Summary: hAT family C-terminal dimerisation region
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FAM200A Edit Wikipedia article
| FAM200A | |||||||||||||||||||||||||
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| Aliases | FAM200A, C7orf38, family with sequence similarity 200 member A | ||||||||||||||||||||||||
| External IDs | HomoloGene: 89159 GeneCards: FAM200A | ||||||||||||||||||||||||
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| Species | Human | Mouse | |||||||||||||||||||||||
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| Location (UCSC) | Chr 7: 99.55 – 99.56 Mb | n/a | |||||||||||||||||||||||
| PubMed search | [2] | n/a | |||||||||||||||||||||||
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C7orf38 is a gene located on chromosome 7 in the human genome.[3] The gene is expressed in nearly all tissue types at very low levels.[4] 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.[5] The protein contains a hAT dimerization domain nears its C-terminus.[6] This domain is highly conserved in transposase enzymes.[7]
Contents
Gene
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.[8] The translated protein contains 573 amino acids.[9]
Protein composition
The 573 amino acid protein has a molecular weight of 66,280.05.[10] 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.[11] 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.[12] There are not sections of strong hydrophobicity or hydrophilicity. Thus, it is not predicted to be a transmembrane protein.
Gene neighborhood
The four genes in closest proximity to C7orf38 on chromosome 7 exhibit similar function, many of which are transcription factors.[13]
| Name | Orientation | Function |
|---|---|---|
| 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 Orientation : 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. |
Paralogs
Eight paralogs are found in the human proteome.[5] Similar to the neighboring genes, many of the paralogs function as zinc fingers, or transcription factors.
| 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
Orthologs to C7orf38 can be traced back evolutionarily through plants.[5] 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 |
|---|---|---|---|---|---|
| Chimp | Pan troglodytes | XP_001139775.1 | 573 | 99 | 99 |
| Macaque monkey | Macaca fascicularis | BAE01234.1 | 573 | 96 | 98 |
| Horse | Equus caballus | XP_001915370.1 | 573 | 81 | 84 |
| Pig | Sus scrofa | XP_001929194 | 1323 | 39 | 61 |
| Cow | Bos taurus | XP_875656.2 | 1320 | 38 | 61 |
| Mouse | Mus musculus | CAM15594.1 | 1157 | 37 | 60 |
| Domestic dog | Canis lupus familiaris | ABF22701.1 | 609 | 37 | 60 |
| Rat | Rattus rattus | NP_001102151.1 | 1249 | 37 | 59 |
| Opossum | Monodelphis domestica | XP_001372983.1 | 608 | 37 | 59 |
| Chicken | Gallus gallus | XP_424913.2 | 641 | 37 | 58 |
| 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 |
| Beatle | Tribolium castaneum | ABF20545.1 | 599 | 35 | 55 |
| Sea squirt | Ciona intestinalis | XP_002119512.1 | 524 | 34 | 52 |
| Hydra | Hydra magnipapillata | XP_002165429.1 | 572 | 29 | 52 |
| Puffer fish | Tetraodon nigroviridis | CAF95678.1 | 539 | 28 | 47 |
| Mosquito | Anopheles gambiae | XP_558399.5 | 591 | 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 |
Structure
Protein
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).[14]
| hAT Dimerization Domain | |||||||||
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| Identifiers | |||||||||
| Symbol | hAT | ||||||||
| Pfam | PF05699 | ||||||||
| InterPro | IPR008906 | ||||||||
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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.[7]
mRNA
The MFOLD program available at Rensselaer BioInformatics Server was used to predict secondary structure of the mature mRNA sequence.[15] The primary sequence of the mRNA secondary structures displayed high levels of conservation in orthologs, suggesting structural importance.
Tissue distribution
The gene appears to be expressed in most tissue types.[16] Very low levels of expression were observed through est profiles, and no deviation was observed between health or developmental states.
References
- ^ a b c 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.
- ^ a b c "NCBI BLAST". Retrieved 2010-05-10.
- ^ "KEGG". Retrieved 2010-05-10.
- ^ a b Essers L, Adolphs RH, Kunze R (2000). "A highly conserved domain of the maize activator transposase is involved in dimerization". Plant Cell. 12 (2): 211–224. doi:10.2307/3870923. PMC 139759. PMID 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.
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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 [1].
Literature references
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Essers L, Adolphs RH, Kunze R; , Plant Cell 2000;12:211-224.: A highly conserved domain of the maize activator transposase is involved in dimerization. PUBMED:10662858 EPMC:10662858
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Rubin E, Lithwick G, Levy AA; , Genetics 2001;158:949-957.: Structure and evolution of the hAT transposon superfamily. PUBMED:11454746 EPMC:11454746
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].
Gene Ontology
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) |
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 (47) |
Full (15550) |
Representative proteomes | UniProt (24759) |
NCBI (37105) |
Meta (16) |
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| RP15 (3525) |
RP35 (7972) |
RP55 (10819) |
RP75 (14052) |
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| Jalview | |||||||||
| HTML | |||||||||
| PP/heatmap | 1 | ||||||||
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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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 (47) |
Full (15550) |
Representative proteomes | UniProt (24759) |
NCBI (37105) |
Meta (16) |
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|---|---|---|---|---|---|---|---|---|---|
| RP15 (3525) |
RP35 (7972) |
RP55 (10819) |
RP75 (14052) |
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| Raw Stockholm | |||||||||
| Gzipped | |||||||||
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
| Seed source: | Albrecht M |
| Previous IDs: | hATC; |
| Type: | Domain |
| Sequence Ontology: | SO:0000417 |
| Author: |
Albrecht M  , Bateman A
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| Number in seed: | 47 |
| Number in full: | 15550 |
| Average length of the domain: | 77.50 aa |
| Average identity of full alignment: | 20 % |
| Average coverage of the sequence by the domain: | 16.16 % |
HMM information
| HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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| Model details: |
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| Model length: | 86 | ||||||||||||
| Family (HMM) version: | 15 | ||||||||||||
| Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 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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