Your browser is unable to support new features implemented in HTML5 and CSS3 to render this site as intended. Your experience may suffer from functionality degradation but the site should remain usable. We strongly recommend the latest version of Google Chrome, OS X Safari or Mozilla Firefox. As Safari is bundled with OS X, if you are unable to upgrade to a newer version of OS X, we recommend using an open source browser. Dismiss message
IPR003604 is a Matrin/U1-C-like, C2H2-type zinc finger.
<p>Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [[cite:PUB00035807], [cite:PUB00035805], [cite:PUB00035806], [cite:PUB00035804], [cite:PUB00014077]]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few [[cite:PUB00035812]]. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.</p> <p>C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short β-hairpin and an α-helix (β/β/α structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 [[cite:PUB00035808]]. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes [[cite:PUB00035809]]. Transcription factors usually contain several Znf's (each with a conserved β/β/α structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short α-helix in the Znf, the Znf spanning 3-4 bases of the DNA [[cite:PUB00035811]]. C2H2 zinc fingers can also bind to RNA and protein targets [[cite:PUB00043274]].</p> <p>This entry represents U1-type zinc finger domains, a family of C2H2-type zinc fingers present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins [[cite:PUB00031914], [cite:PUB00035823]].</p>
This description is obtained from EB-eye REST.
GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .
GO term | Namespace | Name | Definition | Relationships |
---|---|---|---|---|
Molecular function | Nucleic acid binding | Interacting selectively and non-covalently with any nucleic acid. | ||
Molecular function | Zinc ion binding | Interacting selectively and non-covalently with zinc (Zn) ions. |
Transcript | Name | Description | Predicted domains | Domain count |
---|---|---|---|---|
– | PREDICTED: zinc finger protein 593-like [Cucumis sativus] gi|449451052|ref|XP_004143276.1| | 10 | ||
– | PREDICTED: dnaJ homolog subfamily C member 21-like [Glycine max] gi|356511845|ref|XP_003524632.1| | 13 | ||
– | Uncharacterized protein TCM_005599 [Theobroma cacao] gi|508704432|gb|EOX96328.1| | 9 | ||
– | Uncharacterized protein TCM_005599 [Theobroma cacao] gi|508704432|gb|EOX96328.1| | 15 | ||
– | PREDICTED: zinc finger RNA-binding protein-like [Cicer arietinum] gi|502126918|ref|XP_004499491.1| | 11 | ||
– | PREDICTED: zinc finger RNA-binding protein-like [Cicer arietinum] gi|502126918|ref|XP_004499491.1| | 9 | ||
– | C2H2 and C2HC zinc fingers superfamily protein isoform 1 [Theobroma cacao] gi|508719731|gb|EOY11628.1| | 7 | ||
– | PREDICTED: splicing factor 3A subunit 2-like [Cicer arietinum] gi|502155744|ref|XP_004510177.1| | 12 | ||
– | HVA22-like protein a [Medicago truncatula] gi|357476185|ref|XP_003608378.1| | 14 | ||
– | HVA22-like protein a [Medicago truncatula] gi|357476187|ref|XP_003608379.1| | 18 | ||
– | HVA22-like protein a [Medicago truncatula] gi|357476185|ref|XP_003608378.1| | 18 | ||
– | HVA22-like protein a [Medicago truncatula] gi|357476187|ref|XP_003608379.1| | 10 | ||
– | WW domain-binding protein [Medicago truncatula] gi|357475471|ref|XP_003608021.1| | 9 | ||
– | PREDICTED: dnaJ homolog subfamily C member 21-like [Glycine max] gi|356511845|ref|XP_003524632.1| | 12 | ||
– | HVA22-like protein a [Medicago truncatula] gi|357476185|ref|XP_003608378.1| | 8 | ||
– | Uncharacterized protein TCM_037031 [Theobroma cacao] gi|508782264|gb|EOY29520.1| | 7 | ||
– | PREDICTED: zinc finger protein 622-like [Glycine max] gi|356563786|ref|XP_003550140.1| | 11 | ||
– | C2H2 and C2HC zinc fingers superfamily protein isoform 1 [Theobroma cacao] gi|508727165|gb|EOY19062.1| | 12 | ||
– | PREDICTED: U1 small nuclear ribonucleoprotein C-like isoform X1 [Cicer arietinum] gi|502117894|ref|XP_004495998.1| | 13 | ||
– | HVA22-like protein; TAIR: AT1G74520.1 HVA22 homologue A; Swiss-Prot: sp|Q9S7V4|HA22A_ARATH HVA22-like protein a; TrEMBL-Plants: tr|A0A0L9UXN1|A0A0L9UXN1_PHAAN Uncharacterized protein; Found in the gene: LotjaGi1g1v0135400 | 22 | ||
– | Zinc finger protein; TAIR: AT5G61190.1 putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein; Swiss-Prot: sp|Q8AVN9|ZN346_XENLA Zinc finger protein 346; TrEMBL-Plants: tr|A0A072UVJ5|A0A072UVJ5_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi1g1v0190900 | 11 | ||
– | Zinc finger protein; TAIR: AT3G29310.1 calmodulin-binding protein-like protein; Swiss-Prot: sp|Q9LIB3|BAG8_ARATH BAG family molecular chaperone regulator 8, chloroplastic; TrEMBL-Plants: tr|C6TD17|C6TD17_SOYBN Putative uncharacterized protein; Found in the gene: LotjaGi1g1v0509600_LC | 12 | ||
– | Zinc finger protein; TAIR: AT5G61190.1 putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein; Swiss-Prot: sp|Q6PBT9|Z385B_DANRE Zinc finger protein 385B; TrEMBL-Plants: tr|V7B1Q0|V7B1Q0_PHAVU Uncharacterized protein; Found in the gene: LotjaGi1g1v0509700 | 11 | ||
– | U1 small nuclear ribonucleoprotein C; TAIR: AT4G03120.1 C2H2 and C2HC zinc fingers superfamily protein; Swiss-Prot: sp|F6HQ26|RU1C_VITVI U1 small nuclear ribonucleoprotein C; TrEMBL-Plants: tr|A0A072U5H3|A0A072U5H3_MEDTR U1 small nuclear ribonucleoprotein C; Found in the gene: LotjaGi1g1v0744200_LC | 17 | ||
– | Zinc finger matrin-type 2; TAIR: AT3G05760.1 C2H2 and C2HC zinc fingers superfamily protein; Swiss-Prot: sp|Q96NC0|ZMAT2_HUMAN Zinc finger matrin-type protein 2; TrEMBL-Plants: tr|I3SLF9|I3SLF9_LOTJA Uncharacterized protein; Found in the gene: LotjaGi1g1v0747900 | 11 | ||
– | Splicing factor 3A subunit 2; TAIR: AT2G32600.1 hydroxyproline-rich glycoprotein family protein; Swiss-Prot: sp|Q15428|SF3A2_HUMAN Splicing factor 3A subunit 2; TrEMBL-Plants: tr|I1MCD5|I1MCD5_SOYBN Uncharacterized protein; Found in the gene: LotjaGi3g1v0075400 | 13 | ||
– | Splicing factor 3A subunit 2; TAIR: AT2G32600.1 hydroxyproline-rich glycoprotein family protein; Swiss-Prot: sp|Q15428|SF3A2_HUMAN Splicing factor 3A subunit 2; TrEMBL-Plants: tr|A0A1J7GPB1|A0A1J7GPB1_LUPAN Uncharacterized protein; Found in the gene: LotjaGi3g1v0075400 | 13 | ||
– | Zinc finger protein; TAIR: AT5G61190.2 putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein; Swiss-Prot: sp|O59811|REI1_SCHPO Cytoplasmic 60S subunit biogenesis factor SPCC550.15c; TrEMBL-Plants: tr|V7AMM2|V7AMM2_PHAVU Uncharacterized protein; Found in the gene: LotjaGi3g1v0205100 | 11 | ||
– | Zinc finger protein; TAIR: AT5G61190.2 putative endonuclease or glycosyl hydrolase with C2H2-type zinc finger domain-containing protein; Swiss-Prot: sp|O59811|REI1_SCHPO Cytoplasmic 60S subunit biogenesis factor SPCC550.15c; TrEMBL-Plants: tr|V7AMM2|V7AMM2_PHAVU Uncharacterized protein; Found in the gene: LotjaGi3g1v0205100 | 17 | ||
– | HVA22-like protein; TAIR: AT1G74520.1 HVA22 homologue A; Swiss-Prot: sp|Q9S7V4|HA22A_ARATH HVA22-like protein a; TrEMBL-Plants: tr|A0A151T2F4|A0A151T2F4_CAJCA HVA22-like protein; Found in the gene: LotjaGi4g1v0040600 | 21 | ||
– | HVA22-like protein; TAIR: AT1G74520.1 HVA22 homologue A; Swiss-Prot: sp|Q9S7V4|HA22A_ARATH HVA22-like protein a; TrEMBL-Plants: tr|I1KQX1|I1KQX1_SOYBN HVA22-like protein; Found in the gene: LotjaGi4g1v0040700 | 20 | ||
– | HVA22-like protein; TAIR: AT1G69700.1 HVA22 homologue C; Swiss-Prot: sp|Q9S7V4|HA22A_ARATH HVA22-like protein a; TrEMBL-Plants: tr|A0A151T2F4|A0A151T2F4_CAJCA HVA22-like protein; Found in the gene: LotjaGi4g1v0040700 | 20 | ||
– | HVA22-like protein; TAIR: AT1G74520.1 HVA22 homologue A; Swiss-Prot: sp|Q9S7V4|HA22A_ARATH HVA22-like protein a; TrEMBL-Plants: tr|G7JV31|G7JV31_MEDTR TB2/DP1, HVA22 family protein; Found in the gene: LotjaGi4g1v0040800 | 18 | ||
– | U1 small nuclear ribonucleoprotein C; TAIR: AT1G49590.1 C2H2 and C2HC zinc fingers superfamily protein; Swiss-Prot: sp|Q7XA66|ZOP1_ARATH Zinc finger protein ZOP1; TrEMBL-Plants: tr|I3S6A8|I3S6A8_LOTJA Uncharacterized protein; Found in the gene: LotjaGi4g1v0071400 | 15 | ||
– | Chaperone protein DnaJ; TAIR: AT1G74250.1 DNAJ heat shock N-terminal domain-containing protein; Swiss-Prot: sp|Q9C911|JJJ1_ARATH DNAJ protein JJJ1 homolog; TrEMBL-Plants: tr|A0A1J7HZV7|A0A1J7HZV7_LUPAN Uncharacterized protein; Found in the gene: LotjaGi4g1v0254500 | 25 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 10 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 11 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 11 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 11 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 11 | ||
– | Zinc finger protein 385D; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|Q6AXX3|Z385D_RAT Zinc finger protein 385D; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288800_LC | 11 | ||
– | 30S ribosomal protein S3; TAIR: AT2G19380.1 RNA recognition motif (RRM)-containing protein; Swiss-Prot: sp|O64571|UBA1C_ARATH UBP1-associated proteins 1C; TrEMBL-Plants: tr|A0A1J7J0K1|A0A1J7J0K1_LUPAN Uncharacterized protein; Found in the gene: LotjaGi4g1v0288800_LC | 12 | ||
– | Zinc finger protein; TAIR: AT2G24030.1 zinc ion binding / nucleic acid binding protein; Swiss-Prot: sp|Q9UPR6|ZFR2_HUMAN Zinc finger RNA-binding protein 2; TrEMBL-Plants: tr|G7JFL6|G7JFL6_MEDTR C2H2 type zf-met: zinc-finger protein; Found in the gene: LotjaGi4g1v0288900 | 12 | ||
– | Zinc finger RNA-binding protein; TAIR: AT2G19385.1 zinc ion binding protein; Swiss-Prot: sp|O64571|UBA1C_ARATH UBP1-associated proteins 1C; TrEMBL-Plants: tr|V7CCJ3|V7CCJ3_PHAVU Uncharacterized protein; Found in the gene: LotjaGi4g1v0328300 | 13 | ||
– | Zinc finger protein; TAIR: AT4G31420.1 Zinc finger protein 622; Swiss-Prot: sp|Q8H1G5|REIL1_ARATH Cytoplasmic 60S subunit biogenesis factor REI1 homolog 1; TrEMBL-Plants: tr|I3SNF7|I3SNF7_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0065800 | 14 | ||
– | Zinc finger family protein; TAIR: AT2G36930.1 zinc finger (C2H2 type) family protein; Swiss-Prot: sp|B0BLT0|ZN593_XENTR Zinc finger protein 593; TrEMBL-Plants: tr|I3T688|I3T688_LOTJA Uncharacterized protein; Found in the gene: LotjaGi5g1v0082800 | 10 | ||
– | U1 small nuclear ribonucleoprotein C; TAIR: AT4G03120.1 C2H2 and C2HC zinc fingers superfamily protein; Swiss-Prot: sp|F6HQ26|RU1C_VITVI U1 small nuclear ribonucleoprotein C; TrEMBL-Plants: tr|I3S8F7|I3S8F7_LOTJA U1 small nuclear ribonucleoprotein C; Found in the gene: LotjaGi5g1v0261800 | 15 |
A list of co-occurring predicted domains within the L. japonicus gene space:
Predicted domain | Source | Observations | Saturation (%) |
---|---|---|---|
mobidb-lite | MobiDBLite | 1 | 2.13 |