C1orf21

Last updated
C1orf21
Identifiers
Aliases C1orf21 , PIG13, chromosome 1 open reading frame 21
External IDs MGI: 1916649 HomoloGene: 12776 GeneCards: C1orf21
Orthologs
SpeciesHumanMouse
Entrez
Ensembl
UniProt
RefSeq (mRNA)

NM_030806

NM_197990

RefSeq (protein)

NP_110433

NP_932107

Location (UCSC) Chr 1: 184.39 – 184.63 Mb Chr 1: 151.73 – 151.97 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Uncharacterized protein C1orf21, also known as Proliferation-Inducing Protein 13, is a protein that in humans is encoded by the C1orf21 gene. [5] [6] C1orf21 is an intracellular protein that flows between the nucleus and the cytoplasm in the cell. It has been linked with cell growth and reproduction and there has been strong links with various types of cancers. [7] There are no paralogs for this gene, however, many conserved orthologs have been found in all invertebrates. [8] C1orf21 has low to moderate level of expression in most tissues in humans, however, it has the most expression in the skin, lung and prostate.

Contents

Gene

Locus

C1orf198 is a protein-encoding gene found on the reverse strand of chromosome 1 at the locus 1q25.3. [9]

Gene neighborhood

C1orf21 is located on the long arm of chromosome 1. It is found at position 5q23.1.

C1orf21 Cytogenic Band.png

Cytogenic band: 1q25.3

Size

Chromosome one is one of the longest chromosomes, in which C1orf21 spans from 184,385,826 to 184,390,390 bases, resulting with mRNA transcript that is 10,278 nucleotides long with 4 exons. The protein is 121 amino acids long, containing a domain of unknown function known as DUF4612.

Expression

NCBI gene and RNA-Seq revealed that C1orf21 is expressed in all tissues at a low to moderate level, however, it is mostly expressed in the skin, brain and prostate.

Gene level regulation

Promoter

There was over 7 promoters that were predicted, but the true promoter was 1111 base pairs long known as . [10]

Transcription factor binding sites

Many transcription factor (TF) binding sites have been predicted through Genomatix. Some important binding cites include MYRE, MARs, and Bright.

MYRE is a myelin regulatory factor. Myelin is produced in the central nervous system and plays a large role in axons. MARs is a special AT-rich sequence-binding protein 1, predominantly expressed in thymocytes, binds to matrix attachment regions. Bright helps with B cell regulator of IgH transcription.

Protein

Subcellular location

It was predicted that the location of C1orf21 is in the nucleus with 62.2% certainty. The mitochondria was predicted at 17.4%: mitochondrial, while the cytoskeleton, and vascular system at 4.3%. [11]

Structure

C1orf21 protein is 121 amino acids long with a molecular weight of 18,7 kDa with an isoelectric point of 5.08. It is believed that the protein interacts with the nuclear membrane and contains an unknown domain known as DUF4612. For the secondary and tertiary structure it is predicted that there are many alpha helices in the structure, with the rest of the protein having a disordered structure. [12]

PHYRE. An a-helix from 18 amino acids of C1orf21. C1orf21 PHYRE.png
PHYRE. An α-helix from 18 amino acids of C1orf21.


I-TASSER software generated a prediction of the tertiary structure of C1orf21. I-TASSER C1orf21.jpg
I-TASSER software generated a prediction of the tertiary structure of C1orf21.

Protein level regulation

Interacting proteins

Protein

Function

Calcineurin-binding protein cabin-1 (Cabin1)Required for replication-independent chromatin assembly
Centrosomal protein of 162 kDa (CEP162)Required to promote assembly of the transition zone in primary cilia.
CD97 antigenReceptor potentially involved in both adhesion and signaling processes early after leukocyte activation.
Chromosome 11 open reading frame 57 (C11orf57)Unknown
Chromosome 5 open reading frame 51 (C5orf51)Unknown
Homeobox protein Nkx-2.8; (NKX2-8)NKL subclass homeoboxes and pseudogenes
NACHT, LRR and PYD domains-containing protein 13 (NLPR13)Involved in inflammation
Semaphorin-3C (SEMA3C)Binds to plexin family members and plays an important role in the regulation of developmental processes
Zinc finger protein 19 (ZNF19)transcriptional regulation

Homology

Paralogs

Figure 3.  Unrooted phylogenetic tree of C1orf21 orthologs. Adi [Acropora digitifera, Stony coral pulp], Ate [Anabas testudineus], Bbe [Branchiostoma belcheri, crown-of-thorns starfish],  Cat [Cercocebus atys], Cmi [Callorhinchus milli], Ena [Echeneis naucrates], Fgl [Fulmarus glacialis], Gga [Gallus gallus, chicken], Ggg [Gorilla gorilla gorilla], Hbu [Haplochromis burtoni], Hle [Haliaeetus leucocephalus], Hsa [Homo sapiens, human], Mul [Macaca mulatta], Nfu [Nothobranchius furzeri], Oha [Ophiophagus hannah], Ptr [Pan troglodytes], Pvi [Pogona vitticeps, central bearded dragon], Rty [Rhincodon typus], Xla [Xenopus laevis, African clawed frog] Uma [Ursus maritimus]. Tree made with a neighbor-Joining method using a ClustalW-formatted set of sequences as input1.1 Clustal W C1orf21 Tree.png
Figure 3.  Unrooted phylogenetic tree of C1orf21 orthologs. Adi [Acropora digitifera, Stony coral pulp], Ate [Anabas testudineus], Bbe [Branchiostoma belcheri, crown-of-thorns starfish],  Cat [Cercocebus atys], Cmi [Callorhinchus milli], Ena [Echeneis naucrates], Fgl [Fulmarus glacialis], Gga [Gallus gallus, chicken], Ggg [Gorilla gorilla gorilla], Hbu [Haplochromis burtoni], Hle [Haliaeetus leucocephalus], Hsa [Homo sapiens, human], Mul [Macaca mulatta], Nfu [Nothobranchius furzeri], Oha [Ophiophagus hannah], Ptr [Pan troglodytes], Pvi [Pogona vitticeps, central bearded dragon], Rty [Rhincodon typus], Xla [Xenopus laevis, African clawed frog] Uma [Ursus maritimus]. Tree made with a neighbor-Joining method using a ClustalW-formatted set of sequences as input1.1 Clustal W

There are no isoforms or paralogs of C1orf21 that are known.

Orthologs

C1orf21 is found in most classes of vertebrates and some invertebrates. The most distant ortholog of C1orf21 is Acropora digitifera , which diverged an estimated 824 million years ago. [17] There is no traces of the C1orf21 gene in organisms that are traced beyond invertebrates, such as fungi, plants, protists, or single celled organisms. [18]

Homologous domains

The domain of unknown function 4612 (DUF4612) was highly conserved in most orthologs.

SpeciesCommon nameTaxonomic groupDOD

(MYA)

Accession numberSequence length (aa)IdentitySimilarity
Homo sapiens HumanPrimates0NP_110433121100100
Pan troglodytes ChimpanzeePrimates7NP_001229539121100100
Gorilla gorilla gorilla GorillaPrimates9XP_018883443121100100
Macaca mulatta Rhesus macaquePrimates30NP_001247792121100100
Cercocebus atys Sooty mangabeyPrimates30XP_011903171121100100
Ursus maritimus Polar bearCarnivora96XP_0086953661219799
Pogona vitticeps Central bearded dragonAmphioxiformes312XP_0206507641219497
Gallus gallus Red junglefowlGalliformes312XP_4222921219398
Haliaeetus leucocephalus Bald eagleAccipitriformes312XP_0105789921219398
Fulmarus glacialis Northern fulmarProcellariiformes312KFV96345909398
Ophiophagus hannah King cobraSquamata312ETE667281219196
Xenopus tropicalis Western clawed frogAnura352NP_0010726521217785
Nothobranchius furzeri Turquoise killifishCyprinodontiformes435XP_0158270001166173
Echeneis naucrates Live sharksuckerPerciformes435XP_0293557621166173
Haplochromis burtoni Burton's mouthbrooderCichliformes435XP_0059325281166173
Anabas testudineus Blue perchAnabantiformes435XP_0262017021164760
Callorhinchus milii Australian ghostsharkChimaeriformes473XP_0078937871356979
Rhincodon typus Whale SharkOrectolobiformes473XP_020373635916882
Branchiostoma belcheri Belcher's lanceletAmphioxiformes684XP_0196409801143356
Acropora digitifera Stony coral pulpScleractinia824XP_0157472271405565

Function

C1orf21 is most likely involved in the growth of cells, especially in the nucleus where replication of DNA occurs.

Clinical significance

Even though there is not a lot known about C1orf21, there have been some links with diseases. In many studies it has been found that there are links with cancer. Since C1orf21 is associated with cell proliferation, in another study by Sooda et al. there was an interest in the transcript map of the HPC1 locus, to help them identify the susceptibility genes involved in prostate cancer and jaw tumor.  It was seen that overall there are several studies where C1orf21 has been studied on role it plays in cancer for different body areas among many other genes. It was also found that there is a large correlation with affects on keratinocytes since C1orf21 plays a role in ZNF750 silencing.

Related Research Articles

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

CCDC186

CCDC186 is a protein that in humans is encoded by the CCDC186 gene The CCDC186 gene is also known as the CTCL-tumor associated antigen with accession number NM_018017.

MAP11 is a protein that in human is encoded by the gene MAP11. It was previously referred to by the generic name C7orf43. C7orf43 has no other human alias, but in mice can be found as BC037034.

C20orf27

UPF0687 protein C20orf27 is a protein that in humans is encoded by the C20orf27 gene. It is expressed in the majority of the human tissues. One study on this protein revealed its role in regulating cell cycle, apoptosis, and tumorigenesis via promoting the activation of NFĸB pathway.

TMEM63A

Transmembrane protein 63A is a protein that in humans is encoded by the TMEM63A gene. The mature human protein is approximately 92.1 kilodaltons (kDa), with a relatively high conservation of mass in orthologs. The protein contains eleven transmembrane domains and is inserted into the membrane of the lysosome. BioGPS analysis for TMEM63A in humans shows that the gene is ubiquitously expressed, with the highest levels of expression found in T-cells and dendritic cells.

C11orf1 Protein-coding gene in the species Homo sapiens

Chromosome 11 open reading frame one, also known as C11orf1, is a protein-coding gene. It has been found by yeast two hybrid screen to bind to SETDB1 a histone protein methyltransferase enzyme. SETDB1 has been implicated in Huntington's disease, a neurodegenerative disorder.

OSER1

Chromosome 20 open reading frame 111, or C20orf111, is the hypothetical protein that in humans is encoded by the C20orf111 gene. C20orf111 is also known as Perit1, HSPC207, and dJ1183I21.1. It was originally located using genomic sequencing of chromosome 20. The National Center for Biotechnology Information, or NCBI, shows that it is located at q13.11 on chromosome 20, however the genome browser at the University of California-Santa Cruz (UCSC) website shows that it is at location q13.12, and within a million base pairs of the adenosine deaminase locus. It was also found to have an increase in expression in cells undergoing hydrogen peroxide(H
2
O
2
)-induced apoptosis. After analyzing the amino acid content of C20orf111, it was found to be rich in serine residues.

Tetratricopeptide repeat 39A

Tetratricopeptide repeat 39A is a human protein encoded by the TTC39A gene. TTC39A is also known as DEME-6, KIAA0452, and c1orf34. The function of TTC39A is currently not well understood. The main feature within tetratricopeptide repeat 39A is the domain of unknown function 3808 (DUF3808), spanning almost the entire protein. KIAA0452 can also be seen as an isoform of TTC39A because of differences in genome sequence, but overlap in DUF domain.

C5orf34 is a protein that in humans is encoded by the C5orf34 gene (5p12).

C14orf80 Protein-coding gene in the species Homo sapiens

Uncharacterized protein C14orf80 is a protein which in humans is encoded by the chromosome 14 open reading frame 80, C14orf80, gene.

C9orf152 Protein-coding gene in the species Homo sapiens

Chromosome 9 open reading frame 152 is a protein that in humans is encoded by the C9orf152 gene. The exact function of the protein is not completely understood.

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.

C3orf67 Human gene

Chromosome 3 open reading frame 67 or C3orf67 is a protein that in humans is encoded by the gene C3orf67. The function of C3orf67 is not yet fully understood.

C4orf51 Protein-coding gene in the species Homo sapiens

Chromosome 4 open reading frame 51 (C4orf51) is a protein which in humans is encoded by the C4orf51 gene.

C7orf57 Uncharacterized protein in humans

Chromosome 7 open reading frame 57 is an uncharacterized protein found in humans and several other homologs. It is encoded by the C7orf57 gene. This gene is found to be greatly expressed in the Fallopian tubes, testes, lungs, hippocampus, hypothalamus, and caudate. There are three isoforms of the gene. Within the gene sequence 9 exons are present. C7orf57 has been linked to lupus, pancreatic cancer sporadic amyotrophic lateral sclerosis. and gastrointestinal toxicity

TEDC2

Tubulin epsilon and delta complex 2 (TEDC2), also known as Chromosome 16 open reading frame 59 (C16orf59), is a protein that in humans is encoded by the TEDC2 gene. Its NCBI accession number is NP_079384.2.

SKIDA1 Protein-coding gene in the species Homo sapiens

Ski/Dach domain-containing protein 1 is a protein that in humans is encoded by the SKIDA1 gene. It is also known as C10orf140 and DLN-1. It has orthologs in vertebrates. It has two domains: the Ski/Sno/Dac domain and a domain of unknown function, DUF4854. It is associated with multiple types of cancer, like leukemia, ovarian cancer, and colon cancer. It's predicted to be a nuclear protein. It may interact with PRC2.

C1orf185 Protein-coding gene in the species Homo sapiens

Chromosome 1 open reading frame 185, also known as C1orf185, is a protein that in humans is encoded by the C1orf185 gene. In humans, C1orf185 is a lowly expressed protein that has been found to be occasionally expressed in the circulatory system.

C7orf50

C7orf50 is a gene in humans that encodes a protein known as C7orf50. This gene is ubiquitously expressed in the kidneys, brain, fat, prostate, spleen, among 22 other tissues and demonstrates low tissue specificity. C7orf50 is conserved in chimpanzees, Rhesus monkeys, dogs, cows, mice, rats, and chickens, along with 307 other organisms from mammals to fungi. This protein is predicted to be involved with the import of ribosomal proteins into the nucleus to be assembled into ribosomal subunits as a part of rRNA processing. Additionally, this gene is predicted to be a microRNA (miRNA) protein coding host gene, meaning that it may contain miRNA genes in its introns and/or exons.

C6orf136

C6orf136 is a protein in humans encoded by the C6orf136 gene. The gene is conserved in mammals, mollusks, as well some porifera. While the function of the gene is currently unknown, C6orf136 has been shown to be hypermethylated in response to FOXM1 expression in Head Neck Squamous Cell Carcinoma (HNSCC) tissue cells. Additionally, elevated expression of C6orf136 has been associated with improved survival rates in patients with bladder cancer. C6orf136 has three known isoforms.

References

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Further reading