universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42571091   56 SRDFDSRGPPPGAGRCFNCGVDGHWARDCT----AGDWKNKCYRCGERGHIERNCKNSPKKLR 114
Cdd:PTZ00368  65 SRECPEAPPGSGPRSCYNCGQTGHISRECPnrakGGAARRACYNCGGEGHISRDCPNAGKRPG 127

universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42571091   56 SRDFDSRGPPPGAGRCFNCGVDGHWARDCT----AGDWKNKCYRCGERGHIERNCKNSPKKLR 114
Cdd:PTZ00368  65 SRECPEAPPGSGPRSCYNCGQTGHISRECPnrakGGAARRACYNCGGEGHISRDCPNAGKRPG 127

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSriTVEFSRGAPRGSRDFDSRGP------------PPGAGRCFNCGVDGHWARDCTAG 87
Cdd:COG5082   2 SMDDRPRVVDATPTLPIDKLSAN--SIEESSSNPNELRSLRSSGRyedrsvedvsaiREENPVCFNCGQNGHLRRDCPHS 79

                        90       100       110       120
                ....*....|....*....|....*....|....*....|...
gi 42571091  88 D---------------WKNKCYRCGERGHIERNCknSPKKLRR 115
Cdd:COG5082  80 IcyncswdghrsnhcpKPKKCYNCGETGHLSRDC--NPSKDQQ 120

zinc finger;

                           10
                   ....*....|....*..
gi 42571091     92 KCYRCGERGHIERNCKN 108
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17

universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 42571091   56 SRDFDSRGPPPGAGRCFNCGVDGHWARDCT----AGDWKNKCYRCGERGHIERNCKNSPKKLR 114
Cdd:PTZ00368  65 SRECPEAPPGSGPRSCYNCGQTGHISRECPnrakGGAARRACYNCGGEGHISRDCPNAGKRPG 127

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 4 (SRSF4) and similar proteins; This subfamily corresponds to the RRM1 in three serine/arginine (SR) proteins: serine/arginine-rich splicing factor 4 (SRSF4 or SRp75 or SFRS4), serine/arginine-rich splicing factor 5 (SRSF5 or SRp40 or SFRS5 or HRS), serine/arginine-rich splicing factor 6 (SRSF6 or SRp55). SRSF4 plays an important role in both, constitutive and alternative, splicing of many pre-mRNAs. It can shuttle between the nucleus and cytoplasm. SRSF5 regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and essential for enhancer activation. SRSF6 preferentially interacts with a number of purine-rich splicing enhancers (ESEs) to activate splicing of the ESE-containing exon. It is the only protein from HeLa nuclear extract or purified SR proteins that specifically binds B element RNA after UV irradiation. SRSF6 may also recognize different types of RNA sites. Members in this family contain two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides.

                        10        20        30
                ....*....|....*....|....*....|..
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSRG 51
Cdd:cd12337  39 EFEDPRDADDAVYELNGKELCGERVIVEHARG 70

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor 3 (SRSF3) and similar proteins; This subfamily corresponds to the RRM of two serine/arginine (SR) proteins, serine/arginine-rich splicing factor 3 (SRSF3) and serine/arginine-rich splicing factor 7 (SRSF7). SRSF3, also termed pre-mRNA-splicing factor SRp20, modulates alternative splicing by interacting with RNA cis-elements in a concentration- and cell differentiation-dependent manner. It is also involved in termination of transcription, alternative RNA polyadenylation, RNA export, and protein translation. SRSF3 is critical for cell proliferation, and tumor induction and maintenance. It can shuttle between the nucleus and cytoplasm. SRSF7, also termed splicing factor 9G8, plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. Moreover, SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. Both SRSF3 and SRSF7 contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                        10        20        30
                ....*....|....*....|....*....|..
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSRG 51
Cdd:cd12373  42 EFEDPRDAEDAVRALDGRRICGSRVRVELSRG 73

universal minicircle sequence binding protein (UMSBP); Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 42571091   62 RGPPPGAGR--CFNCGVDGHWARDC----TAGDWKNKCYRCGERGHIERNCKNS 109
Cdd:PTZ00368  95 NRAKGGAARraCYNCGGEGHISRDCpnagKRPGGDKTCYNCGQTGHLSRDCPDK 148

RNA recognition motif (RRM) found in vertebrate serine/arginine-rich splicing factor 7 (SRSF7); This subgroup corresponds to the RRM of SRSF7, also termed splicing factor 9G8, is a splicing regulatory serine/arginine (SR) protein that plays a crucial role in both constitutive splicing and alternative splicing of many pre-mRNAs. Its localization and functions are tightly regulated by phosphorylation. SRSF7 is predominantly present in the nuclear and can shuttle between nucleus and cytoplasm. It cooperates with the export protein, Tap/NXF1, helps mRNA export to the cytoplasm, and enhances the expression of unspliced mRNA. SRSF7 inhibits tau E10 inclusion through directly interacting with the proximal downstream intron of E10, a clustering region for frontotemporal dementia with Parkinsonism (FTDP) mutations. SRSF7 contains a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a CCHC-type zinc knuckle motif in its median region, and a C-terminal RS domain rich in serine-arginine dipeptides. The RRM domain is involved in RNA binding, and the RS domain has been implicated in protein shuttling and protein-protein interactions.

                        10        20        30
                ....*....|....*....|....*....|....*
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSRGAPR 54
Cdd:cd12646  42 EFEDPRDAEDAVRGLDGKVICGSRVRVELSTGMPR 76

RNA recognition motif 1 (RRM1) found in vertebrate serine/arginine-rich splicing factor 5 (SRSF5); This subgroup corresponds to the RRM1 of SRSF5, also termed delayed-early protein HRS, or pre-mRNA-splicing factor SRp40, or splicing factor, arginine/serine-rich 5 (SFRS5). SFSF5 is an essential splicing regulatory serine/arginine (SR) protein that regulates both alternative splicing and basal splicing. It is the only SR protein efficiently selected from nuclear extracts (NE) by the splicing enhancer (ESE) and it is necessary for enhancer activation. SRSF5 also functions as a factor required for insulin-regulated splice site selection for protein kinase C (PKC) betaII mRNA. It is involved in the regulation of PKCbetaII exon inclusion by insulin via its increased phosphorylation by a phosphatidylinositol 3-kinase (PI 3-kinase) signaling pathway. Moreover, SRSF5 can regulate alternative splicing in exon 9 of glucocorticoid receptor pre-mRNA in a dose-dependent manner. SRSF5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), followed by a C-terminal RS domains rich in serine-arginine dipeptides. The specific RNA binding by SRSF5 requires the phosphorylation of its SR domain.

                        10        20        30
                ....*....|....*....|....*....|.
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSR 50
Cdd:cd12595  39 EFEDPRDADDAVYELDGKELCNERVTIEHAR 69

RNA recognition motif 1 (RRM1) found in serine/arginine-rich splicing factor 1 (SRSF1) and similar proteins; This subgroup corresponds to the RRM1 of SRSF1, also termed alternative-splicing factor 1 (ASF-1), or pre-mRNA-splicing factor SF2, P33 subunit. SRSF1 is a splicing regulatory serine/arginine (SR) protein involved in constitutive and alternative splicing, nonsense-mediated mRNA decay (NMD), mRNA export and translation. It also functions as a splicing-factor oncoprotein that regulates apoptosis and proliferation to promote mammary epithelial cell transformation. SRSF1 is a shuttling SR protein and contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), separated by a long glycine-rich spacer, and a C-terminal RS domains rich in serine-arginine dipeptides.

                        10        20        30
                ....*....|....*....|....*....|.
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSR 50
Cdd:cd12597  49 EFEDPRDAEDAVYGRDGYDYDGYRLRVEFPR 79

RNA recognition motif (RRM) found in serine/arginine-rich splicing factor SRSF10, SRSF12 and similar proteins; This subfamily corresponds to the RRM of SRSF10 and SRSF12. SRSF10, also termed 40 kDa SR-repressor protein (SRrp40), or FUS-interacting serine-arginine-rich protein 1 (FUSIP1), or splicing factor SRp38, or splicing factor, arginine/serine-rich 13A (SFRS13A), or TLS-associated protein with Ser-Arg repeats (TASR). It is a serine-arginine (SR) protein that acts as a potent and general splicing repressor when dephosphorylated. It mediates global inhibition of splicing both in M phase of the cell cycle and in response to heat shock. SRSF10 emerges as a modulator of cholesterol homeostasis through the regulation of low-density lipoprotein receptor (LDLR) splicing efficiency. It also regulates cardiac-specific alternative splicing of triadin pre-mRNA and is required for proper Ca2+ handling during embryonic heart development. In contrast, the phosphorylated SRSF10 functions as a sequence-specific splicing activator in the presence of a nuclear cofactor. It activates distal alternative 5' splice site of adenovirus E1A pre-mRNA in vivo. Moreover, SRSF10 strengthens pre-mRNA recognition by U1 and U2 snRNPs. SRSF10 localizes to the nuclear speckles and can shuttle between nucleus and cytoplasm. SRSF12, also termed 35 kDa SR repressor protein (SRrp35), or splicing factor, arginine/serine-rich 13B (SFRS13B), or splicing factor, arginine/serine-rich 19 (SFRS19), is a serine/arginine (SR) protein-like alternative splicing regulator that antagonizes authentic SR proteins in the modulation of alternative 5' splice site choice. For instance, it activates distal alternative 5' splice site of the adenovirus E1A pre-mRNA in vivo. Both, SRSF10 and SRSF12, contain a single N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), followed by a C-terminal RS domain rich in serine-arginine dipeptides.

                        10        20        30
                ....*....|....*....|....*....|..
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSRG 51
Cdd:cd12312  48 QFEDVRDAEDALYYLDRTRFLGREIEIQFAQG 79

Zinc knuckle; The zinc knuckle is a zinc binding motif composed of the the following CX2CX4HX4C where X can be any amino acid. The motifs are mostly from retroviral gag proteins (nucleocapsid). Prototype structure is from HIV. Also contains members involved in eukaryotic gene regulation, such as C. elegans GLH-1. Structure is an 18-residue zinc finger.

                          10
                  ....*....|....*..
gi 42571091    69 GRCFNCGVDGHWARDCT 85
Cdd:pfam00098   1 GKCYNCGEPGHIARDCP 17

zinc finger;

                           10
                   ....*....|....*..
gi 42571091     92 KCYRCGERGHIERNCKN 108
Cdd:smart00343   1 KCYNCGKEGHIARDCPS 17

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).

                        10        20
                ....*....|....*....|....*...
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVE 47
Cdd:cd00590  45 EFESPEDAEKALEALNGTELGGRPLKVS 72

RNA recognition motif (RRM) found in fission yeast pre-mRNA-splicing factor Srp1p, Arabidopsis thaliana arginine/serine-rich-splicing factor RSp31 and similar proteins; This subfamily corresponds to the RRM of Srp1p and RRM2 of plant SR splicing factors. Srp1p is encoded by gene srp1 from fission yeast Schizosaccharomyces pombe. It plays a role in the pre-mRNA splicing process, but is not essential for growth. Srp1p is closely related to the SR protein family found in Metazoa. It contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a glycine hinge and a RS domain in the middle, and a C-terminal domain. The family also includes a novel group of arginine/serine (RS) or serine/arginine (SR) splicing factors existing in plants, such as A. thaliana RSp31, RSp35, RSp41 and similar proteins. Like vertebrate RS splicing factors, these proteins function as plant splicing factors and play crucial roles in constitutive and alternative splicing in plants. They all contain two RRMs at their N-terminus and an RS domain at their C-terminus.

                        10        20        30
                ....*....|....*....|....*....|.
gi 42571091  20 EFGDPRDADDARHYLDGRDFDGSRITVEFSR 50
Cdd:cd12233  40 EFEDSEDATKALEALHGSRIDGSVLTVEFVK 70