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0  structures 116  species 0  interactions 339  sequences 5  architectures

Family: RNF111_N (PF15303)

Summary: E3 ubiquitin-protein ligase Arkadia N-terminus

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "RNF111". More...

RNF111 Edit Wikipedia article

RNF111
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases RNF111, ARK, ring finger protein 111, hRNF111
External IDs MGI: 1934919 HomoloGene: 9741 GeneCards: RNF111
Gene location (Human)
Chromosome 15 (human)
Chr. Chromosome 15 (human)[1]
Chromosome 15 (human)
Genomic location for RNF111
Genomic location for RNF111
Band n/a Start 58,865,175 bp[1]
End 59,097,419 bp[1]
RNA expression pattern
PBB GE RNF111 218761 at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001270528
NM_001270529
NM_001270530
NM_017610
NM_001330331

NM_033604

RefSeq (protein)

NP_001257457
NP_001257458
NP_001257459
NP_001317260
NP_060080

NP_291082

Location (UCSC) Chr 15: 58.87 – 59.1 Mb Chr 15: 70.43 – 70.5 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

E3 ubiquitin-protein ligase Arkadia is an enzyme that in humans is encoded by the RNF111 gene.[5][6]

Function

The protein encoded by this gene contains a RING finger domain, a motif known to be involved in protein-protein and protein-DNA interactions. The mouse counterpart of this gene (Rnf111/arkadia) has been shown to genetically interact with the transforming growth factor (TGF) beta-like factor Nodal, and act as a modulator of the nodal signaling cascade, which is essential for the induction of mesoderm during embryonic development.[6]

Interactions

RNF111 has been shown to interact with Mothers against decapentaplegic homolog 7[7] and Mothers against decapentaplegic homolog 3.[7][8]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000157450 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000032217 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Episkopou V, Arkell R, Timmons PM, Walsh JJ, Andrew RL, Swan D (Apr 2001). "Induction of the mammalian node requires Arkadia function in the extraembryonic lineages". Nature. 410 (6830): 825–30. PMID 11298452. doi:10.1038/35071095. 
  6. ^ a b "Entrez Gene: RNF111 ring finger protein 111". 
  7. ^ a b Koinuma D, Shinozaki M, Komuro A, Goto K, Saitoh M, Hanyu A, Ebina M, Nukiwa T, Miyazawa K, Imamura T, Miyazono K (Dec 2003). "Arkadia amplifies TGF-beta superfamily signalling through degradation of Smad7". The EMBO Journal. 22 (24): 6458–70. PMC 291827Freely accessible. PMID 14657019. doi:10.1093/emboj/cdg632. 
  8. ^ Yuzawa H, Koinuma D, Maeda S, Yamamoto K, Miyazawa K, Imamura T (Jan 2009). "Arkadia represses the expression of myoblast differentiation markers through degradation of Ski and the Ski-bound Smad complex in C2C12 myoblasts". Bone. 44 (1): 53–60. PMID 18950738. doi:10.1016/j.bone.2008.09.013. 

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.

E3 ubiquitin-protein ligase Arkadia N-terminus Provide feedback

This domain is found at the N-terminus of E3 ubiquitin-protein ligase Arkadia [1].

Literature references

  1. Episkopou V, Arkell R, Timmons PM, Walsh JJ, Andrew RL, Swan D;, Nature. 2001;410:825-830.: Induction of the mammalian node requires Arkadia function in the extraembryonic lineages. PUBMED:11298452 EPMC:11298452


This tab holds annotation information from the InterPro database.

InterPro entry IPR029306

This domain is found at the N terminus of E3 ubiquitin-protein ligase Arkadia. Arkadia plays a role in embryonic development [PUBMED:11298452]. Proteins containing this domain also include protein C18orf25 from humans.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(11)
Full
(339)
Representative proteomes UniProt
(528)
NCBI
(1696)
Meta
(0)
RP15
(31)
RP35
(81)
RP55
(193)
RP75
(266)
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PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(11)
Full
(339)
Representative proteomes UniProt
(528)
NCBI
(1696)
Meta
(0)
RP15
(31)
RP35
(81)
RP55
(193)
RP75
(266)
Alignment:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(11)
Full
(339)
Representative proteomes UniProt
(528)
NCBI
(1696)
Meta
(0)
RP15
(31)
RP35
(81)
RP55
(193)
RP75
(266)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download    
Gzipped Download   Download   Download   Download   Download   Download   Download   Download    

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.

Note: You can also download the data file for the tree.

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: Jackhmmer:Q96B23
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R , Coggill P , Hetherington K
Number in seed: 11
Number in full: 339
Average length of the domain: 243.50 aa
Average identity of full alignment: 47 %
Average coverage of the sequence by the domain: 37.78 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.0 27.0
Trusted cut-off 27.3 38.4
Noise cut-off 23.6 23.2
Model length: 277
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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