U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002280013  11 KWCDFCKIYIANNPLSIR-THEIGKRHKDNVTKRL 44
Cdd:pfam06220   4 YYCDYCDCYLTHDSPSVRkSHNGGRKHKDNVKDYY 38

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1002280013  92 SAAPGDGWEFDSTSGYYYDKSTGLYFDSNSGFYYSDGLGKWVTQEEAYA 140
Cdd:cd16165     1 SADGAGDWVLDSKSGYYYNAATRYYYDPKTGMYYSDETGKWTTQPPEHA 49

U1-like zinc finger; Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.

                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 1002280013    8 QGNKWCDFCKIYIANNPlSIRTHEIGKRHKDNVTKR 43
Cdd:smart00451   1 TGGFYCKLCNVTFTDEI-SVEAHLKGKKHKKNVKKR 35

OCRE domain found in Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) and similar proteins found in plant; ZOP1 is a novel plant-specific nucleic acid-binding protein required for both RNA-directed DNA methylation (RdDM) and pre-mRNA splicing. It promotes RNA polymerase IV (Pol IV)-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. As a pre-mRNA splicing factor, ZOP1 associates with several typical splicing proteins as well as with RNA polymerase II (RNAP II and Pol II). It also shows both RdDM-dependent and -independent roles in transcriptional silencing. ZOP1 contains an N-terminal C2H2-type ZnF domain and an OCtamer REpeat (OCRE) domain that is usually related to RNA processing.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1002280013  92 SAAPGDGWEFDSTSGYYYDKSTGLYFDSNSGFYYSDGLGKWVTQEEAYA 140
Cdd:cd16165     1 SADGAGDWVLDSKSGYYYNAATRYYYDPKTGMYYSDETGKWTTQPPEHA 49

OCRE domain found in Suppressor of ABI3-5 (SUA) and similar proteins; SUA is an RNA-binding protein located in the nucleus and expressed in all plant tissues. It functions as a splicing factor that influences seed maturation by controlling alternative splicing of ABI3. The suppression of the cryptic ABI3 intron indicates a role of SUA in mRNA processing. SUA also interacts with the prespliceosomal component U2AF65, the larger subunit of the conserved pre-mRNA splicing factor U2AF. SUA contains two RNA recognition motifs surrounding a zinc finger domain, an OCtamer REpeat (OCRE) domain, and a Gly-rich domain close to the C-terminus.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1002280013  92 SAAPGDGWEFDSTSGYYYDKSTGLYFDSNSGFYYSDGLGKWvtqeeaYAWAKTSQA 147
Cdd:cd16166     1 KAAPPSGFVYDPASGYYYDASSGYYYDANTGLYYDAASGRW------YSYDEETGQ 50

OCRE domain found in RNA-binding protein 5 (RBM5) and similar proteins; RBM5 is also called protein G15, H37, putative tumor suppressor LUCA15, or renal carcinoma antigen NY-REN-9. It is a known modulator of apoptosis. It acts as a tumor suppressor or an RNA splicing factor. RBM5 shows high sequence similarity to RNA-binding protein 6 (RBM6 or NY-LU-12 or g16 or DEF-3). Both of them specifically binds poly(G) RNA. RBM5 contains two N-terminal RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1002280013  90 DTSAapgdgWEFDSTSGYYYDKSTGLYFDSNSGFYYSDglgkwVTQEEAYaWAKTSQA 147
Cdd:cd16168     4 DTST-----YQYDESSGYYYDPITGLYYDPNSQYYYNS-----LTQQYLY-WDGEKQT 50

OCRE domain found in angiogenic factor VG5Q and similar proteins; VG5Q, also called angiogenic factor with G patch and FHA domains 1 (AGGF1), or G patch domain-containing protein 7, or vasculogenesis gene on 5q protein, functions as a potent angiogenic factor in promoting angiogenesis through interacting with TWEAK (also known as TNFSF12), which is a member of the tumor necrosis factor (TNF) superfamily that induces angiogenesis in vivo. VG5Q can bind to the surface of endothelial cells and promote cell proliferation, suggesting that it may act in an autocrine fashion. The chromosomal translocation t(5;11) and the E133K variant in VG5Q are associated with Klippel-Trenaunay syndrome (KTS), a disorder characterized by diverse effects in the vascular system. In addition to a forkhead-associated (FHA) domain and a G-patch motif, VG5Q contains an N-terminal OCtamer REpeat (OCRE) domain that is characterized by a 5-fold, imperfectly repeated octameric sequence.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1002280013  98 GWEFDSTSGYYYDKSTGLYFDSNSGFYYSDGLGKWVTQEEA 138
Cdd:cd16164     7 GFVYDEATGMYYDPSTGYYYDSETQLYYDPNTGTYYYYDEE 47

U1 zinc finger; This family consists of several U1 small nuclear ribonucleoprotein C (U1-C) proteins. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site (ss) at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' ss is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' ss. Binding of TIA-1 in the vicinity of a 5' ss helps to stabilize U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator. This domain is probably a zinc-binding. It is found in multiple copies in some members of the family.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002280013  11 KWCDFCKIYIANNPLSIR-THEIGKRHKDNVTKRL 44
Cdd:pfam06220   4 YYCDYCDCYLTHDSPSVRkSHNGGRKHKDNVKDYY 38

OCRE domain found in RNA-binding protein 6 (RBM6) and similar proteins; RBM6, also called lung cancer antigen NY-LU-12, or protein G16, or RNA-binding protein DEF-3, has been predicted to be a nuclear factor based on its nuclear localization signal. It shows high sequence similarity to RNA-binding protein 5 (RBM5 or LUCA15 or NY-REN-9). Both specifically binds poly(G) RNA. RBM6 contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, a nuclear localization signal, and a G-patch/D111 domain. In contrast to RBM5, RBM6 has an additional unique domain, the POZ (poxvirus and zinc finger) domain, which may be involved in protein-protein interactions and inhibit binding of target sequences by zinc fingers.

                          10        20
                  ....*....|....*....|....*..
gi 1002280013  99 WEFDSTSGYYYDKSTGLYFDSNSGFYY 125
Cdd:cd16163     9 YRSDPDSGYIYDPETGYYYDPVTGLYY 35

OCRE domain found in RNA-binding protein RBM5, RBM10, and similar proteins; RBM5 is a known modulator of apoptosis. It may also act as a tumor suppressor or an RNA splicing factor; it specifically binds poly(G) RNA. RBM10, a paralog of RBM5, may play an important role in mRNA generation, processing, and degradation in several cell types. The rat homolog of human RBM10 is protein S1-1, a hypothetical RNA binding protein with poly(G) and poly(U) binding capabilities. Both RBM5 and RBM10, contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), an OCtamer REpeat (OCRE) domain, two C2H2-type zinc fingers, and a G-patch/D111 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002280013  95 PGDGWEFDSTSGYYYDKSTGLYFDSNSG-FYYSDG 128
Cdd:cd16162    12 ETSGYYYDPTTGLYYDPNSQYFYNSQTQqYLYWDQ 46