C12orf24

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]

FAM216A
Identifiers
AliasesFAM216A, C12orf24, HSU79274, family with sequence similarity 216 member A
External IDsMGI: 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 MbChr 5: 122.5 – 122.51 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse
Chromosome 12
C12Orf24
AlliasesFAM216A, HSU79274
External IDsNCBI: NM_013300.3

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]

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

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 paniscusBonoboPrimate6.7XP_00383253128195.796.1
Pan troglodytesChimpanzeePrimate6.7PNI6472025692.793
Gulo guloWolverineCarnivore96VCW5018325479.986.6
Orcinus orcaKiller WhaleOdontoceti96XP_00427677825678.884.2
Delphinapteruss leucasBeluga WhaleOdonoceti96XP_02245374125678.484.2
Mondon monocerosNarwhalOdontoceti96XP_02908471125678.484.2
Tursiops truncatusBottlenose DolphinOdontoceti96XP_01980606625678.484.2
Callhorhinus ursinusNorthern Fur SealCarnivore96XP_02574556925377.785
Felis catusHouse CatCarnivore96XP_00399470525375.584.2
Puma concolorPumaCarnivore96XP_02578930425375.584.2
Acinonyx jubatusCheetahCarnivore96XP_02689998025375.184.2
Equus asinusDonkeyEquidae96XP_01471417425374.780.6
Camelus ferusWild Bactrian CamelArtidoctyla96XP_00617813225673.682.8
Loxodonta africanaAfrican Bush ElephantProboscidea105XP_01059817525476.283.2
Ciona intestinalisSea VaseTunicata676XP_00212448626816.928.9
Acanthaster planciCrown-of-thorns StarfishEchinodermata684XP_0221098343681729.7
Actinia tenebrosaAustralian Red Waratah Sea AnemoneCnidaria824XP_03155655343316.124.8
Pocillopora damicornisCauliflower CoralCnidaria824XP_0270479534151623.7
Orbicella faveolataMountainous Star CoralCnidaria824XP_02062333043515.423.2

References
  1. GRCh38: Ensembl release 89: ENSG00000204856 - Ensembl, May 2017
  2. 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. "FAM216A family with sequence similarity 216 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov.
  6. "Genepaint - Home of High Resolution Gene Expression Data". gp3.mpg.de.
  7. "PSORT II server - GenScript". www.genscript.com.
  8. "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. "Genomatix: Annotation & Analysis". www.genomatix.de. Retrieved 2 May 2020.
  14. "Human hg38 chr12%3A110468611%2D110490386 UCSC Genome Browser v397". genome.ucsc.edu.
  15. "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.
  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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