The domain within your query sequence starts at position 6 and ends at position 136; the E-value for the RPR domain shown below is 1.26e-42.

TFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYV
IDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSKIVRVLNLWQKNNVFKS
EIIQPLLDMAA

RPR

• SMART accession number: SM00582
• Description: domain present in proteins, which are involved in regulation of nuclear pre-mRNA
• Interpro abstract (IPR006569):

  The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. CTD recognition is dependent on the phosphorylation state of the CTD itself, which varies during the course of transcription but has also been linked to the isomerization state of the CTD's proline residues. Several RNA-processing factors recognise the CTD by means of a conserved CTD-interacting domain (CID). Factors with CID domains include the serine/arginine-rich-like factors SCAF4 and SCAF8, Nrd1 (which is implicated in polyadenylation-independent RNA 3'-end formation) and Pcf11. Pcf11 is a conserved and essential subunit of the yeast cleavage factor 1A, which is required for 3'-RNA processing and transcription termination [ (PUBMED:15241417) (PUBMED:15665873) ].

  The CID domain is a right-handed superhelix of eight alpha-helices forming a compact domain. The CID fold closely resembles that of VHS domains IPR002014 and is related to armadillo-repeat proteins IPR000225 except for the two amino-terminal helices. Amino acid residues in the hydrophobic core of the domain are highly conserved across CID domains [ (PUBMED:15241417) (PUBMED:15665873) ].

There are 9580 RPR domains in 9578 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Doerks T, Copley RR, Schultz J, Ponting CP, Bork P
• Systematic identification of novel protein domain families associated with nuclear functions.
• Genome Res. 2002; 12: 47-56

A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.

Structure (3D structures containing this domain)

3D Structures of RPR domains in PDB

PDB code	Title
1sz9	The RNA polymerase II CTD in mRNA processing: beta-turn recognition and beta-spiral model
1sza	The RNA polymerase II CTD in mRNA processing: beta-turn recognition and beta-spiral model
2bf0	crystal structure of the rpr of pcf11
2diw	Solution structure of the RPR domain of Putative RNA-binding protein 16
2km4	Solution structure of Rtt103 CTD interacting domain
2l0i	Solution structure of Rtt103 CTD-interacting domain bound to a Ser2 phosphorylated CTD peptide
2lo6	Structure of Nrd1 CID bound to phosphorylated RNAP II CTD
2mow	2MOW
3clj	Structure of the RNA polymerase II CTD-interacting domain of Nrd1
3d9i	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9j	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9k	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9l	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9m	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9n	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9o	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
3d9p	Snapshots of the RNA processing factor SCAF8 bound to different phosphorylated forms of the Carboxy-Terminal Domain of RNA-Polymerase II
4flb	CID of human RPRD2
4fu3	CID of human RPRD1B
4hfg	CID of human RPRD1B
4jxt	CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD
4nac	Crystal Structure of the N-terminal Domain of p15RS
4q94	4Q94
4q96	4Q96

Links (links to other resources describing this domain)

• INTERPRO: IPR006569