Ccdc78

Last updated
CCDC78
Identifiers
Aliases CCDC78 , C16orf25, CNM4, JFP10, hsCcdc78, coiled-coil domain containing 78
External IDs OMIM: 614666 MGI: 2685784 HomoloGene: 105408 GeneCards: CCDC78
Orthologs
SpeciesHumanMouse
Entrez

124093

381077

Ensembl

ENSG00000162004

ENSMUSG00000071202

UniProt

A2IDD5

D3Z5T1

RefSeq (mRNA)

NM_001031737
NM_173476
NM_001378030
NM_001378031
NM_001378033

Contents

NM_001165929

RefSeq (protein)

NP_001026907
NP_001364959
NP_001364960
NP_001364962

NP_001159401

Location (UCSC) Chr 16: 0.72 – 0.73 Mb Chr 17: 26.01 – 26.01 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Coiled-coil domain-containing 78 (CCDC78) is a protein in humans encoded by the CCDC78 gene. It has several aliases including C16orf25, FLJ34512, CNM4, and JFP10. [5] It is located on the (-) strand on chromosome 16 (16p13.3). Its gene neighborhood includes NARFL (also on the minus strand), HAGHL, FAM173A, and METRN. The CCDC78 gene is 10,892 base pairs long, and the protein contains 438 amino acids. [6] The protein weighs approximately 4.852 KDal. [7] There are several isoforms, including one indicated with a unique congenital myopathy. [8] Several expression profiles show it has ubiquitous expression at moderate levels. Although no paralogs exist several orthologs do.

Function

The function of this gene is currently unknown. There is evidence that CCDC78 plays a role in skeletal muscle contraction. This is supported by structural similarities to other muscle proteins and by localization assays. CCDC78's predicted structure was similar to that of tropomyosin (see below). [9] The gene product is found primarily in the perinuclear region, the sarcolemmal membrane, and in the reticular pattern of the sarcoplasm. However, localization assays predict it to also be found in the cytoplasm. [8]

mRNA

Transcript Variants of CCDC78 according to AceView.png

General Properties: [6]

Transcript Variants: There are 13 known alternative splicing patterns. [5] These can be seen in the adjacent image. One of these is indicated in disease. [8]

Protein

General Properties: [7]

Expression

When looking at EST profiles in humans, CCDC78 seems to show ubiquitous expression at moderate levels. [6]

Predicted post-translational modification: Phosphorylation of several serine residues has been predicted by using tools at ExPasy. [10]

Predicted secondary structure

Secondary structure of CCDC78 was predicted using the protein secondary structure prediction tool PELE. As would be expected with a coiled-coil domain containing protein, there are several α-helices. [7] The model was predicted to be 98% accurate to 65% of the protein. The predicted image can be seen below. This predicted model is closely related to tropomyosin - a contractile protein. [9]

Protein-protein interactions

Only one protein has been found to interact with CCDC78. An analysis performed from IntAct showed an interaction between CCDC78 and dAK1_1 in Yersinia pestis. [11]

Homology

CCDC78 has no known paralogs in the human genome. However, it has several orthologs in other organisms. Orthologs can be found throughout the animal kingdom. CCDC78 is highly conserved in mammals. [7] The coiled-coil domain is highly conserved throughout all orthologs, demonstrating the importance of these domains.

Clinical relevance

A mutation in this gene has been shown to cause a unique congenital myopathy. [8] This mutation is caused by alternative splicing - a 222 bp in-frame insertion. A group of researchers from the University of Michigan analyzed a family with a dominantly inherited congenital myopathy. After linkage analysis followed by whole-exome capture and next-generation sequencing, they found CCDC78 to be present in affected individuals and absent in >10,000 controls. [8] They then successfully modeled this congenital myopathy in zebrafish. CCDC78 has also been associated with an immune response to Hepatitis B. [12]

Related Research Articles

<span class="mw-page-title-main">CCDC130</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain containing 130 is a protein that in humans is encoded by the CCDC130 gene. It is part of the U4/U5/U6 tri-snRNP in the U5 portion. This tri-snRNP comes together with other proteins to form complex B of the mature spliceosome. The mature protein is approximately 45 kilodaltons (kDa) and is extremely hydrophilic due to the abnormally high number of charged and polar amino acids. CCDC130 is a highly conserved protein, it has orthologous genes in some yeasts and plants that were found using nucleotide and protein versions of the basic local alignment search tool (BLAST) from the National Center for Biotechnology Information. GEO profiles for CCDC130 have shown that this protein is ubiquitously expressed, but the highest levels of expression are found in T-lymphocytes.

Uncharacterized LOC644249 gene., also known as RP11-195B21.3, is about 1058 base pairs long and is found in Homo sapiens on chromosome 9q12. More specifically, the sequence is located on Chromosome: 9; NC_000009.11(67977457..67987991 bp). This gene’s protein product is the “coiled-coil domain-containing protein 29” which is 291 amino acids long and may contain a conserved domain in the superfamily, pfam 12001. In particular, this conserved domain contains the domain of unknown function DUF3496 which is about 110 amino acids long, functionally uncharacterized, and found in eukaryotes. Other possible motifs for the protein product exist but the DUF3496 remains the most likely. This protein may play a role as a transmembrane protein.

<span class="mw-page-title-main">Coiled-coil domain containing protein 120</span> Protein-coding gene in humans

Coiled coil domain containing protein 120 (CCDC120), also known as JM11 protein, is a protein that, in humans, is encoded by the CCDC120 gene. The function of CCDC120 has not been formally identified but structural components, conservation, and interactions can be identified computationally.

<span class="mw-page-title-main">CCDC144A</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain-containing protein 144A is a protein that in humans is encoded by the CCDC144A gene. An alias of this gene is called KIAA0565. There are four members of the CCDC family: CCDC 144A, 144B, 144C and putative CCDC 144 N-terminal like proteins.

<span class="mw-page-title-main">CCDC94</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain containing 94 (CCDC94), is a protein that in humans is encoded by the CCDC94 gene. The CCDC94 protein contains a coiled-coil domain, a domain of unknown function (DUF572), an uncharacterized conserved protein (COG5134), and lacks a transmembrane domain.

<span class="mw-page-title-main">CCDC82</span> Protein-coding gene in the species Homo sapiens

Coiled-Coil Domain Containing protein 82 (CCDC82) is a protein that in humans, is encoded for by the gene of the same name, CCDC82. The CCDC82 gene is expressed in nearly all of human tissues at somewhat low rates. As of today, there are no patents involving CCDC82 and the function remains unknown.

<span class="mw-page-title-main">CCDC138</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain-containing protein 138, also known as CCDC138, is a human protein encoded by the CCDC138 gene. The exact function of CCDC138 is unknown.

<span class="mw-page-title-main">Coiled-coil domain containing 42B</span> Protein-coding gene in the species Homo sapiens

Coiled Coil Domain Containing protein 42B, also known as CCDC42B, is a protein encoded by the protein-coding gene CCDC42B.

<span class="mw-page-title-main">CCDC47</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain 47 (CCDC47) is a gene located on human chromosome 17, specifically locus 17q23.3 which encodes for the protein CCDC47. The gene has several aliases including GK001 and MSTP041. The protein itself contains coiled-coil domains, the SEEEED superfamily, a domain of unknown function (DUF1682) and a transmembrane domain. The function of the protein is unknown, but it has been proposed that CCDC47 is involved in calcium ion homeostasis and the endoplasmic reticulum overload response.

<span class="mw-page-title-main">FAM71D</span> Protein-coding gene in the species Homo sapiens

FAM71D, also known as chromosome 14 open reading frame 54 (C14orf54), is a protein that in humans is encoded by the FAM71D gene on Chromosome 14. Orthologs of FAM71D reach as far back in evolution to Reptiles, however, it is closer in homology to primates than any other orthologs. FAM71D has 6 paralogs: FAM71A, FAM71B, FAM71C, FAM71E1, FAM71F1, and FAM71F2 which encode a protein of unknown function.

<span class="mw-page-title-main">GPATCH11</span> Protein-coding gene in the species Homo sapiens

GPATCH11 is a protein that in humans is encoded by the G-patch domain containing protein 11 gene. The gene has four transcript variants encoding two functional protein isoforms and is expressed in most human tissues. The protein has been found to interact with several other proteins, including two from a splicing pathway. In addition, GPATCH11 has orthologs in all taxa of the eukarya domain.

<span class="mw-page-title-main">Proser1</span>

PROSER1 is a protein that in humans is encoded by the PROSER1 gene.

<span class="mw-page-title-main">C14orf93</span> Protein-coding gene in the species Homo sapiens

C14orf93 is a protein that is encoded in humans by the C14orf93 gene. It is a globular protein with a conserved C-terminus that is localized to the nucleus. While expressed relatively highly in all tissues except nervous tissue, it is expressed particularly highly in T cells and other immune tissues.

<span class="mw-page-title-main">Coiled-coil domain containing 166</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain containing 166 is a protein that in humans is encoded by the CCDC166 gene. Its function is currently unknown. It contains a coiled-coil domain, hence the current origin of its name. It is primarily expressed in the testes.

<span class="mw-page-title-main">TMEM171</span> Protein-coding gene in the species Homo sapiens

Transmembrane protein 171 (TMEM171) is a protein that in humans is encoded by the TMEM171 gene.

<span class="mw-page-title-main">CCDC198</span> Mammalian protein found in Homo sapiens

Coiled-Coil Domain Containing 198 (CCDC198) is a gene that encodes for a protein of the same name.

<span class="mw-page-title-main">Ccdc60</span> Protein-coding gene in humans

Coiled-coil domain containing 60 is a protein that in humans is encoded by the CCDC60 gene that is most highly expressed in the trachea, salivary glands, bladder, cervix, and epididymis.

<span class="mw-page-title-main">CCDC121</span> Protein-coding gene in the species Homo sapiens

Coiled-coil domain containing 121 (CCDC121) is a protein encoded by the CCDC121 gene in humans. CCDC121 is located on the minus strand of chromosome 2 and encodes three protein isoforms. All isoforms of CCDC121 contain a domain of unknown function referred to as DUF4515 or pfam14988.

<span class="mw-page-title-main">MIPOL1</span> Protein-coding gene in the species Homo sapiens

MIPOL1 , also known as CCDC193 , is a protein that in humans is encoded by the MIPOL1 gene. Mutation of this gene is associated with mirror-image polydactyly in humans, which is a rare genetic condition characterized by mirror-image duplication of digits.

<span class="mw-page-title-main">CCDC184</span> CCDC184 Bioinformatics analysis

Coiled-coil domain-containing 184 (CCDC184) is a protein which, in humans, is encoded by the CCDC184 gene

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000162004 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000071202 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. 1 2 GeneCards. "CCDC78 Gene". The Human Gene Compendium. Retrieved 2 May 2013.
  6. 1 2 3 "CCDC78". National Center for Biotechnology Information.
  7. 1 2 3 4 Biology WorkBench. San Diego Supercomputer Center http://seqtool.sdsc.edu/CGI/BW.cgi#!.{{cite web}}: Missing or empty |title= (help)[ permanent dead link ]
  8. 1 2 3 4 5 Majczenko K, Davidson AE, Camelo-Piragua S, Agrawal PB, Manfready RA, Li X, Joshi S, Xu J, Peng W, Beggs AH, Li JZ, Burmeister M, Dowling JJ (August 2012). "Dominant mutation of CCDC78 in a unique congenital myopathy with prominent internal nuclei and atypical cores". American Journal of Human Genetics. 91 (2): 365–71. doi:10.1016/j.ajhg.2012.06.012. PMC   3415545 . PMID   22818856.
  9. 1 2 "Phyre2". Structural Bioinformatics Group.[ permanent dead link ]
  10. ↑ "ExPASy: SIB Bioinformatics Resource Portal - Home". ExPasy. Swiss Institute of Bioinformatics.
  11. ↑ "3 binary interactions found for search term Ccdc78". IntAct Molecular Interaction Database. EMBL-EBI. Retrieved 2018-08-25.
  12. ↑ Davila S, Froeling FE, Tan A, Bonnard C, Boland GJ, Snippe H, Hibberd ML, Seielstad M (April 2010). "New genetic associations detected in a host response study to hepatitis B vaccine". Genes and Immunity. 11 (3): 232–8. doi:10.1038/gene.2010.1. PMID   20237496.
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