Summary: hAT family C-terminal dimerisation region
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This is the Wikipedia entry entitled "FAM200A". More...
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FAM200A Edit Wikipedia article
|, C7orf38, family with sequence similarity 200 member A|
C7orf38 is a gene located on chromosome 7 in the human genome. The gene is expressed in nearly all tissue types at very low levels. Evolutionarily, it can be found throughout the kingdom animalia. While the function of the protein is not fully understood by the scientific community, bioinformatic tools have shown that the protein bares much similarity to zinc finger or transposase proteins. Many of its orthologs, paralogs, and neighboring genes have been shown to possess zinc finger domains. The protein contains a hAT dimerization domain nears its C-terminus. This domain is highly conserved in transposase enzymes.
C7orf38 is located on chromosome 7 at q22.1. Its genomic sequence contains 5,612 bp. The predominant transcript contains two exons and is 2,507 bp in length. The translated protein contains 573 amino acids.
The 573 amino acid protein has a molecular weight of 66,280.05. The isoelectric point was found to occur at a pH of 5.775, about 1.6 pH lower than that of the average human pH. Two deviations from prototypical human proteins are evident. The protein contains a less than expected number of glycine residues, and is rich in leucine residues. There are not sections of strong hydrophobicity or hydrophilicity. Thus, it is not predicted to be a transmembrane protein.
The four genes in closest proximity to C7orf38 on chromosome 7 exhibit similar function, many of which are transcription factors.
|ZNF789||Start: 98,908,451 bp from pter
End: 98,923,153 bp from pter Size: 14,703 bases Orientation: plus strand
|The gene encodes the zinc finger protein 789. Functionally, the gene has been proposed to participate in regulation of transcription. It is expected to use zinc ion binding.|
|ZNF394||Start: 98,928,790 bp from pter
End: 98,935,813 bp from pter Size: 7,024 bases OrientationÂ : minus strand
|The gene encodes zinc finger protein 394. Over expression over ZNF394 inhibits the transchription of c-jun and Ap-1. Suggesting that it is a transcriptional repressor.|
|ZKSCAN5||Start: 98,940,209 bp from pter
End: 98,969,381 bp from pter Size: 29,173 bases Orientation: plus strand
|The gene encodes zinc finger with KRAB and SCAN domains 5. This gene encodes a zinc finger protein of the Kruppel family. The protein contains a SCAN box and a KRAB A domain.|
|ZNF655||Start: 98,993,981 bp from pter
End: 99,012,012 bp from pter Size: 18,032 bases Orientation: plus strand
|The gene encodes zinc finger protein 655. Numerous alternatively spliced transcripts encoding distinct isoforms have been discovered.|
|Mihuya||Start: 99,149,738 bp from pter
End: 99,149,626 bp from pter Size: 112 bases Orientation: plus strand
|The Mihuya gene does not encode a large or known functional protein. The antisense relationship to C7orf38 raises the possibility for regulation of expression.|
|Name||NCBI Accession Number||Length (AA)||% Identity to C7orf38||% Similarity to C7orf38|
|hypothetical protein LOC285550||NP_001138663.1||657||79||91|
|zinc finger MYM-type protein 6||NP_009098.3||1325||38||60|
|SCAN domain-containing protein 3||NP_443155.1||1325||39||60|
|zinc finger BED domain-containing protein 5||NP_067034.2||692||35||57|
|transposon-derived Buster3 transposase-like||NP_071373.2||594||32||53|
|general transcription factor II-I repeat domain-containing protein 2B||NP_001003795.1||949||25||46|
|GTF2I repeat domain containing 2||NP_775808.2||949||24||45|
|EPM2A interacting protein 1||NP_055620.1||607||22||42|
Orthologs to C7orf38 can be traced back evolutionarily through plants. The following is not an extensive list of orthologs. It is intended to provide an evolutionary overview of the conservation of C7orf38.
|Common name||Genus & species||NCBI accession number||Length (AA)||% Identity to C7orf38||% Similarity to C7orf38|
|Macaque monkey||Macaca fascicularis||BAE01234.1||573||96||98|
|Domestic dog||Canis lupus familiaris||ABF22701.1||609||37||60|
|Frog||Xenopus (Silurana) tropicalis||ABF20551.1||656||37||56|
|Zebra fish||Danio rerio||XP_001340213.1||609||37||56|
|Pea aphid||Acyrthosiphon pisum||XP_001943527.1||659||36||54|
|Sea squirt||Ciona intestinalis||XP_002119512.1||524||34||52|
|Puffer fish||Tetraodon nigroviridis||CAF95678.1||539||28||47|
|Sea urchin||Strongylocentrotus purpuratus||ABF20546.1||625||27||47|
|Grass plant||Sorghum bicolor||XP_002439156.1||524||25||40|
|Broad leaf tree||Populus trichocarpa||XP_002319808.1||788||21||39|
CBLast was used to determine a structurally related protein with experimentally determined structure. The protein Hermes DNA transposase, of the Hermes DBD superfamily, was shown to be structurally similar (Evalue: 1E-6).
|hAT Dimerization Domain|
The hAT dimerization domain is found at the C-terminus of transposase elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerization domain forms extremely stable dimers in vitro.
The MFOLD program available at Rensselaer BioInformatics Server was used to predict secondary structure of the mature mRNA sequence. The primary sequence of the mRNA secondary structures displayed high levels of conservation in orthologs, suggesting structural importance.
The gene appears to be expressed in most tissue types. Very low levels of expression were observed through est profiles, and no deviation was observed between health or developmental states.
- GRCh38: Ensembl release 89: ENSG00000221909 - Ensembl, May 2017
- "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
- "University of California Santa Cruz". Retrieved 2010-05-10.
- "NCBI UniGene". Retrieved 2010-05-10.
- "NCBI BLAST". Retrieved 2010-05-10.
- "KEGG". Retrieved 2010-05-10.
- Essers L, Adolphs RH, Kunze R (2000). "A highly conserved domain of the maize activator transposase is involved in dimerization". Plant Cell. 12 (2): 211â€“224. doi:10.2307/3870923. JSTORÂ 3870923. PMCÂ 139759. PMIDÂ 10662858.
- "Fam200A". Retrieved 2010-05-10.
- "NCBI Protein Accession Number". Retrieved 2010-05-10.
- "AAStats. SDSC Biology WorkBench". Retrieved 2010-05-10.[permanent dead link]
- "IP. SDSC Biology WorkBench". Retrieved 2010-05-10.[permanent dead link]
- "SAPS. SDSC Biology WorkBench". Retrieved 2010-05-10.[permanent dead link]
- "AceView". Retrieved 2010-05-10.
- "Hermes DNA Transposase". Retrieved 2010-05-10.
- "Fam200A". Archived from the original on 2010-05-22. Retrieved 2010-05-10.
- "NCBI UniGene". Retrieved 2010-04-22.
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.
hAT family C-terminal dimerisation region Provide feedback
This dimerisation region is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation region forms extremely stable dimers in vitro .
This tab holds annotation information from the InterPro database.
InterPro entry IPR008906
This dimerisation domain is found at the C terminus of the transposases of elements belonging to the Activator superfamily (hAT element superfamily). The isolated dimerisation domain forms extremely stable dimers in vitro [ PUBMED:10662858 , PUBMED:11454746 ].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||protein dimerization activity (GO:0046983)|
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
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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 and the UniProtKB sequence database. More...
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We make a range of alignments for each Pfam-A family:
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You can see the alignments as HTML or in three different sequence viewers:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
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.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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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.
|Seed source:||Albrecht M|
|Author:||Albrecht M , Bateman A|
|Number in seed:||47|
|Number in full:||22680|
|Average length of the domain:||77.90 aa|
|Average identity of full alignment:||20 %|
|Average coverage of the sequence by the domain:||15.99 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
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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 Dimer_Tnp_hAT domain has been found. There are 10 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.