User:Htafer/SCARNA6: Difference between revisions
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{{Infobox RNA family |
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{{Rfam_box|acc=RF00478| description=Small Cajal body specific RNA 6 |abbreviation=SCARNA6 |avg_length=256.00 |avg_identity=54.00 |type=Gene; snRNA; snoRNA; scaRNA; |se=Moxon SJ, Daub J, INFERNAL |ss=Published; {{PMID|12032087}}, Daub J |release=10.0}} |
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| Name = Small Cajal body specific RNA 6 |
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| image = [[File:RF00478.jpg|300px|SCARNA6]] |
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| Symbol = SCARNA6 |
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| Rfam = RF00478 |
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| RNA_type = Gene; snRNA; snoRNA; scaRNA; |
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}} |
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[[File: 4rfam_scaRNA6_stk.svg|frame|left|alt=Alternative representation of the '''SCARNA6''' consensus structure.| |
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Representation of the '''SCARNA6''' consensus structure. ]] |
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In [[molecular biology]], '''Small Cajal body specific RNA 6''' (also known as '''scaRNA6''' or '''U88''') is a [[small nucleolar RNA]] found in [[cajal body|Cajal bodies]]. It is predicted to [[Methylation|methylate]] residue 41 in [[U5| U5 spliceosomal RNA]] as well as position 65 in [[U4| U4 spliceosomal RNA]]. |
In [[molecular biology]], '''Small Cajal body specific RNA 6''' (also known as '''scaRNA6''' or '''U88''') is a [[small nucleolar RNA]] found in [[cajal body|Cajal bodies]]. It is predicted to [[Methylation|methylate]] residue 41 in [[U5| U5 spliceosomal RNA]] as well as position 65 in [[U4| U4 spliceosomal RNA]]. |
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scaRNAs are a specific class of [[small nucleolar RNA]]s that localise to the [[cajal body|Cajal bodies]] and guide the modification of [[RNA polymerase II]] transcribed [[spliceosome|spliceosomal]] RNAs [[U1 spliceosomal RNA|U1]], [[U2 spliceosomal RNA|U2]], [[U4 spliceosomal RNA|U4]], [[U5 spliceosomal RNA|U5]] and [[U12 minor spliceosomal RNA|U12]].<ref name=" |
scaRNAs are a specific class of [[small nucleolar RNA]]s that localise to the [[cajal body|Cajal bodies]] and guide the modification of [[RNA polymerase II]] transcribed [[spliceosome|spliceosomal]] RNAs [[U1 spliceosomal RNA|U1]], [[U2 spliceosomal RNA|U2]], [[U4 spliceosomal RNA|U4]], [[U5 spliceosomal RNA|U5]] and [[U12 minor spliceosomal RNA|U12]].<ref name="pmid12032087">{{Cite journal | last1 = Darzacq | first1 = Xavier | last2 = Jády | first2 = Beáta E. | last3 = Verheggen | first3 = Céline | last4 = Kiss | first4 = Arnold M. | last5 = Bertrand | first5 = Edouard | last6 = Kiss | first6 = Tamás | title = Cajal body-specific small nuclear RNAs: A novel class of 2'-''O''-methylation and pseudouridylation guide RNAs | doi = 10.1093/emboj/21.11.2746 | journal = [[The EMBO Journal]] | volume = 21 | issue = 11 | pages = 2746–2756 | pmc = 126017 | year = 2002 | pmid = 12032087}}</ref> |
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U88 is composed of a [[SnoRNA#H.2FACAbox|H/ACA box]] domain as well as a [[SnoRNA#C.2FDbox|C/D box]] domain. Further it contains two CAB boxes that promotes its localization into the [[cajal body|Cajal bodies]]. The length of SCARNA6 |
U88 is composed of a [[SnoRNA#H.2FACAbox|H/ACA box]] domain as well as a [[SnoRNA#C.2FDbox|C/D box]] domain. Further it contains two CAB boxes that promotes its localization into the [[cajal body|Cajal bodies]]. The length of SCARNA6 |
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ranges from 225 nt in [[Canis]] to 276 nt in [[Monodelphis]], slightly shorter than the closely related [[SCARNA5]]<ref name="pmid11387227">{{ |
ranges from 225 nt in [[Canis]] to 276 nt in [[Monodelphis]], slightly shorter than the closely related [[SCARNA5]]<ref name="pmid11387227">{{Cite journal | last1 = Huttenhofer | first1 = Alexander| last2 = Kiefmann | first2 = Martin| last3 = Meier-Ewert | first3 = Sebastian| last4 = O'Brien | first4 = John| last5 = Lehrach | first5 = Hans| last6 = Bachellerie | first6 = Jean-Pierre | last7 = Brosius | first7 = Jürgen| title = RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse| doi = 10.1093/emboj/20.11.2943 | journal = [[The EMBO Journal]]| volume = 20 | issue = 11 | pages = 2943–2953 | date = 1 June 2001| pmid = 11387227| pmc = 125495}}</ref>. |
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While found experimentally in the intron of human ATG16L1 mRNA |
While found experimentally in the intron of human ATG16L1 mRNA |
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<ref name="pmid12032087"/> |
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<ref name="darzacq_2002" >{{cite journal | last = Darzacq | first = X | coauthors = Jady BE, Verheggen C, Kiss AM, Bertrand E, Kiss T | year = 2002 | title = Cajal body-specific small nuclear RNAs: a novel class of 2'-O-methylation and pseudouridylation guide RNAs | journal = EMBO J. | volume = 21 | pages = 2746–2756 | pmid = 12032087 | doi = 10.1093/emboj/21.11.2746 | issue = 11 | pmc = 126017}}</ref> |
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, it can be traced throughout [[gnathostome]] evolution. Interestingly, SCARNA6 relocated to different introns several times during vertebrate evolution, however without changing host gene. |
, it can be traced throughout [[gnathostome]] evolution. Interestingly, SCARNA6 relocated to different introns several times during vertebrate evolution, however without changing host gene. |
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* {{Rfam|id=|name=Small Cajal body specific RNA 5}} |
* {{Rfam|id=|name=Small Cajal body specific RNA 5}} |
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* [http://www-snorna.biotoul.fr/plus.php?id=U87 snoRNABase entry for SCARNA12] |
* [http://www-snorna.biotoul.fr/plus.php?id=U87 snoRNABase entry for SCARNA12] |
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[[Category:Small nuclear RNA]] |
[[Category:Small nuclear RNA]] |
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[[Category:Spliceosome]] |
[[Category:Spliceosome]] |
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Latest revision as of 09:00, 14 October 2019
| Small Cajal body specific RNA 6 | |
|---|---|
 | |
| Identifiers | |
| Symbol | SCARNA6 |
| Rfam | RF00478 |
| Other data | |
| RNA type | Gene; snRNA; snoRNA; scaRNA; |
| PDB structures | PDBe |
In molecular biology, Small Cajal body specific RNA 6 (also known as scaRNA6 or U88) is a small nucleolar RNA found in Cajal bodies. It is predicted to methylate residue 41 in U5 spliceosomal RNA as well as position 65 in U4 spliceosomal RNA.
scaRNAs are a specific class of small nucleolar RNAs that localise to the Cajal bodies and guide the modification of RNA polymerase II transcribed spliceosomal RNAs U1, U2, U4, U5 and U12.[1]
U88 is composed of a H/ACA box domain as well as a C/D box domain. Further it contains two CAB boxes that promotes its localization into the Cajal bodies. The length of SCARNA6 ranges from 225 nt in Canis to 276 nt in Monodelphis, slightly shorter than the closely related SCARNA5[2]. While found experimentally in the intron of human ATG16L1 mRNA [1] , it can be traced throughout gnathostome evolution. Interestingly, SCARNA6 relocated to different introns several times during vertebrate evolution, however without changing host gene.
An interesting peculiarity of both SCARNA5 and SCARNA6 is the absence of well-conserved target sequences. Possibly, the H/ACA domain, which ,similar to SCARNA10, contains conserved CAB boxes in its hairpin loops, only mediates transport to the Cajal body.
References
[edit]- ^ a b Darzacq, Xavier; Jády, Beáta E.; Verheggen, Céline; Kiss, Arnold M.; Bertrand, Edouard; Kiss, Tamás (2002). "Cajal body-specific small nuclear RNAs: A novel class of 2'-O-methylation and pseudouridylation guide RNAs". The EMBO Journal. 21 (11): 2746–2756. doi:10.1093/emboj/21.11.2746. PMC 126017. PMID 12032087.
- ^ Huttenhofer, Alexander; Kiefmann, Martin; Meier-Ewert, Sebastian; O'Brien, John; Lehrach, Hans; Bachellerie, Jean-Pierre; Brosius, Jürgen (1 June 2001). "RNomics: an experimental approach that identifies 201 candidates for novel, small, non-messenger RNAs in mouse". The EMBO Journal. 20 (11): 2943–2953. doi:10.1093/emboj/20.11.2943. PMC 125495. PMID 11387227.