgatgtagttacaaactctccagagccataattagagcaaactaattgaagttgtgttttgacacactttccaaattcacgggtgccggatgacatattcacaacactgctgccgcacaaccatggcgacggcaaaatcattaggctaataacgcttatttgcattcttatcatgccggcagctcgcccttaaatactgtttccactactgctcctttactgtaagtttccaccgaaagatattaacagtaattattagtactttagtggaattttaatgttaaagaataacaatgtgcattaacatacattgaatggcaattctttttcttaaccacccatcggaaggtttgggggttcttccttggccctctccccagagctcaagggtaaccagatgcgatttcagcttcatttacaattcagggtccacacccagtgggatctgaagtcaggtttctgaaccattctgctccaaaagtttgatgagaaaaatctttctttcttttttttaagtacaataaaatgaaatagttaaggagaaattttttcc</dnaseq>|
 
}}
 
}}
−
[[Category:Intronic(AS)]]
+
[[Category:Intronic(AS)]][[Category:NONHSAG053456]][[Category:Transcripts]]
−
 
 
−
{{lncrnadb|
 
−
tID = NONHSAT134764|
 
−
ltID = NRON|
 
−
ann = <tab class=wikitable sep=tab head=top>
 
−
Section Description
 
−
ID NRON
 
−
Characteristics noncoding repressor of NFAT (NRON). ~2.7 kb. Composed of three exons, which can be alternatively spliced to yield transcripts ranging in size from 0.8 to 3.7 kb.
 
−
Expression Expressed in relatively low levels. Present in mouse embryos and enriched in cells derived from human and mouse placenta, muscle, and lymphoid tissues such as the spleen, thymus and lymph nodes, with differential expression of isoforms.
 
−
Function Identified in a shRNA knock down screening for conserved long noncoding RNAs that modulate the activity of nuclear factor of activated T cells (NFAT). Knockdown of human or mouse NRON sequences in human embryonic kidney (HEK) 293 cells or mouse 3T3 and Jurkat cell lines resulted in significantly increased NFAT activity. Knockdown of NRON increases NFAT transcription factor activity by specifically affecting NFAT nuclear trafficking. This effect is observed on the activity of multiple NFAT family members (NFATc1, NFATc2, NFATc3, and NFATc4). Using an RNA-protein affinity purification strategy with part of NRON sequence, 11 proteins were reported to putatively bind NRON. These included: calmodulin-binding protein (IQGAP1), a nuclear transport factor (KPNB1), the structural subunit of a phosphatase (PPP2R1A), a component of the proteasome (PSMD11) and an RNA helicase (DDX3X); as well as three members of the importin-beta superfamily, factors which mediate the nucleocytoplasmic transport of cargoes such as NFAT. Direct interaction was demonstrated with importin-beta 1 (KPNB1). In summary, having a repressive effect on NFAT signaling, NRON is proposed to regulate NFAT's subcellular localization as an RNA component of a protein complex that acts to represses NFAT activity. It has presumed implications in immune response and developmental processes regulated by NFAT.
 
−
Conservation NRON contains blocks of sequence which are highly conserved back to chicken. In particular, it contains two large regions of 300 to 400 bases regions of near-perfect sequence conservation between rodents and primates.
 
−
</tab>|
 
−
}}
 

Latest revision as of 10:50, 11 August 2019

Please input one-sentence summary here.

Annotated Information

Name

Approved symbol: NRON

Approved name: non-coding repressor of NFAT

HGNC ID: HGNC:37079

Previous names: non-protein coding RNA, repressor of NFAT

Alias symbols: NCRNA00194

Alias names: noncoding repressor of NFAT; non-protein coding RNA 194

RefSeq ID: NR_045006

LncBook ID: HSALNT0289382

Characteristics

noncoding repressor of NFAT (NRON). ~2.7 kb. Composed of three exons, which can be alternatively spliced to yield transcripts ranging in size from 0.8 to 3.7 kb, is a cytoplasmic lncRNA[1].

Disease

AIDS

Function

Identified in a shRNA knock down screening for conserved long noncoding RNAs that modulate the activity of nuclear factor of activated T cells (NFAT). Knockdown of human or mouse NRON sequences in human embryonic kidney (HEK) 293 cells or mouse 3T3 and Jurkat cell lines resulted in significantly increased NFAT activity. Knockdown of NRON increases NFAT transcription factor activity by specifically affecting NFAT nuclear trafficking. This effect is observed on the activity of multiple NFAT family members (NFATc1, NFATc2, NFATc3, and NFATc4). Using an RNA-protein affinity purification strategy with part of NRON sequence, 11 proteins were reported to putatively bind NRON. These included: calmodulin-binding protein (IQGAP1), a nuclear transport factor (KPNB1), the structural subunit of a phosphatase (PPP2R1A), a component of the proteasome (PSMD11) and an RNA helicase (DDX3X); as well as three members of the importin-beta superfamily, factors which mediate the nucleocytoplasmic transport of cargoes such as NFAT. Direct interaction was demonstrated with importin-beta 1 (KPNB1). In summary, having a repressive effect on NFAT signaling, NRON is proposed to regulate NFAT's subcellular localization as an RNA component of a protein complex that acts to represses NFAT activity. It has presumed implications in immune response and developmental processes regulated by NFAT.

NRON acts as a scaffold to maintain the structure of a ribonucleoprotein complex which can retain the transcription factor NFAT in the cytoplasm, meaning that NRON plays a significant role in the immune response[1].

Expression

Expressed in relatively low levels. Present in mouse embryos and enriched in cells derived from human and mouse placenta, muscle, and lymphoid tissues such as the spleen, thymus and lymph nodes, with differential expression of isoforms.

NRON expression level is much lower in CRSsNP patients compared to both the control group and CRSwNP group, Previously reported highly expressed in human immune cells including macrophages, dendritic cells, and neutrophils.[1]

Conservation

NRON contains blocks of sequence which are highly conserved back to chicken. In particular, it contains two large regions of 300 to 400 bases regions of near-perfect sequence conservation between rodents and primates.

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

  • Department of Otolaryngology-Head and Neck Surgery, Eye Ear Nose and Throat Hospital, Fudan University, 83 Fenyang Road, Xuhui District, Shanghai, 200031 People's Republic of China.
  • Shanghai Key Clinical Disciplines of Otorhinolaryngology, Shanghai, People's Republic of China.

References

  1. ↑ 1.0 1.1 1.2 Ma Y, Zheng C and Shi L. The kinase LRRK2 is differently expressed in chronic rhinosinusitis with and without nasal polyps[J]. Clin Transl Allergy, 2018, 8: 8.


Annotation originally sourced from lncRNAdb.

Basic Information

Transcript ID

NONHSAT134764

Source

NONCODE4.0

Same with

,

Classification

intronic(AS)

Length

2730 nt

Genomic location

chr9-:129170054..129172783

Exon number

1

Exons

129170054..129172783

Genome context

Sequence
000001 cacatctcta atgtaaacaa cccagcaagg gaagtagtac cctatatgtg ggggaaaagt ggttcagaga ggttaagtaa 000080
000081 ctcacccaaa gtcacacagc tgaagaaaat ggctgggcta ggatgtgcgt tcatgctctt tccaccatgc catgttgctt 000160
000161 tactgagatg acacagggca caaagtaagt gcaaacacag acctgttcat tttccattca ggaagcccat ttgccacgac 000240
000241 caatgcaact ccaacctacc aggctgactg tagaatgggt tttcctcatg ggcaacacat acacacatgc atgcatgcgc 000320
000321 gtgcatgcgt gcacacacac acacacacac acacacacac acaaaaccaa atcactgtgc attggacaag gggaaaaaaa 000400
000401 agctgccact ggaagatgaa ggaaatcaca attccaaact ccccaagttc ctaaatgcat aaagtacgtg cagcttgacg 000480
000481 gcatatggca aatcaattac tagtttaaat cttaaaacaa aaacatggca agtgtggtgc agaaataatc aagaacaacg 000560
000561 gttaggttta gattacagtg ggccactaga gttttgaata caattaatca tcattccagg caatgggaag ccatattgac 000640
000641 acttattcct aatttgaata tttaattagg gtgaagttct tcatcaaatt atcgcagaac tgggagaaag cctggaagac 000720
000721 ttacacaatt actatcttaa ccccttccca gctgctcacc tgtgaacaca gccattctag tcccagctcc gcaggggagg 000800
000801 ttgcctgtgc ccagtctctg atgctgtggg gtgctggagg ggtgctggtg actggagttg caactgcagc aggcgggagc 000880
000881 cacgtggtgg caaaggaaag gtctaagggg atgccctgct catgcttagg ctaagttctg cattgaaccc tggacacaga 000960
000961 cagaaagcca gcatgcatgg gtgctcactg ggcaccaggg tggtgctttc tgtgtccccc cccaatttaa ttctcatgac 001040
001041 aaatcctgca aaggaggcat ttctatcccc atttcacaga ggaagaaaca ggctcagaga gtgataaaac tcactcaaag 001120
001121 taacaccgcc tgtgagtggt gtaaagaagg cccaagggac acacacacac acacacacac acacacacac acacacacac 001200
001201 acacagagtt actcaccaaa agtgatgaca aagagaacac gcaaaggccc acaaaaatgt tttcaaggct gtattttgga 001280
001281 tcatctgcac cgtgtggcta aatcaaagga aaaccaaaac ccaggcctct tcaatcagca ttctaaaatt taactcttgg 001360
001361 gttcaaaatg cattactgag ccccccccca caatggaagt cacgatgccg ttgtggccag gggctcagca gaatggtgga 001440
001441 ggtgggggca gcaaagctca aggaacagtc ccacaaggcc gatttgaggc aaggtgacaa ggtggccatc caaaccccgc 001520
001521 agagtaggac tcgagaaggt gggcgctgcg ggacaggtgt ccttggggag gggaatgttt gcaacaggac aaaaaaatgt 001600
001601 gaactctttc ttctttcaag atggccaagg ctcaatgata gcatttagaa ctatacatca gcttggtgat tacgttcctt 001680
001681 aatgtacgcc tttgctatct gaaaagactt ttactaacat ttcatagata ctatgtgatt ctacgtgacc aaaaacaaca 001760
001761 cattttgcca cataatctcc ccgaaggact caggacacgg ccaagggctg agtgcacaca tgggactgga ccacggtagg 001840
001841 tccagagacc tttctgcttc cagcctccac cgagaagccg aaaaggaggg acatcctgat agtttcaggt tagccatctc 001920
001921 tccttaaaag cctgtgacgg gttcacttac cctcttgtgg aaaaggctcc atttgcagtg gccactttca gcaggaagtg 002000
002001 gatcgccagg cagaaggagg gagccgcccc agccccctgc ctgggcccac tgcaggcaca gaccccggat ccggatccat 002080
002081 caggcctgcg tggggggagc gaatggcatc gggaactttg aaactttcct ttgtatatta cattaatcca tataagaaaa 002160
002161 tctcttttaa tgaggagtga tgtagttaca aactctccag agccataatt agagcaaact aattgaagtt gtgttttgac 002240
002241 acactttcca aattcacggg tgccggatga catattcaca acactgctgc cgcacaacca tggcgacggc aaaatcatta 002320
002321 ggctaataac gcttatttgc attcttatca tgccggcagc tcgcccttaa atactgtttc cactactgct cctttactgt 002400
002401 aagtttccac cgaaagatat taacagtaat tattagtact ttagtggaat tttaatgtta aagaataaca atgtgcatta 002480
002481 acatacattg aatggcaatt ctttttctta accacccatc ggaaggtttg ggggttcttc cttggccctc tccccagagc 002560
002561 tcaagggtaa ccagatgcga tttcagcttc atttacaatt cagggtccac acccagtggg atctgaagtc aggtttctga 002640
002641 accattctgc tccaaaagtt tgatgagaaa aatctttctt tctttttttt aagtacaata aaatgaaata gttaaggaga 002720
002721 aattttttcc
[back to top]
Retrieved from "https://ngdc.cncb.ac.cn/lncrnawiki1/index.php?title=NONHSAT134764&oldid=1276250"