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2  structures 91  species 0  interactions 336  sequences 8  architectures

Family: POM121 (PF15229)

Summary: POM121 family

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 "POM121". More...

POM121 Edit Wikipedia article

POM121
Identifiers
Aliases POM121, P145, POM121A, POM121 transmembrane nucleoporin
External IDs MGI: 2137624 HomoloGene: 70878 GeneCards: POM121
Gene location (Human)
Chromosome 7 (human)
Chr. Chromosome 7 (human)[1]
Chromosome 7 (human)
Genomic location for POM121
Genomic location for POM121
Band 7q11.23 Start 72,879,365 bp[1]
End 72,951,440 bp[1]
RNA expression pattern
PBB GE POM121 213360 s at fs.png

PBB GE POM121 212178 s at fs.png
More reference expression data
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_001257190
NM_172020

NM_148932

RefSeq (protein)

NP_001244119
NP_742017

NP_683734

Location (UCSC) Chr 7: 72.88 – 72.95 Mb Chr 7: 135.38 – 135.39 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Nuclear envelope pore membrane protein POM 121 is a protein that in humans is encoded by the POM121 gene.[5][6][7] Alternatively spliced variants that encode different protein isoforms have been described but the full-length nature of only one has been determined.[8]

Function

The nuclear envelope creates distinct nuclear and cytoplasmic compartments in eukaryotic cells. It consists of two concentric membranes perforated by nuclear pores, large protein complexes that form aqueous channels to regulate the flow of macromolecules between the nucleus and the cytoplasm. These complexes are composed of at least 100 different polypeptide subunits, many of which belong to the nucleoporin family. This gene encodes a member of the FG-repeat-containing nucleoporins. The protein encoded by this gene is an integral membrane protein that localizes to the central spoke ring complex and participates in anchoring the nuclear pore complex to the nuclear envelope.[8]

Antibodies against this protein can be used to identify the nuclear envelope in immunofluorescence experiments.[9]

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000196313 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000053293 - Ensembl, May 2017
  3. ^ "Human PubMed Reference:". 
  4. ^ "Mouse PubMed Reference:". 
  5. ^ Hallberg E, Wozniak RW, Blobel G (Aug 1993). "An integral membrane protein of the pore membrane domain of the nuclear envelope contains a nucleoporin-like region". J Cell Biol. 122 (3): 513–21. doi:10.1083/jcb.122.3.513. PMC 2119659Freely accessible. PMID 8335683. 
  6. ^ Ishikawa K, Nagase T, Suyama M, Miyajima N, Tanaka A, Kotani H, Nomura N, Ohara O (Dec 1998). "Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro". DNA Res. 5 (3): 169–76. doi:10.1093/dnares/5.3.169. PMID 9734811. 
  7. ^ Funakoshi T, Maeshima K, Yahata K, Sugano S, Imamoto F, Imamoto N (Oct 2007). "Two distinct human POM121 genes: requirement for the formation of nuclear pore complexes". FEBS Lett. 581 (25): 4910–6. doi:10.1016/j.febslet.2007.09.021. PMID 17900573. 
  8. ^ a b "Entrez Gene: POM121 POM121 membrane glycoprotein (homo sapiens)". 
  9. ^ Kihlmark M, Imreh G, Hallberg E (October 2001). "Sequential degradation of proteins from the nuclear envelope during apoptosis". J. Cell Sci. 114 (Pt 20): 3643–53. PMID 11707516. 

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.

POM121 family Provide feedback

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Literature references

  1. Funakoshi T, Maeshima K, Yahata K, Sugano S, Imamoto F, Imamoto N;, FEBS Lett. 2007;581:4910-4916.: Two distinct human POM121 genes: requirement for the formation of nuclear pore complexes. PUBMED:17900573 EPMC:17900573


This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

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
(34)
Full
(336)
Representative proteomes UniProt
(487)
NCBI
(1102)
Meta
(0)
RP15
(44)
RP35
(88)
RP55
(234)
RP75
(314)
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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
(34)
Full
(336)
Representative proteomes UniProt
(487)
NCBI
(1102)
Meta
(0)
RP15
(44)
RP35
(88)
RP55
(234)
RP75
(314)
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
(34)
Full
(336)
Representative proteomes UniProt
(487)
NCBI
(1102)
Meta
(0)
RP15
(44)
RP35
(88)
RP55
(234)
RP75
(314)
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:A6NNC1
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Eberhardt R , Coggill P , Hetherington K
Number in seed: 34
Number in full: 336
Average length of the domain: 186.70 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 27.12 %

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 27.0
Noise cut-off 25.1 26.7
Model length: 234
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the POM121 domain has been found. There are 2 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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