Biology:C17orf78

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Short description: Mammalian protein found in Homo sapiens

Uncharacterized protein C17orf78 is a protein encoded by the C17orf78 gene in humans.[1] 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.[2] The function of C17orf78 is not well defined.

Gene

Location

C17orf78 (Chromosome 17 Open Reading Frame 78) is found on the long arm cytogenetic band 17q12.[3] The genomic sequence spans from base pair position 37,375,985 to 37,392,708 on the forward strand, and constitutes a length of 16,723 base pairs.[4] The neighboring genes include TADA2A, DUSP14, and ACACA.[5]

Exons and Introns

C17orf78 has 7 exon regions within its encoding area.[1] C17orf78 also has a total of 6 intron regions spanning its sequence.[6][3]

Transcripts

C17orf78 has two splice variant isoforms.[7] Isoform 1 is encoded by a mRNA sequence that is 1920 base pairs in length.[8] Isoform 2 derives from a mRNA sequence of 1678 base pairs.[9]

Protein

The primary sequence of C17orf78 has been predicted to be 30.55kDa, with an isoelectric point of 9.62.[10]

Uncharacterized protein C17orf78 isoform 1 (C17orf78-204) has a span of 275 amino acids, including all 7 exons.[11][12] C17orf78 isoform 1 is the principle protein.

Uncharacterized protein C17orf78 isoform 2 (C17orf78-203) has a span of 159 amino acids, constituted from 5 exon regions, which include the 1st, 2nd, 3rd, 6th, and 7th exons of the principle protein.[13][12]

Expression

C17orf78 has high expression in the human small intestine, particularly the duodenum[2][14] and has been detected in small expression levels in the testes and other tissues.[15] Fetal expression lowers in all tissues over time with development except for the intestines, which shows increasing expression over time.[16][2]

Subcellular Location

Predictive analysis of C17orf78 by Psort2[17] places the primary location in the nucleus because of a nuclear localization signal. C17orf78 is also potentially a transmembrane protein due to the presence of a transmembrane region.[18][8]

Structure

Protein

C17orf78 secondary structure has been predicted to have several alpha helices and strands as well as beta sheets.[19][20]

Regulation

DNA Promoter

The Genomatix[21] tool Gene2Promoter found one viable promoter region. The region was found to span from base pairs 37374332 to 37376025.

mRNA

The mRNA secondary structure for C17orf78 was found by the online tool RNAfold[22] show a moderate affinity for stem-loop (hairpin) structures.

Post Translational Modification

Phosphorylation is predicted to occur at a number of sites on C17orf78.[23] PKC-phosphorylation and CK2 phosphorylation are predicted to have various sites on C17orf78 with high confidence.[24]

N-linked glycosylation is predicted to occur at three locations on C17orf78.[24] Asparagine linked glycosylation was predicted to occur on C17orf78 orthologs with high confidence.

Myristolyation has been predicted to occur on C17orf78 by the ExPASy tool Motif Scan.[24]

Homology & Evolution

The evolution rate for c17orf78 compared to fibrinogen alpha and cytochrome c

C17orf78 orthologs have been identified in mammals, birds, and reptiles.[1] It is a rapidly evolving gene, with around 40 base pairs mutating every 100 million years.[1] There are no known paralogs of this gene in humans.[25]

Scientific Name Common Name Taxonomic Group Date of Divergence (MYA) Accession Number Protein Length (aa) Identity (%) Similarity (%)
Homo sapiens Human Primates 0 NP_775896.3 275 100 100
Mus musculus Mouse Rodentia 89 NP_001033021.2 290 59.7 72.0
Sus scrofa Wild Boar Artiodactyla 94 XP_013845397.2 287 69.7 80.8
Ovis aries Sheep Artiodactyla 94 XP_027831111.1 280 68.3 79.4
Eptesicus fuscus Big Brown Bat Chiroptera 94 XP_028013352.1 287 66.7 74.7
Mustela erminea Stoat Carnivora 94 XP_032175349.1 300 58.8 67.7
Orycteropus afer afer Aardvark Tubulidentata 102 XP_007946081.1 286 71.2 80.9
Loxodonta africana African Bush Elephant Proboscidea 102 XP_003414613.1 282 67.6 77.8
Elephantulus edwardii Cape Elephant Shrew Macroscelidea 102 XP_006881725.1 312 57.6 67.5
Phascolarctos cinereus Koala Diprotodontia 160 XP_020847101.1 286 53.3 66.2
Vombatus ursinus Common Wombat Diprotodontia 160 XP_027726443.1 245 45.6 59.8
Trachemys scripta elegans Red-Eared Slider Turtle Testudines 318 XP_034608235.1 257 31.6 46.2
Apertyx rowi Okarito Kiwi Apterygiformes 318 XP_025937346.1 270 31.3 50.2
Chelonia mydas Green Sea Turtle Testudines 318 XP_027675993.1 270 28.9 39.7
Terrapene carolina triunguis Three-Toed Box Turtle Testudines 318 XP_029768387.1 299 28.4 41.0
Pelodiscus sinensis Chinese Softshell Turtle Testudines 318 XP_025035086.1 258 28.2 40.8
Melopsittacus undulatus Budgerigar Psittaciformes 318 XP_012985804.2 255 26.7 41.1
Oxyura jamaicensis Ruddy Duck Anseriformes 318 XP_035199171.1 270 25.8 41.2
Chelonoidis abingdonii Pinta Island Tortoise Testudines 318 XP_032635246.1 262 24.2 36.3
Anas platyrhynchos Mallard Anseriformes 318 XP_021123240.1 232 23.3 34.3

References

  1. ↑ 1.0 1.1 1.2 1.3 "C17orf78 chromosome 17 open reading frame 78 [Homo sapiens (human) - Gene - NCBI"]. https://www.ncbi.nlm.nih.gov/gene/284099. 
  2. ↑ 2.0 2.1 2.2 "C17orf78 Gene Expression - Gene - NCBI". https://www.ncbi.nlm.nih.gov/gene/284099?report=expression&bioproject=PRJEB4337. 
  3. ↑ 3.0 3.1 "Gene: C17orf78 (ENSG00000278505) - Summary - Homo sapiens - Ensembl genome browser 100". https://uswest.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000278505;r=17:37375985-37392708. 
  4. ↑ "Symbol report for C17orf78". https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:26831. 
  5. ↑ "AceView: Gene:C17orf78, a comprehensive annotation of human, mouse and worm genes with mRNAs or ESTsAceView.". https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=c17orf78&submit=Go. 
  6. ↑ "Human hg38 chr17:37,375,985-37,392,708 UCSC Genome Browser v397". https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr17:37375985-37392708&hgsid=831979755_Ux5XISB6qdV9P7P6fTz714t7KBat. 
  7. ↑ "Gene: C17orf78 (ENSG00000278505) - Summary - Homo sapiens - Ensembl genome browser 100". http://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000278505;r=17:37375985-37392708. 
  8. ↑ 8.0 8.1 (in en-US) Homo sapiens chromosome 17 open reading frame 78 (C17orf78), transcript variant 1, mRNA. 2020-04-25. http://www.ncbi.nlm.nih.gov/nuccore/NM_173625.5. 
  9. ↑ (in en-US) Homo sapiens chromosome 17 open reading frame 78 (C17orf78), transcript variant 2, mRNA. 2019-06-01. http://www.ncbi.nlm.nih.gov/nuccore/NM_001321399.2. 
  10. ↑ "ExPasy Compute pI/Mw". 2020-05-05. https://web.expasy.org/cgi-bin/compute_pi/pi_tool. [yes|permanent dead link|dead link}}]
  11. ↑ "uncharacterized protein C17orf78 isoform 1 [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/NP_775896.3. 
  12. ↑ 12.0 12.1 "Gene: C17orf78 (ENSG00000278505) - Splice variants - Homo sapiens - Ensembl genome browser 100". https://uswest.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000278505;r=17:37375985-37392708. 
  13. ↑ "uncharacterized protein C17orf78 isoform 2 [Homo sapiens - Protein - NCBI"]. https://www.ncbi.nlm.nih.gov/protein/NP_001308328.1. 
  14. ↑ "Tissue expression of C17orf78 - Summary - The Human Protein Atlas". https://www.proteinatlas.org/ENSG00000278505-C17orf78/tissue. 
  15. ↑ "C17orf78 Gene Expression - Gene - NCBI". https://www.ncbi.nlm.nih.gov/gene/284099?report=expression&bioproject=PRJEB2445. 
  16. ↑ Szabo, Linda; Morey, Robert; Palpant, Nathan J.; Wang, Peter L.; Afari, Nastaran; Jiang, Chuan; Parast, Mana M.; Murry, Charles E. et al. (2015-06-16). "Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development". Genome Biology 16 (1): 126. doi:10.1186/s13059-015-0690-5. ISSN 1474-760X. PMID 26076956. 
  17. ↑ "PSORT II server". http://www.genscript.com/cgi-bin/tools/psort2.pl. 
  18. ↑ "SOSUI: Result". http://harrier.nagahama-i-bio.ac.jp/sosui/cgi-bin/adv_sosui.cgi. 
  19. ↑ "I-TASSER server for protein structure and function prediction". https://zhanglab.ccmb.med.umich.edu/I-TASSER/. 
  20. ↑ "Bioinformatics Toolkit". https://toolkit.tuebingen.mpg.de/jobs/1464143. 
  21. ↑ "Genomatix - NGS Data Analysis & Personalized Medicine". https://www.genomatix.de/. 
  22. ↑ "RNAfold web server". http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi. 
  23. ↑ "NetPhos 3.1 Server - prediction results". http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5EC7117200002E735448F980&wait=20. 
  24. ↑ 24.0 24.1 24.2 "Motif Scan" (in en). https://myhits.sib.swiss/cgi-bin/motif_scan. 
  25. ↑ "Human BLAT Search". https://genome.ucsc.edu/cgi-bin/hgBlat. 



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