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0  structures 758  species 0  interactions 987  sequences 24  architectures

Family: Med13_N (PF11597)

Summary: Mediator complex subunit 13 N-terminal

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 "MED13". More...

MED13 Edit Wikipedia article

MED13
Identifiers
Aliases MED13, ARC250, DRIP250, HSPC221, THRAP1, TRAP240, mediator complex subunit 13
External IDs MGI: 3029632 HomoloGene: 21067 GeneCards: MED13
Gene location (Human)
Chromosome 17 (human)
Chr. Chromosome 17 (human)[1]
Chromosome 17 (human)
Genomic location for MED13
Genomic location for MED13
Band n/a Start 61,942,605 bp[1]
End 62,065,282 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_005121

NM_001080931

RefSeq (protein)

NP_005112

NP_001074400

Location (UCSC) Chr 17: 61.94 – 62.07 Mb Chr 17: 86.27 – 86.36 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Mediator complex subunit 13 is a protein that in humans is encoded by the MED13 gene.[5][6]

Function

This gene encodes a component of the mediator complex (also known as TRAP, SMCC, DRIP, or ARC), a transcriptional coactivator complex thought to be required for the expression of almost all genes. The mediator complex is recruited by transcriptional activators or nuclear receptors to induce gene expression, possibly by interacting with RNA polymerase II and promoting the formation of a transcriptional pre-initiation complex. The product of this gene is proposed to form a sub-complex with MED12, cyclin C, and CDK8 that can negatively regulate transactivation by mediator.[5]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000108510 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000034297 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ a b "Entrez Gene: Mediator complex subunit 13". Retrieved 2012-05-11. 
  6. ^ Tuchin DA, Erve PR, Schumer W (1976). "Prevention of endotoxin--induced irreversible platelet aggregation in vitro". Surgical Forum. 27 (62): 22–3. PMID 1019863. 

Further reading

This article incorporates text from the United States National Library of Medicine, which is in the public domain.


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

This is the Wikipedia entry entitled "Mediator (coactivator)". More...

Mediator (coactivator) Edit Wikipedia article

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.

Mediator complex subunit 13 N-terminal Provide feedback

Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood [4].

Literature references

  1. Samuelsen CO, Baraznenok V, Khorosjutina O, Spahr H, Kieselbach T, Holmberg S, Gustafsson CM; , Proc Natl Acad Sci U S A 2003;100:6422-6427.: TRAP230/ARC240 and TRAP240/ARC250 Mediator subunits are functionally conserved through evolution. PUBMED:12738880 EPMC:12738880

  2. Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, , Mol Cell. 2004;14:553-557.: A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II. PUBMED:15175151 EPMC:15175151

  3. Sato S, Tomomori-Sato C, Parmely TJ, Florens L, Zybailov B, Swanson SK, Banks CA, Jin J, Cai Y, Washburn MP, Conaway JW, Conaway RC; , Mol Cell. 2004;14:685-691.: A set of consensus mammalian mediator subunits identified by multidimensional protein identification technology. PUBMED:15175163 EPMC:15175163

  4. Carrera I, Janody F, Leeds N, Duveau F, Treisman JE; , Proc Natl Acad Sci U S A. 2008;105:6644-6649.: Pygopus activates Wingless target gene transcription through the mediator complex subunits Med12 and Med13. PUBMED:18451032 EPMC:18451032


This tab holds annotation information from the InterPro database.

InterPro entry IPR021643

Mediator is a large complex of up to 33 proteins that is conserved from plants through fungi to humans - the number and representation of individual subunits varying with species [PUBMED:12738880],[PUBMED:15175151]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Med13 is part of the ancillary kinase module, together with Med12, CDK8 and CycC, which in yeast is implicated in transcriptional repression, though most of this activity is likely attributable to the CDK8 kinase. The large Med12 and Med13 proteins are required for specific developmental processes in Drosophila, zebrafish, and Caenorhabditis elegans but their biochemical functions are not understood [PUBMED:18451032].

Domain organisation

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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
(84)
Full
(987)
Representative proteomes UniProt
(1534)
NCBI
(2286)
Meta
(0)
RP15
(117)
RP35
(404)
RP55
(716)
RP75
(1016)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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  Seed
(84)
Full
(987)
Representative proteomes UniProt
(1534)
NCBI
(2286)
Meta
(0)
RP15
(117)
RP35
(404)
RP55
(716)
RP75
(1016)
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
(84)
Full
(987)
Representative proteomes UniProt
(1534)
NCBI
(2286)
Meta
(0)
RP15
(117)
RP35
(404)
RP55
(716)
RP75
(1016)
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.

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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: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 84
Number in full: 987
Average length of the domain: 308.10 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 18.59 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.0 26.1
Noise cut-off 25.8 25.9
Model length: 323
Family (HMM) version: 9
Download: download the raw HMM for this family

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