Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
5  structures 645  species 2  interactions 11953  sequences 434  architectures

Family: Dimer_Tnp_hAT (PF05699)

Summary: hAT family C-terminal dimerisation region

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 "FAM200A". More...

FAM200A Edit Wikipedia article

FAM200A
CBLASTHermesTransposase.jpg
Identifiers
Aliases FAM200A, C7orf38, family with sequence similarity 200 member A
External IDs HomoloGene: 89159 GeneCards: FAM200A
Gene location (Human)
Chromosome 7 (human)
Chr. Chromosome 7 (human)[1]
Chromosome 7 (human)
Genomic location for FAM200A
Genomic location for FAM200A
Band n/a Start 99,546,308 bp[1]
End 99,558,536 bp[1]
Orthologs
Species Human Mouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_145111

n/a

RefSeq (protein)

NP_659802

n/a

Location (UCSC) Chr 7: 99.55 – 99.56 Mb n/a
PubMed search [2] n/a
Wikidata
View/Edit Human

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]

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]

C7orf38 Gene Loci.

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.

Hydrophilicity Analysis.

Gene neighborhood

The four genes in closest proximity to C7orf38 on chromosome 7 exhibit similar function, many of which are transcription factors.[13]

Gene Neighborhood
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
Identifiers
Symbol hAT
Pfam PF05699
InterPro IPR008906

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]

Hermes DNA Transposase.

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.

MFOLD Secondary Structure Prediction.

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.

Est profile based on tissue type.
Est profile based on health state.
Est profile based on developmental stage.

References

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000221909 - Ensembl, May 2017
  2. ^ "Human PubMed Reference:". 
  3. ^ "University of California Santa Cruz". Retrieved 2010-05-10. 
  4. ^ "NCBI UniGene". Retrieved 2010-05-10. 
  5. ^ a b c "NCBI BLAST". Retrieved 2010-05-10. 
  6. ^ "KEGG". Retrieved 2010-05-10. 
  7. ^ 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. PMC 139759Freely accessible. PMID 10662858. doi:10.2307/3870923. 
  8. ^ "Fam200A". Retrieved 2010-05-10. 
  9. ^ "NCBI Protein Accession Number". Retrieved 2010-05-10. 
  10. ^ "AAStats. SDSC Biology WorkBench". Retrieved 2010-05-10. [permanent dead link]
  11. ^ "IP. SDSC Biology WorkBench". Retrieved 2010-05-10. [permanent dead link]
  12. ^ "SAPS. SDSC Biology WorkBench". Retrieved 2010-05-10. [permanent dead link]
  13. ^ "AceView". Retrieved 2010-05-10. 
  14. ^ "Hermes DNA Transposase". Retrieved 2010-05-10. 
  15. ^ "Fam200A". Retrieved 2010-05-10. 
  16. ^ "NCBI UniGene". Retrieved 2010-04-22. 

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.

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

  1. 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

  2. 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.

Domain organisation

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

Loading domain graphics...

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...

View options

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
(11953)
Representative proteomes UniProt
(16757)
NCBI
(24047)
Meta
(16)
RP15
(4137)
RP35
(8307)
RP55
(10358)
RP75
(12284)
Jalview View  View  View  View  View  View  View  View  View 
HTML View                 
PP/heatmap 1                

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

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

Format an alignment

  Seed
(47)
Full
(11953)
Representative proteomes UniProt
(16757)
NCBI
(24047)
Meta
(16)
RP15
(4137)
RP35
(8307)
RP55
(10358)
RP75
(12284)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

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
(11953)
Representative proteomes UniProt
(16757)
NCBI
(24047)
Meta
(16)
RP15
(4137)
RP35
(8307)
RP55
(10358)
RP75
(12284)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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: Albrecht M
Previous IDs: hATC;
Type: Domain
Sequence Ontology: SO:0000417
Author: Albrecht M , Bateman A
Number in seed: 47
Number in full: 11953
Average length of the domain: 77.10 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 16.75 %

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 21.4 21.4
Trusted cut-off 21.4 21.4
Noise cut-off 21.3 21.3
Model length: 86
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls

Hide

The tree shows the occurrence of this domain across different species. More...

Loading...

Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

Interactions

There are 2 interactions for this family. More...

DBD_Tnp_Hermes DBD_Tnp_Hermes

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 5 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.

Loading structure mapping...