C12orf24

Last updated
FAM216A
Identifiers
Aliases FAM216A , C12orf24, HSU79274, family with sequence similarity 216 member A
External IDs MGI: 1916198 HomoloGene: 8328 GeneCards: FAM216A
Orthologs
SpeciesHumanMouse
Entrez

29902

68948

Ensembl

ENSG00000204856

ENSMUSG00000029463

UniProt

Q8WUB2

Q9DB54

RefSeq (mRNA)

NM_013300

NM_026883

RefSeq (protein)

NP_037432

NP_081159

Location (UCSC) Chr 12: 110.47 – 110.49 Mb Chr 5: 122.5 – 122.51 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Chromosome 12 Chromosome Picture.jpg
Chromosome 12
C12Orf24
AlliasesFAM216A, HSU79274
External IDsNCBI: NM_013300.3

C12orf24 (Chromosome 12, open reading frame 24) is a gene in humans ( Homo sapiens ) that encodes a protein known as FAM216A. [5] This gene is primarily expressed in the testis and brain, but has constitutive expression in 25 other tissues. [5] [6] FAM216A is an intracellular protein that has been predicted to reside within the nucleus of cells. [7] The exact function of C12orf24 is unknown. FAM216A is highly expressed in Sertoli cells of the testis as well as different stage spermatids. [8]

Contents

Gene

Locus

C12orf24 is a protein-encoding gene found on the forward strand of chromosome 12 at the locus 12q24.11. C12orf24 is located on the long arm of chromosome 12. [9]

Gene Locus.png

mRNA

FAM216A has 2 isoforms X1 and X2 that are both shorter than the main protein, which is known as FAM216A. Isoform X2 has 2 variants which are the same length and isoform X1 only has 1 variant. [5]

NameTranscript IDBase pair lengthProtein length
FAM216ANP_037432.21,101273
FAM216A_X1XP_011536548.11,148234
FAM216A_X2XP_024304727.11,142179
FAM216A_X2XP_005253932.11,040179

Size

Chromosome 12 is a medium-sized chromosome, on which C12orf24 spans from 110,468,415 to 110,490,387 which is 21,973 bases long. The resulting mRNA transcript is 1,101 bases, 822 of which is the coding sequence. The resulting protein is 273 amino acids long. [10] [5]

ExonStartEndLength in base pairs
ENSE00001474815110,468,845110,469,018174
ENSE00003514548110,473,078110,473,07741
ENSE00003459833110,485,078110,485,199122
ENSE00003639607110,486,325110,486,454130
ENSE00003553453110,486,534110,486,717184
ENSE00003571489110,487,861110,487,94383
ENSE00003568139110,490,019110,490,385367

Expression

C12orf24 is primarily expressed in the brain, spinal cord, and testis of humans. [6] [11] Within the testis C12orf24 is expressed in Sertoli cells. [8] Within the brain C12orf24 is expressed within neuropils. [12]

Gene regulation

Promoter

According to the UCSC Genome Browser and Genomatix Eldorado there are two promoters of C12orf24 and no enhancers or other regulatory elements. [13] [14] Only one of the two predicted promoters binds transcription factors. [14]

Transcription factors

There are many transcription factors predicted to bind to the promoter region of C12orf24 by Genomatix and the UCSC Genome Browser. [14] [13]

NameFunctionBinding sequence
ZKSCAN3C2H2 zinc finger transcription factors 2ccctcCCCCaccgtaactccggg
SPZ1Testis-specific bHLH-Zip transcription factorsaGGAGggaaat
WT1Wilms tumor suppressorcggtgggGGAGgggcagga
E2F7Cell cycle regulatorcacaggaGGGAaatata
MZF1Myeloid zinc finger 1 factorsgcGGGGagcag
ETSFHuman and murine ETS1 factorsgtttgacaGGAAggtggctca
ZNF7C2H2 zinc finger transcription factors 18cgggaGGCTgaggca
NKX2NKX homeodomain factorsgccctcAAGTgagaggcgg
MYODMyoblast determining factor

ctgggaCAGCtgctccc

Protein

Cellular location

According to the PSORT program of Genescript, C12orf24 is 69.6% likely to be a nuclear protein. [7] NCBI Gene predicts that C12orf24 is an intracellular protein. [5]

Structure

Protein FAM261A has 2 charge runs, a positive run from amino acids 200-229 and a negative charge run from amino acids 238–268. [15] Methionine, histidine, and serine are all seen at a higher than expected rate in FAM216A while valine is seen at a significantly lower than expected rate. [15]

The CFSSP (Chou and Fassman Secondary Structure Prediction Server) predicts a secondary structure for FAM216A that has multiple alpha helices with a few large beta pleated sheets. [16] [17] I-TASSER structure prediction program shows a 3D structure of FAM216A that has many alpha helices and a few coil turns with no beta pleated sheets. [18]

3D Structure of FAM216A 3D Structure of FAM216A.jpg
3D Structure of FAM216A

Protein level regulation

There are 8 predicted sites of sumoylation on FAM216A, with only 2 of them having a high probability of occurrence. [19] There are 7 predicted sites of glycation on FAM216A. [20] There is no predicted signal peptide for FAM216A, which may prevent the protein from being glycosylated. [21] There is 42 predicted sites for phosphorylation, however given the predicted structure of the protein not all 42 sites will be accessible for phosphorylation. [22]

Interacting proteins

There are only a few known proteins that are predicted to interact with FAM216A. [23] [24] [25]

ProteinFunction
E6HPV type 8 protein that prevents apoptosis in infected cells
MAGEA10Possible roles in embryonal development, tumor transformation, and tumor development
DKC1Required for ribosome biogenesis and telomere maintenance
RCF4Replication factor C subunit 4. Possible required for elongation of multiprimed DNA
CCDC34Coiled-coil domain containing 34. Involved in the cell cycle
NIFKNucleolar protein interacting with the FHA domain of MKI67
PSMA4Protease responsible for degrading most intracellular proteins

Homology

Paralogs

The only paralog for FAM216A is FAM216B. [26]

Orthologs

According to the NCBI Gene page for C12orf24, there are at least 182 organisms with an ortholog of C12orf24. [27] The farthest back known orthologs are in sea corals which diverged from humans 824 million years ago. [28] [29]

Genus and speciesCommon nameTaxonomic groupDate of divergence (MYA)Accession numberSequence lengthSequence identitySequence similarity
Pan paniscus BonoboPrimate6.7XP_00383253128195.796.1
Pan troglodytes ChimpanzeePrimate6.7PNI6472025692.793
Gulo gulo WolverineCarnivore96VCW5018325479.986.6
Orcinus orca Killer whaleOdontoceti96XP_00427677825678.884.2
Delphinapteruss leucas Beluga whaleOdonoceti96XP_02245374125678.484.2
Mondon monoceros NarwhalOdontoceti96XP_02908471125678.484.2
Tursiops truncatus Bottlenose dolphinOdontoceti96XP_01980606625678.484.2
Callhorhinus ursinus Northern fur sealCarnivore96XP_02574556925377.785
Felis catus House catCarnivore96XP_00399470525375.584.2
Puma concolor PumaCarnivore96XP_02578930425375.584.2
Acinonyx jubatus CheetahCarnivore96XP_02689998025375.184.2
Equus asinus DonkeyEquidae96XP_01471417425374.780.6
Camelus ferus Wild Bactrian camelArtidoctyla96XP_00617813225673.682.8
Loxodonta africana African bush elephantProboscidea105XP_01059817525476.283.2
Ciona intestinalis Sea vaseTunicata676XP_00212448626816.928.9
Acanthaster planci Crown-of-thorns starfishEchinodermata684XP_0221098343681729.7
Actinia tenebrosa Australian red Waratah Sea anemoneCnidaria824XP_03155655343316.124.8
Pocillopora damicornis Cauliflower coralCnidaria824XP_0270479534151623.7
Orbicella faveolata Mountainous star coralCnidaria824XP_02062333043515.423.2

Related Research Articles

<span class="mw-page-title-main">TSBP1</span> Protein found in humans

TSBP1 is a protein that in humans is encoded by the TSBP1 gene. C6orf10 is an open reading frame on chromosome 6 containing a protein that is ubiquitously expressed at low levels in the adult genome and may play a role during fetal development. C6orf10 has been found to be linked to both neurodegenerative and autoimmune diseases in adults. Expression of this gene is highest in the testis but is also seen in other tissue types such as the brain, lens of the eye and the medulla. TSBP1 was previously known as C6orf10.

<span class="mw-page-title-main">Interferon-inducible GTPase 5</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">ERICH2</span> Protein-coding gene in the species Homo sapiens

Glutamate Rich Protein 2 is a protein in humans encoded by the gene ERICH2. This protein is expressed heavily in male tissues specifically in the testes, and proteins are specifically found in the nucleoli fibrillar center and the vesicles of these testicular cells. The protein has multiple protein interactions which indicate that it may play a role in histone modification and proper histone functioning.

<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">TEX9</span> Protein-coding gene in the species Homo sapiens

Testis-expressed protein 9 is a protein that in humans is encoded the TEX9 gene. TEX9 that encodes a 391-long amino acid protein containing two coiled-coil regions. The gene is conserved in many species and encodes orthologous proteins in eukarya, archaea, and one species of bacteria. The function of TEX9 is not yet fully understood, but it is suggested to have ATP-binding capabilities.

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<span class="mw-page-title-main">TMEM155</span> Protein-coding gene in the species Homo sapiens

Transmembrane protein 155 is a protein that in humans is encoded by the TMEM155 gene. It is located on human chromosome 4, spanning 6,497 bases. It is also referred to as FLJ30834 and LOC132332. This protein is known to be expressed mainly in the brain, placenta, and lymph nodes and is conserved throughout most placental mammals. The function and structure of this protein is still not well understood, but its level of expression has been studied pertaining to various pathologies.

<span class="mw-page-title-main">C5orf46</span> Protein-coding gene in the species Homo sapiens

C5orf46 is a protein coding gene located on chromosome 5 in humans. It is also known as sssp1, or skin and saliva secreted protein 1. There are two known isoforms known in humans, with isoform 2 being the longer of the two. The protein encoded is predicted to have one transmembrane domain, and has a predicted molecular weight of 9,692 Da, and a basal isoelectric point of 4.67.

<span class="mw-page-title-main">C16orf90</span> Protein-coding gene in the species Homo sapiens

C16orf90 or chromosome 16 open reading frame 90 produces uncharacterized protein C16orf90 in homo sapiens. C16orf90's protein has four predicted alpha-helix domains and is mildly expressed in the testes and lowly expressed throughout the body. While the function of C16orf90 is not yet well understood by the scientific community, it has suspected involvement in the biological stress response and apoptosis based on expression data from microarrays and post-translational modification data.

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

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<span class="mw-page-title-main">C1orf94</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">Fam89A</span> Human protein and gene

ProteinFAM89A is a protein which in humans is encoded by the FAM89A gene. It is also known as chromosome 1 open reading frame 153 (C1orf153). Highest FAM89A gene expression is observed in the placenta and adipose tissue. Though its function is largely unknown, FAM89A is found to be differentially expressed in response to interleukin exposure, and it is implicated in immune responses pathways and various pathologies such as atherosclerosis and glioma cell expression.

<span class="mw-page-title-main">LSMEM2</span> Protein-coding gene in the species Homo sapiens

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<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">FAM166C</span>

Family with Sequence Similarity 166, member C (FAM166C), is a protein encoded by the FAM166C gene. The protein FAM166C is localized in the nucleus. It has a calculated molecular weight of 23.29 kDa. It also contains DUF2475, a protein of unknown function from amino acid 19–85. The FAM166C protein is nominally expressed in the testis, stomach, and thyroid.

<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">ZFP62</span> Gene in Humans

Zinc Finger Protein 62, also known as "ZNF62," "ZNF755," or "ZET," is a protein that in humans is encoded by the ZFP62 gene. ZFP62 is part of the C2H2 Zinc Finger family of genes.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000204856 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000029463 - 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 3 4 5 "FAM216A family with sequence similarity 216 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov.
  6. 1 2 "Genepaint - Home of High Resolution Gene Expression Data". gp3.mpg.de.
  7. 1 2 "PSORT II server - GenScript". www.genscript.com.
  8. 1 2 "Tissue expression of FAM216A - Staining in testis - The Human Protein Atlas". www.proteinatlas.org.
  9. ↑ "FAM216A Gene - GeneCards | F216A Protein | F216A Antibody". www.genecards.org.
  10. ↑ "Transcript: FAM216A-201 (ENST00000377673.10) - Exons - Homo sapiens - Ensembl genome browser 100". uswest.ensembl.org.
  11. ↑ "Tissue expression of FAM216A - Staining in cerebral cortex - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2 May 2020.
  12. ↑ "Tissue expression of FAM216A - Staining in cerebral cortex - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2 May 2020.
  13. 1 2 "Genomatix: Annotation & Analysis". www.genomatix.de. Retrieved 2 May 2020.[ permanent dead link ]
  14. 1 2 3 "Human hg38 chr12%3A110468611%2D110490386 UCSC Genome Browser v397". genome.ucsc.edu.
  15. 1 2 "SAPS Results". www.ebi.ac.uk.
  16. ↑ "CFSSP: Chou & Fasman Secondary Structure Prediction Server". www.biogem.org. Retrieved 2 May 2020.
  17. ↑ Ashok Kumar, T. (2013). CFSSP: Chou and Fasman Secondary Structure Prediction server. WIDE SPECTRUM: Research Journal. 1(9):15-19.
  18. ↑ "I-TASSER results". zhanglab.ccmb.med.umich.edu. Retrieved 2 May 2020.[ permanent dead link ]
  19. ↑ "SUMOplot™ Analysis Program | Abcepta". www.abcepta.com. Retrieved 2 May 2020.
  20. ↑ "NetGlycate 1.0 Server - prediction results". www.cbs.dtu.dk. Retrieved 2 May 2020.
  21. ↑ "NetNGlyc 1.0 Server - prediction results". www.cbs.dtu.dk. Retrieved 2 May 2020.
  22. ↑ "NetPhos 3.1 Server - prediction results". www.cbs.dtu.dk. Retrieved 2 May 2020.
  23. ↑ "FAM216A protein (human) - STRING interaction network". string-db.org. Retrieved 1 May 2020.
  24. ↑ "Search Results – The Molecular INTeraction Database" . Retrieved 1 May 2020.
  25. ↑ "PSICQUIC View". www.ebi.ac.uk. Retrieved 1 May 2020.
  26. ↑ "protein FAM216B [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov.
  27. ↑ "FAM216A family with sequence similarity 216 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2 May 2020.
  28. ↑ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2 May 2020.
  29. ↑ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2 May 2020.
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