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 transposaseenzymes.[7]
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 compositionedit
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 neighborhoodedit
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.
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
Orthologsedit
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
Structureedit
Proteinedit
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]
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]
mRNAedit
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 distributionedit
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.
Referencesedit
^ abcGRCh38: 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.
fam200a, c7orf38, gene, located, chromosome, human, genome, gene, expressed, nearly, tissue, types, very, levels, evolutionarily, found, throughout, kingdom, animalia, while, function, protein, fully, understood, scientific, community, bioinformatic, tools, ha. 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 FAM200AIdentifiersAliasesFAM200A C7orf38 family with sequence similarity 200 member AExternal IDsHomoloGene 89159 GeneCards FAM200AGene location Human Chr Chromosome 7 human 1 Band7q22 1Start99 546 300 bp 1 End99 558 536 bp 1 RNA expression patternBgeeHumanMouse ortholog Top expressed inganglionic eminenceAchilles tendonislet of Langerhanscerebellar hemispherestromal cell of endometriumanterior pituitaryspermgastrocnemius muscleBrodmann area 9prefrontal cortexn aMore reference expression dataBioGPSn aGene ontologyMolecular functionprotein binding DNA binding transcription factor activity RNA polymerase II specific DNA bindingCellular componentintegral component of membrane membrane cytoplasm nucleoplasmBiological processregulation of transcription by RNA polymerase IISources Amigo QuickGOOrthologsSpeciesHumanMouseEntrez221786n aEnsemblENSG00000221909n aUniProtQ8TCP9n aRefSeq mRNA NM 145111n aRefSeq protein NP 659802n aLocation UCSC Chr 7 99 55 99 56 Mbn aPubMed search 2 n aWikidataView Edit Human Contents 1 Gene 2 Protein composition 3 Gene neighborhood 4 Paralogs 5 Orthologs 6 Structure 6 1 Protein 6 2 mRNA 7 Tissue distribution 8 ReferencesGene editC7orf38 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 nbsp Protein composition editThe 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 nbsp Gene neighborhood editThe four genes in closest proximity to C7orf38 on chromosome 7 exhibit similar function many of which are transcription factors 13 nbsp 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 editEight 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 42Orthologs editOrthologs 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 amp 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 39Structure editProtein edit 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 DomainIdentifiersSymbolhATPfamPF05699InterProIPR008906Available protein structures Pfam structures ECOD PDBRCSB PDB PDBe PDBjPDBsumstructure 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 nbsp mRNA edit 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 nbsp Tissue distribution editThe 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 nbsp nbsp nbsp References edit 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 JSTOR 3870923 PMC 139759 PMID 10662858 Fam200A 24 February 2010 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 Retrieved from https en wikipedia org w index php title FAM200A amp oldid 1116930564, wikipedia, wiki, book, books, library,
