Biology:C12orf24

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Short description: Protein-coding gene in humans


A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example
C12Orf24

C12orf24 (Chromosome 12, open reading frame 24) is a gene in humans (Homo sapiens) that encodes a protein known as FAM216A.[1] This gene is primarily expressed in the testis and brain, but has constitutive expression in 25 other tissues.[1][2] FAM216A is an intracellular protein that has been predicted to reside within the nucleus of cells.[3] The exact function of C12orf24 is unknown. FAM216A is highly expressed in Sertoli cells of the testis as well as different stage spermatids.[4]

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.[5]

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.[1]

Name Transcript ID Base pair length Protein length
FAM216A NP_037432.2 1,101 273
FAM216A_X1 XP_011536548.1 1,148 234
FAM216A_X2 XP_024304727.1 1,142 179
FAM216A_X2 XP_005253932.1 1,040 179

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.[6][1]

Exon Start End Length in base pairs
ENSE00001474815 110,468,845 110,469,018 174
ENSE00003514548 110,473,078 110,473,077 41
ENSE00003459833 110,485,078 110,485,199 122
ENSE00003639607 110,486,325 110,486,454 130
ENSE00003553453 110,486,534 110,486,717 184
ENSE00003571489 110,487,861 110,487,943 83
ENSE00003568139 110,490,019 110,490,385 367

Expression

C12orf24 is primarily expressed in the brain, spinal cord, and testis of humans.[2][7] Within the testis C12orf24 is expressed in Sertoli cells.[4] Within the brain C12orf24 is expressed within neuropils.[8]

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.[9][10] Only one of the two predicted promoters binds transcription factors.[10]

Transcription factors

There are many transcription factors predicted to bind to the promoter region of C12orf24 by Genomatix and the UCSC Genome Browser.[10][9]

Name Function Binding sequence
ZKSCAN3 C2H2 zinc finger transcription factors 2 ccctcCCCCaccgtaactccggg
SPZ1 Testis-specific bHLH-Zip transcription factors aGGAGggaaat
WT1 Wilms tumor suppressor cggtgggGGAGgggcagga
E2F7 Cell cycle regulator cacaggaGGGAaatata
MZF1 Myeloid zinc finger 1 factors gcGGGGagcag
ETSF Human and murine ETS1 factors gtttgacaGGAAggtggctca
ZNF7 C2H2 zinc finger transcription factors 18 cgggaGGCTgaggca
NKX2 NKX homeodomain factors gccctcAAGTgagaggcgg
MYOD Myoblast determining factor

ctgggaCAGCtgctccc

Protein

Cellular location

According to the PSORT program of Genescript, C12orf24 is 69.6% likely to be a nuclear protein.[3] NCBI Gene predicts that C12orf24 is an intracellular protein.[1]

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.[11] 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.[11]

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.[12][13] 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.[14]

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.[15] There are 7 predicted sites of glycation on FAM216A.[16] There is no predicted signal peptide for FAM216A, which may prevent the protein from being glycosylated.[17] There is 42 predicted sites for phosphorylation, however given the predicted structure of the protein not all 42 sites will be accessible for phosphorylation.[18]

Interacting proteins

There are only a few known proteins that are predicted to interact with FAM216A.[19][20][21]

Protein Function
E6 HPV type 8 protein that prevents apoptosis in infected cells
MAGEA10 Possible roles in embryonal development, tumor transformation, and tumor development
DKC1 Required for ribosome biogenesis and telomere maintenance
RCF4 Replication factor C subunit 4. Possible required for elongation of multiprimed DNA
CCDC34 Coiled-coil domain containing 34. Involved in the cell cycle
NIFK Nucleolar protein interacting with the FHA domain of MKI67
PSMA4 Protease responsible for degrading most intracellular proteins

Homology

Paralogs

The only paralog for FAM216A is FAM216B.[22]

Orthologs

According to the NCBI Gene page for C12orf24, there are at least 182 organisms with an ortholog of C12orf24.[23] The farthest back known orthologs are in sea corals which diverged from humans 824 million years ago.[24][25]

Genus and species Common name Taxonomic group Date of divergence (MYA) Accession number Sequence length Sequence identity Sequence similarity
Pan paniscus Bonobo Primate 6.7 XP_003832531 281 95.7 96.1
Pan troglodytes Chimpanzee Primate 6.7 PNI64720 256 92.7 93
Gulo gulo Wolverine Carnivore 96 VCW50183 254 79.9 86.6
Orcinus orca Killer whale Odontoceti 96 XP_004276778 256 78.8 84.2
Delphinapteruss leucas Beluga whale Odonoceti 96 XP_022453741 256 78.4 84.2
Mondon monoceros Narwhal Odontoceti 96 XP_029084711 256 78.4 84.2
Tursiops truncatus Bottlenose dolphin Odontoceti 96 XP_019806066 256 78.4 84.2
Callhorhinus ursinus Northern fur seal Carnivore 96 XP_025745569 253 77.7 85
Felis catus House cat Carnivore 96 XP_003994705 253 75.5 84.2
Puma concolor Puma Carnivore 96 XP_025789304 253 75.5 84.2
Acinonyx jubatus Cheetah Carnivore 96 XP_026899980 253 75.1 84.2
Equus asinus Donkey Equidae 96 XP_014714174 253 74.7 80.6
Camelus ferus Wild Bactrian camel Artidoctyla 96 XP_006178132 256 73.6 82.8
Loxodonta africana African bush elephant Proboscidea 105 XP_010598175 254 76.2 83.2
Ciona intestinalis Sea vase Tunicata 676 XP_002124486 268 16.9 28.9
Acanthaster planci Crown-of-thorns starfish Echinodermata 684 XP_022109834 368 17 29.7
Actinia tenebrosa Australian red Waratah Sea anemone Cnidaria 824 XP_031556553 433 16.1 24.8
Pocillopora damicornis Cauliflower coral Cnidaria 824 XP_027047953 415 16 23.7
Orbicella faveolata Mountainous star coral Cnidaria 824 XP_020623330 435 15.4 23.2

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 "FAM216A family with sequence similarity 216 member A [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene?LinkName=nuccore_gene&from_uid=1519243283. 
  2. ↑ 2.0 2.1 "Genepaint - Home of High Resolution Gene Expression Data". https://gp3.mpg.de/viewer/setInfo/ES1158/0. 
  3. ↑ 3.0 3.1 "PSORT II server - GenScript". https://www.genscript.com/tools/psort. 
  4. ↑ 4.0 4.1 "Tissue expression of FAM216A - Staining in testis - The Human Protein Atlas". https://www.proteinatlas.org/ENSG00000204856-FAM216A/tissue/testis#img. 
  5. ↑ "FAM216A Gene - GeneCards | F216A Protein | F216A Antibody". https://www.genecards.org/cgi-bin/carddisp.pl?gene=FAM216A. 
  6. ↑ "Transcript: FAM216A-201 (ENST00000377673.10) - Exons - Homo sapiens - Ensembl genome browser 100". https://useast.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000204856;r=12:110468845-110490385;t=ENST00000377673. 
  7. ↑ "Tissue expression of FAM216A - Staining in cerebral cortex - The Human Protein Atlas". https://www.proteinatlas.org/ENSG00000204856-FAM216A/tissue/cerebral+cortex. Retrieved 2 May 2020. 
  8. ↑ "Tissue expression of FAM216A - Staining in cerebral cortex - The Human Protein Atlas". https://www.proteinatlas.org/ENSG00000204856-FAM216A/tissue/cerebral+cortex#img. Retrieved 2 May 2020. 
  9. ↑ 9.0 9.1 "Genomatix: Annotation & Analysis". https://www.genomatix.de/cgi-bin/eldorado/eldorado.pl?s=0072db4bf894b5ae575c86f2f73b0fc6;SHOW_ANNOTATION=FAM216A;ELDORADO_VERSION=E35R1911. Retrieved 2 May 2020. 
  10. ↑ 10.0 10.1 10.2 "Human hg38 chr12%3A110468611%2D110490386 UCSC Genome Browser v397". https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr12%3A110468611%2D110490386&hgsid=825194485_mAfHOI03bRnfAaNNAzaAX3bG6ahF. 
  11. ↑ 11.0 11.1 "SAPS Results". https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=saps-I20200503-000856-0993-93001342-p2m. 
  12. ↑ "CFSSP: Chou & Fasman Secondary Structure Prediction Server". http://www.biogem.org/tool/chou-fasman/index.php. Retrieved 2 May 2020. 
  13. ↑ Ashok Kumar, T. (2013). CFSSP: Chou and Fasman Secondary Structure Prediction server. WIDE SPECTRUM: Research Journal. 1(9):15-19.
  14. ↑ "I-TASSER results". https://zhanglab.ccmb.med.umich.edu/I-TASSER/output/S537044/. Retrieved 2 May 2020. 
  15. ↑ "SUMOplot™ Analysis Program | Abcepta". http://www.abcepta.com/sumoplot. Retrieved 2 May 2020. 
  16. ↑ "NetGlycate 1.0 Server - prediction results". http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5EADFB7D000077A57C0760B9&wait=20. Retrieved 2 May 2020. 
  17. ↑ "NetNGlyc 1.0 Server - prediction results". http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5EADFB8E000065B5F8C6D05B&wait=20. Retrieved 2 May 2020. 
  18. ↑ "NetPhos 3.1 Server - prediction results". http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5EAE0595000051E7E77F4285&wait=20. Retrieved 2 May 2020. 
  19. ↑ "FAM216A protein (human) - STRING interaction network". https://string-db.org/cgi/network.pl?taskId=luFVPqWUlyAk. Retrieved 1 May 2020. 
  20. ↑ "Search Results – The Molecular INTeraction Database". https://mint.bio.uniroma2.it/index.php/results-interactions/?id=FAM216A. Retrieved 1 May 2020. 
  21. ↑ "PSICQUIC View". http://www.ebi.ac.uk/Tools/webservices/psicquic/view/results.xhtml?conversationContext=1. Retrieved 1 May 2020. 
  22. ↑ "protein FAM216B [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/974576752. 
  23. ↑ "FAM216A family with sequence similarity 216 member A [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene/29902. Retrieved 2 May 2020. 
  24. ↑ "BLAST: Basic Local Alignment Search Tool". https://blast.ncbi.nlm.nih.gov/Blast.cgi. Retrieved 2 May 2020. 
  25. ↑ "TimeTree :: The Timescale of Life". http://timetree.org/. Retrieved 2 May 2020. 



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