Wikipedia

FAM200A

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]

FAM200A
Identifiers
AliasesFAM200A, C7orf38, family with sequence similarity 200 member A
External IDsHomoloGene: 89159; GeneCards: FAM200A; OMA:FAM200A - orthologs
Orthologs
SpeciesHumanMouse
Entrez

221786

n/a

Ensembl

ENSG00000221909

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UniProt

Q8TCP9

n/a

RefSeq (mRNA)

NM_145111

n/a

RefSeq (protein)

NP_659802

n/a

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

Gene

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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

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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

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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

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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_071373.2 863 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

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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 CAM15863.1 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

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Protein

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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
SymbolhAT
PfamPF05699
InterProIPR008906
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

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

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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

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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

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000221909 – Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  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. doi:10.2307/3870923. JSTOR 3870923. PMC 139759. PMID 10662858.
  8. ^ "Fam200A". 24 February 2010. 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". Archived from the original on 2010-05-22. Retrieved 2010-05-10.
  16. ^ "NCBI UniGene". Retrieved 2010-04-22.
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