C19orf47

Last updated

Chromosome 19 open reading frame 47 is a protein that in humans is encoded by the C19orf47 gene. Aliases include Chromosome 19 Open Reading Frame 47, FLJ36888, DKZp686P05129, and LOCI26526. [1]

Contents

Gene

Homo sapiens C19orf47 is located in cytogenetic band 19q13.2. It covers 28.98 kilobases from 40,854,420 to 40,825,543 on the minus strand. [2] The gene has 8 exons in the isoform 1 precursor, the last of which is the longest and comprises over half of the mRNA transcript. [1]

mRNA

Transcription of Homo sapiens C19orf47 produces 13 different mRNAs, with 12 alternatively spliced variants and 1 unspliced form. Isoforms and the proteins encoded by them are shown in the table below. Homo sapiens C19orf47 has broad expression in heart, testes, and other tissues.

Isoforms of C19orf47.

Isoform numberNucleotide AccessionmRNA length (bp)Protein AccessionProtein Length (aa)
NM1NM_001256440.12104NP_001243369.1422
NM2NM_001256441.23611NP_001243370.1385
X1 XM_017026291.2 3608 XP_016881780.1 384
X2 XM_005258520.3 3625 XP_005258577.1 421
X3 XM_017026292.3 1407 XP_016881781.1 366
X4 XM_017026293.3 1404 XP_016881782.1 365
X5 XM_047438175.1 1421 XP_047294131.1 402
X6 XM_024451364.2 3507 XP_024307132.1 344
X7 XM_047438176.1 3504 XP_047294132.1 343
X8 XM_024451365.2 4638 XP_024307133.1 385
X8 XM_047438177.1 4671 XP_047294133.1 385
X9 XM_011526460.3 3524 XP_011524762.1 381
X10 XM_047438178.1 3668 XP_047294134.1 355
X11 XM_047438179.1 3241 XP_047294135.1 281
Conceptual translation of C19orf47 using SIXFRAME. Exon-exon boundaries are in blue, start codon is in green, and stop codon is red. PolyA signal sequence is shown in dark orange, polyA sites are shown in orange. Base pair and amino acid numbering is shown. Conserved amino acids in close orthologs are shown bolded. Conceptual translation of C19orf47.png
Conceptual translation of C19orf47 using SIXFRAME. Exon-exon boundaries are in blue, start codon is in green, and stop codon is red. PolyA signal sequence is shown in dark orange, polyA sites are shown in orange. Base pair and amino acid numbering is shown. Conserved amino acids in close orthologs are shown bolded.

Protein

The C19orf47 gene isoform 1 precursor encodes for a 422 amino acid protein. The protein is located in the nucleoplasm and nucleus of the cell.

SAM domain is shown in red and nuclear localization site shown in yellow. Amidation site shown with yellow circle, N-glycosylation site shown with blue circle, cAMP- and cGMP-dependent protein kinase phosphorylation sites shown with purple rhombus, Casein kinase II phosphorylation is shown with light blue triangles, N-myristoylation sites shown with green squares, and protein kinase C phosphorylation sites shown with light purple diamonds. Protein cartoon of human C19orf47.png
SAM domain is shown in red and nuclear localization site shown in yellow. Amidation site shown with yellow circle, N-glycosylation site shown with blue circle, cAMP- and cGMP-dependent protein kinase phosphorylation sites shown with purple rhombus, Casein kinase II phosphorylation is shown with light blue triangles, N-myristoylation sites shown with green squares, and protein kinase C phosphorylation sites shown with light purple diamonds.
C19orf47 tertiary structure from iCn3D C19orf47 tertiary structure from iCn3D.png
C19orf47 tertiary structure from iCn3D

Interacting Proteins

The following proteins have predicted interactions with C19orf47. Interacting proteins with C19orf47 in humans. Notes with important information are shown.

Abbreviated NameFull NameAdditional Notes
PARK2Parkin RBR E3 Ubiquitin Protein LigaseComponent of multiprotein E3 ubiquitin ligase complex. Mutations are known to cause Parkinson’s disease.
NSP3Non-structural protein 3SARS-CoV-2 protein
ORF14Open reading frame 14SARS-CoV-2 protein
MYCV-Myc Avian Myelocytomatosis Viral Oncogene Homolog 2 3Proto-oncogene, forms a heterodimer with related transcription factor for MAX.
DDX39BDExD-Box Helicase 39BRNA-dependent ATPase that mediates ATP hydrolysis during mRNA splicing.
C17orf85Nuclear Cap-Binding Protein Subunit 3Associates with NCBP1/CBP80 to form an alternative cap-binding complex (CBC) which plays a key role in mRNA export.
NXF1Nuclear RNA Export Factor 1Member of a family of nuclear RNA export factor genes.
THOC2THO Complex 2Multiprotein complex binds specifically to spliced mRNAs to facilitate mRNA export.
YWHAQTyrosine 3-Monooxygenase/Tryptophan 5-Monooxygenase Activation Protein, Theta PolypeptideMediates signal transduction by binding to phosphoserine-containing proteins.

Homology

C19orf47 is found in organisms including mammals, reptiles, amphibian, fish, insects, and plant. [3]

Current orthologs of human C19orf47. Sequence identity and similarity are shown.

C19orf47Genus, SpeciesCommon NameTaxonomic GroupDate of Divergence (MYA)Accession NumberSequence Length (aa)IdentitySimilarity
MammaliaHomo sapiens Human Primates0NP_001243369.1422100.0%100.0%
Mus musculus Mouse Rodentia87XP_036009244.139775.5%80.2%
Castor canadensis American Beaver Rodentia87XP_020022531.138271.3%74.7%
ReptiliaGopherus flavomarginatus Bolson Tortoise Testudines319XP_050784538.138663.3%72.9%
Dermochelys coriacea Leatherback Sea Turtle Testudines319XP_038238045.244962.3%72.0%
Varanus komodoensis Komodo Dragon Squamata319XP_044281356.139560.2%69.2%
Alligator sinensis Chinese Alligator Crocodylia319XP_025068843.138854.7%63.3%
AvesHaliaeetus leucocephalus Bald Eagle Falconiformes319XP_010564700.138060.2%69.1%
Phalacrocorax carbo Great Cormorant Suliformes319XP_009501755.138158.5%67.3%
Gallus gallus Chicken Galliformes319XP_015129410.437436.6%45.5%
AmphibiaXenopus tropicalis Frog Anura352NP_001005016.139854.2%64.5%
FishProtopterus annectens West African Lungfish Lepidosireniformes408XP_043937251.139346.4%57.0%
Latimeria chalumnae West Indian Ocean Coelacanth Coelacanthiformes415XP_014348608.138158.2%69.7%
Danio rerio Zebrafish Cypriniformes429NP_001038706.139248.6%59.5%
Leucoraja erinacea Little Skate Rajiformes462XP_055519598.139553.0%64.2%
Petromyzon marinus Sea Lamprey Petromyzontiformes563XP_032803651.145241.6%52.4%
ArthropodsRhipicephalus sanguineus Brown Dog Tick Ixodida686XP_037499932.142829.3%39.9%
Biomphalaria glabrata Bloodfluke Planorb Planorbidae 686XP_055879100.137026.6%36.0%
Polistes fuscatus Northern Paper Wasp Hymenoptera686XP_043494673.140924.1%39.3%
PlantsGossypium anomalum Wild Cotton Malvales1530KAG8495680.126611.5%20.6%

Clinical Significance

One study discusses the identification of four novel mutations in the TUBB4A gene associated with laryngeal and cervical dystonia, a rare neurological disorder. These mutations were found in several affected families, and the study highlights the complexity of this genetic condition, with evidence of incomplete penetrance in some cases. Laryngeal dystonia, often the initial symptom, is a prominent feature of the disease. Of note, there was presence of a variant in the C19orf47 gene in one family. It was shown that the variant in the gene TUBB4A was more likely to be the source of the phenotype, as C19orf47 has low expression in the brain. [4]

Related Research Articles

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

HIKESHI is a protein important in lung and multicellular organismal development that, in humans, is encoded by the HIKESHI gene. HIKESHI is found on chromosome 11 in humans and chromosome 7 in mice. Similar sequences (orthologs) are found in most animal and fungal species. The mouse homolog, lethal gene on chromosome 7 Rinchik 6 protein is encoded by the l7Rn6 gene.

TMEM156 is a gene that encodes the transmembrane protein 156 (TMEM156) in Homo sapiens. It has the clone name of FLJ23235.

Uncharacterized protein Chromosome 16 Open Reading Frame 71 is a protein in humans, encoded by the C16orf71 gene. The gene is expressed in epithelial tissue of the respiratory system, adipose tissue, and the testes. Predicted associated biological processes of the gene include regulation of the cell cycle, cell proliferation, apoptosis, and cell differentiation in those tissue types. 1357 bp of the gene are antisense to spliced genes ZNF500 and ANKS3, indicating the possibility of regulated alternate expression.

<span class="mw-page-title-main">C17orf53</span>

C17orf53 is a gene in humans that encodes a protein known as C17orf53, uncharacterized protein C17orf53. It has been shown to target the nucleus, with minor localization in the cytoplasm. Based on current findings C17orf53 is predicted to perform functions of transport, however further research into the protein could provide more specific evidence regarding its function.

<span class="mw-page-title-main">C16orf46</span> Human gene

Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.

<span class="mw-page-title-main">Transmembrane protein 44</span>

Transmembrane protein 44 is a protein that in humans is encoded by the TMEM44 gene.

<span class="mw-page-title-main">C9orf25</span> Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 25 (C9orf25) is a domain that encodes the FAM219A gene. The terms FAM219A and C9orf25 are aliases and can be used interchangeably. The function of this gene is not yet completely understood.

<span class="mw-page-title-main">C19orf44</span> Mammalian protein found in Homo sapiens

Chromosome 19 open reading frame 44 is a protein that in humans is encoded by the C19orf44 gene. C19orf44 is an uncharacterized protein with an unknown function in humans. C19orf44 is non-limiting implying that the protein exists in other species besides human. The protein contains one domain of unknown function (DUF) that is highly conserved throughout its orthologs. This protein is most highly expressed in the testis and ovary, but also has significant expression in the thyroid and parathyroid. Other names for this protein include: LOC84167.

<span class="mw-page-title-main">CFAP299</span> Protein-coding gene in the species Homo sapiens

Cilia- and flagella-associated protein 299 (CFAP299), is a protein that in humans is encoded by the CFAP299 gene. CFAP299 is predicted to play a role in spermatogenesis and cell apoptosis.

<span class="mw-page-title-main">C9orf50</span> Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 50 is a protein that in humans is encoded by the C9orf50 gene. C9orf50 has one other known alias, FLJ35803. In humans the gene coding sequence is 10,051 base pairs long, transcribing an mRNA of 1,624 bases that encodes a 431 amino acid protein.

<span class="mw-page-title-main">C17orf78</span> Mammalian protein found in Homo sapiens

Uncharacterized protein C17orf78 is a protein encoded by the C17orf78 gene in humans. The name denotes the location of the parent gene, being at the 78th open reading frame, on the 17th human chromosome. The protein is highly expressed in the small intestine, especially the duodenum. The function of C17orf78 is not well defined.

<span class="mw-page-title-main">FAM214B</span> Protein-coding gene in the species Homo sapiens

The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.

<span class="mw-page-title-main">FAM120AOS</span> Protein-coding gene in the species Homo sapiens

FAM120AOS, or family with sequence similarity 120A opposite strand, codes for uncharacterized protein FAM120AOS, which currently has no known function. The gene ontology describes the gene to be protein binding. Overall, it appears that the thyroid and the placenta are the two tissues with the highest expression levels of FAM120AOS across a majority of datasets.

<span class="mw-page-title-main">C11orf98</span> Protein-coding gene in the species Homo sapiens

C11orf98 is a protein-encoding gene on chromosome 11 in humans of unknown function. It is otherwise known as c11orf48. The gene spans the chromosomal locus from 62,662,817-62,665,210. There are 4 exons. It spans across 2,394 base pairs of DNA and produces an mRNA that is 646 base pairs long.

<span class="mw-page-title-main">C4orf19</span> Human C4orf19 gene

C4orf19 is a protein which in humans is encoded by the C4orf19 gene.

<span class="mw-page-title-main">C2orf80</span> Gene

C2orf80 is a protein that in humans is encoded by the c2orf80 gene. The gene c2orf80 also goes by the alias GONDA1. In humans, c2orf80 is exclusively expressed in the brain. While relatively little is known about the function of c2orf80, medical studies have shown a strong association between variations in c2orf80 and IDH-mutant gliomas, 46,XY gonadal dysgenesis, and a possible association with blood pressure.

<span class="mw-page-title-main">THAP3</span> Protein in Humans

THAP domain-containing protein 3 (THAP3) is a protein that, in Homo sapiens (humans), is encoded by the THAP3 gene. The THAP3 protein is as known as MGC33488, LOC90326, and THAP domain-containing, apoptosis associated protein 3. This protein contains the Thanatos-associated protein (THAP) domain and a host-cell factor 1C binding motif. These domains allow THAP3 to influence a variety of processes, including transcription and neuronal development. THAP3 is ubiquitously expressed in H. sapiens, though expression is highest in the kidneys.

<span class="mw-page-title-main">NOXRED1</span> Human gene

NADP-dependent oxidoreductase domain-containing protein 1 is a protein that in humans is encoded by the NOXRED1 gene. An alias of this gene is Chromosome 14 Open Reading Frame 148 (c14orf148). This gene is located on chromosome 14, at 14q24.3. NOXRED1 is predicted to be involved in pyrroline-5-carboxylate reductase activity as part of the L-proline biosynthetic pathway. It is expressed in a wide variety of tissues at a relatively low level, including the testes, thyroid, skin, small intestine, brain, kidney, colon, and more.

<span class="mw-page-title-main">C13orf46</span> C13of46 Gene and Protein

Chromosome 13 Open Reading Frame 46 is a protein which in humans is encoded by the C13orf46 gene. In humans, C13orf46 is ubiquitously expressed at low levels in tissues, including the lungs, stomach, prostate, spleen, and thymus. This gene encodes eight alternatively spliced mRNA transcript, which produce five different protein isoforms.

<span class="mw-page-title-main">Chromosome 5 open reading frame 47</span> Human C5ORF47 Gene

Chromosome 5 Open Reading Frame 47, or C5ORF47, is a protein which, in humans, is encoded by the C5ORF47 gene. It also goes by the alias LOC133491. The human C5ORF47 gene is primarily expressed in the testis.

References

  1. 1 2 "Supplemental Information 2: Nucleotide sequence alignments of TiLV segment 9 sequences (n = 25) retrieved from the GenBank database at NCBI". doi: 10.7717/peerj.13157/supp-2 .{{cite web}}: Missing or empty |url= (help)
  2. "AceView: Gene:C19orf47, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2023-12-16.
  3. "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2023-12-16.
  4. Bally, Julien F.; Camargos, Sarah; Oliveira dos Santos, Camila; Kern, Drew S.; Lee, Teresa; Pereira da Silva-Junior, Francisco; Puga, Renato David; Cardoso, Francisco; Barbosa, Egberto Reis; Yadav, Rachita; Ozelius, Laurie J.; de Carvalho Aguiar, Patricia; Lang, Anthony E. (2021-04-06). "DYT-TUBB4A (DYT4 Dystonia): New Clinical and Genetic Observations". Neurology. 96 (14): e1887–e1897. doi:10.1212/WNL.0000000000010882. ISSN   0028-3878. PMC   8105968 . PMID   32943487.