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0  structures 30  species 0  interactions 80  sequences 1  architecture

Family: PGC7_Stella (PF15549)

Summary: PGC7/Stella/Dppa3 domain

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This is the Wikipedia entry entitled "DPPA3". More...

DPPA3 Edit Wikipedia article

DPPA3
Identifiers
Aliases DPPA3, STELLA, developmental pluripotency associated 3, Pgc7
External IDs HomoloGene: 138483 GeneCards: DPPA3
Gene location (Human)
Chromosome 12 (human)
Chr. Chromosome 12 (human)[1]
Chromosome 12 (human)
Genomic location for DPPA3
Genomic location for DPPA3
Band 12p13.31 Start 7,711,454 bp[1]
End 7,717,559 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_199286

n/a

RefSeq (protein)

NP_954980

n/a

Location (UCSC) Chr 12: 7.71 – 7.72 Mb n/a
PubMed search [2] n/a
Wikidata
View/Edit Human

Developmental pluripotency-associated protein 3 is a protein that in humans is encoded by the DPPA3 gene.[3]

This gene encodes a protein that in mice may function as a maternal factor during the preimplantation stage of development. In mice, this gene may play a role in transcriptional repression, cell division, and maintenance of cell pluripotentiality. In humans, related intronless loci are located on chromosomes 14 and X.[3]

References

Further reading


This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

PGC7/Stella/Dppa3 domain Provide feedback

The domain belongs to a fast evolving family known only from the placental mammals [1-3]. The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization [3]. This suggests that it might bind methylated DNA sequences directly [4]. The conserved core includes a postively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion [4]. Most placental mammals contain 3-6 paralogs of this domain family. The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins [4].

Literature references

  1. Payer B, Saitou M, Barton SC, Thresher R, Dixon JP, Zahn D, Colledge WH, Carlton MB, Nakano T, Surani MA;, Curr Biol. 2003;13:2110-2117.: Stella is a maternal effect gene required for normal early development in mice. PUBMED:14654002 EPMC:14654002

  2. Clark AT, Rodriguez RT, Bodnar MS, Abeyta MJ, Cedars MI, Turek PJ, Firpo MT, Reijo Pera RA;, Stem Cells. 2004;22:169-179.: Human STELLAR, NANOG, and GDF3 genes are expressed in pluripotent cells and map to chromosome 12p13, a hotspot for teratocarcinoma. PUBMED:14990856 EPMC:14990856

  3. Nakamura T, Arai Y, Umehara H, Masuhara M, Kimura T, Taniguchi H, Sekimoto T, Ikawa M, Yoneda Y, Okabe M, Tanaka S, Shiota K, Nakano T;, Nat Cell Biol. 2007;9:64-71.: PGC7/Stella protects against DNA demethylation in early embryogenesis. PUBMED:17143267 EPMC:17143267

  4. Iyer LM, Abhiman S, Aravind L;, Prog Mol Biol Transl Sci. 2011;101:25-104.: Natural history of eukaryotic DNA methylation systems. PUBMED:21507349 EPMC:21507349


This tab holds annotation information from the InterPro database.

InterPro entry IPR029096

Dppa3 (developmental pluripotency-associated protein 3), also known as Stella or PGC7, belongs to family known only in placental mammals [PUBMED:14654002, PUBMED:14990856, PUBMED:17143267]. The PGC7/Stella/Dppa3 protein protects imprinted regions from demethylation post-fertilization [PUBMED:17143267]. This suggests that it might bind methylated DNA sequences directly [PUBMED:21507349]. Dppa3 also seems to be involved in the demethylation process during reprogramming of embryonic germ cell precursors [PUBMED:23595900]. Most placental mammals contain 3-6 paralogues of this family.

The conserved core of Dppa3 includes a positively charged helical segment and a C-terminal CXCXXC motif that is predicted to chelate a metal ion [PUBMED:21507349]. The CXCXXC motif is also conserved in a subset of fungal MBD4-like proteins [PUBMED:21507349].

Gene Ontology

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Domain organisation

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(18)
Full
(80)
Representative proteomes UniProt
(98)
NCBI
(231)
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(0)
RP15
(21)
RP35
(28)
RP55
(41)
RP75
(72)
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  Seed
(18)
Full
(80)
Representative proteomes UniProt
(98)
NCBI
(231)
Meta
(0)
RP15
(21)
RP35
(28)
RP55
(41)
RP75
(72)
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  Seed
(18)
Full
(80)
Representative proteomes UniProt
(98)
NCBI
(231)
Meta
(0)
RP15
(21)
RP35
(28)
RP55
(41)
RP75
(72)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Manual
Previous IDs: DPPA3;
Type: Family
Author: Iyer LM, Aravind L, Eberhardt RY, Coggill P
Number in seed: 18
Number in full: 80
Average length of the domain: 147.20 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 84.03 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 32.3 32.3
Trusted cut-off 35.0 33.2
Noise cut-off 28.6 28.6
Model length: 166
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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