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SPMAP1

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SPMAP1
Identifiers
AliasesSPMAP1, chromosome 17 open reading frame 98, sperm microtubule associated protein 1
External IDsMGI: 1919465; HomoloGene: 19140; GeneCards: SPMAP1; OMA:SPMAP1 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

388381

72215

Ensembl

ENSG00000275489
ENSG00000276913

ENSMUSG00000018543

UniProt

A8MV24

Q9DAQ5

RefSeq (mRNA)

NM_001080465

NM_028156

RefSeq (protein)

NP_001073934

NP_082432

Location (UCSC)Chr 17: 38.84 – 38.84 MbChr 11: 97.66 – 97.67 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

C17orf98 is a protein which in humans is coded by the gene c17orf98. The protein is derived from Homo sapiens chromosome 17[5]. The C17orf98 gene consists of a 552 basepair sequence. Its mRNA has three exons and no alternative splice sites. The protein has 154 amino acids, with no abnormal amino acid levels[6]. C17orf98 has a domain of unknown function (DUF4542) superfamily and is 17.6kDal in weight[7][8].

C17orf98 does not belong to any other families nor does it have any isoforms[9]. The protein has orthologs with high percent similarity in mammals and reptiles. The protein has additional distantly related orthologs across the metazoan kingdom, culminating with the sponge family.[10].

Protein structure of C17orf98 (homo sapiens) with beta sheets and alpha helixes

Like most proteins, C17orf98 is known to be highly expressed in the testes[11]. The protein has also been known to have elevated levels in cancer[12]. The protein has been shown to be expressed in proximity to or within intermediate filaments and the nucleolus[13]. Additionally, c17orf98 has transcription factors which are also active in hematopoietic cells, the immune system, the cardiovascular system, among others[14]. The gene is over-expressed in many cancer types, including kidney renal clear cell carcinoma and lung squamous cell carcinoma[15].

Gene

Background

GeneCards determined that C17orf98 has five enhancer sequences. The role of the se sequences may provide insight into the function of C17orf98. Four of the five enhancers are active in the thymus. All five enhancers are active in the H1 hESC. Additionally, all five enhancers are active in iPS DF 19.11 derived from foreskin fibroblasts [16]. C17orf98 has 11 Alu repeats[17]. C17orf98 gene has six sites on the sequence of possible O-GlcNAc sites[18]. C17orf98 does not have any alternative splice sites[19]. C17orf98 does not have any miRNA binding sites[20].

C17orf98 Select Transcription Factors

Transcription factors analysis The 5' UTR sequence of C17orf98 is highly conserved in primates. No non-mammalian 5'UTR mathces were able to be determined[21][22].

mRNA stucture Unafold entry on c17orf98 5’ UTR

Variants

SNPs

Protein

Structure

C17orf98 is a 17.6kDal protein[23]. There are no positive or negative charge clusters. There are no transmembrane components. The isoelectric point pI/Mw: 9.80 / 17564.67[24].

There are no N-terminal signal peptides. There are no transmembrane domains. Cleavage motifs were not found. There are no ER membrane retention signals, nor peroxisomal targeting signal. SKL2 is not present, thus a secondary peroxisome signal is not present. There are no vacuolar targeting signals. There are no RNA binding motifs are actinin type actin binding motifs. There are no N-myristoylation pattern or prenylation pattern[25]. The results of the k-NN prediction is cytoplasmic localization[26]. C17orf98 is not a signal peptide[27]. The protein is a soluble[28].

Kinase finder at Cuckoo determined kinase binding sites for c17orf98. There are many serine, threonine, and tyrosine binding sites[29].The lack of transmembrane domains is affirmed by Enzim, who also notes the entropy of the model as 17.0158. Additionally, the entropy of the best path is 17.0158[30]. Serine and threonine kinase binding sites are the most prevalent above the statistically significant threshold.

I-Tasser generated 3D stucture of c17orf98 (incomplete coverage)
SWISS-MODEL 3D structure of c17orf98

The c17orf98 protein is 17.6 kDal in weight. It is hydrophobic and soluble. Thus, it does not insert in the membrane. Additionally, there are no transmembrane domains in the protein sequence. There are no localization signals in the protein. The protein has five alpha helix regions, and two beta sheet regions.

Binding Sites

phosphorylation sites

Amino Acid Sequence

Homo Sapiens

MAYLSECRLRLEKGFILDGVAVSTAARAYGRSRPKLWSAIPPYNAQQDYHARSYFQ SHVVPPLLRVVPPLLRKTDQDHGGTGRDGWIVDYIHIFGQGQRYLNRRNWAGTGHS LQQVTGHDHYNADLKPIDGFNGRFGYRRNTPALRQSTSVFGEVTHFPLF

Associated Proteins

There are no known associated proteins[31] [32] [33] [34].

Expression

Protein abundance in Homo sapiens whole organism is quite low. No data is available for other species. The gene has a 0.44 percent abundance[35]. There are Geo Profile derived factors affecting to expression of c17orf98[36].

Cellular Expression

C17orf98 protein has been found to be expressed in the intermediate filaments and the nucleoli[37]. A C17orf98 antibody is available from Sigma-Aldrich[38]. Additionally, C17orf98 localizes in the cytoplasm. Distantly related c17orf98 ortholgs in organsisms such as Macrostomum lignano and Amphimedon queenslandica exhibit nuclear expression[39]. Nuclear localization signals are present in distantly related organisms in non-conserved sites.

Tissue

Like most proteins, C17orf98 protein is highly expressed in the testes[40]. The protein is expressed on adult tissues as well as fetal tissue. The protein has been found to be mildly expressed in connective tissue[41].

Cancer

Protein expression is elevated in many cancer patients. Specifically, protein expression has been shown to be high on colorectal, breast, prostate, and lung[42]. C17orf98 is expressed in papillary thryoid cancer as well[43]. Additionally, mutations were found in c17orf98 in endometrial, stomach, coloratura, and kidney cancer[44]. C17orf98 expression is elevated in cancer patients with BRCA. In Kidney renal clear cell carcinoma patients, c17orf98 expression dramatically decreased compared to the non cancerous state[45]. In 80% of chromophobe renal cell carcinoma patients, at least one gene duplication c17orf98 was present[46].

Evolution

C17orf98 is a slow mutating protein. It resembles Cytochrome C in its rate of amino acid changes, as determined by the molecular clock equations[47].

Unrooted c17orf98 Phylogenetic Tree with 20 orthologs (see table below)

Paralogs

There are no known Homo sapiens paralogs for C17orf98[48].

Orthologs

The protein has additional distantly related orthologs across the metazoan kingdom. It's most distant relative is in the sponge family. There is no known ortholog in ctenophores, nematodes, bacteria, fungus, plants, or zebrafish[49]. Interestingly, there are only two fish with the c17orf 98 gene. Model organisms such as C. elegans, and Drosophila melanogaster, do not have the gene.


C17orf98 Orthologs[50]

Sequence # Genus and Species Common Name Accession # Protein Length MYA Div Seq Id Confidence
1 Homo sapiens Human NP_001073934 154 0 100% na
2 Camelus ferus Wild Bactrian Camel XP_006176436 154 96 83% 2.00E-94
3 Pteropus alecto Black Flying Fox XP_006924784 154 96 81% 1.00E-92
4 Lipotes vexilifer Yangtze River Dolphin XP_007465208 154 96 81% 6.00E-89
5 Condylura cristat Star Nosed Mole XP_004684322 154 96 75% 5.00E-78
6 Myotis brandtii Brandt's Bat EPQ05064 171 96 78% 6.00E-78
7 Marmata marmata marmata Alpine Marmot XP_015362150.1 154 90 81% 3.00E-94
8 Octodon degus Chilean Rodent XP_004633931 153 90 73% 1.00E-76
9 Alligator sinensis Chinese Alligator XP_006022630 154 312 63% 8.00E-68
10 Anolis carolinensis Lizard XP_003222553 154 312 62% 6.00E-67
11 Xenopus laevis African Clawed Frog XP_018090228 244 352 51% 4.00E-38
12 Rhincodon typus Whale Shark XP_020388051.1 164 476 53% 5.00E-52
13 Acanthaster planci Starfish XP_022086463 209 684 48% 1.00E-37
14 Mizuhopecten yessoensis Scallop XP_021340301 275 797 45% 5.00E-06
15 Lottia gigantea Sea Snail XP_009063876 173 797 45% 2.00E-37
16 Lingula anatine Lamp Shell XP_013388744.1 211 797 43% 2.00E-35
17 Biomphalaria glabrata Freshwater Snail XP_013088317 198 797 41% 6.00E-15
18 Nematostella vectensis Sea Anemone XP_001629616 173 824 48% 2.00E-35
19 Stylophora pistillata Coral XP_022795125 226 824 46% 3.00E-38
20 Macrostonum lignano Flatworm PAA73615 235 824 36% 4.00E-25
21 Amphimedon queenslandica Sponge XP_003389909 275 951.8 32% 2.00E-12

C17orf98

  1. ^ a b c ENSG00000276913 GRCh38: Ensembl release 89: ENSG00000275489, ENSG00000276913 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000018543 – 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. ^ Zody, M.C., et al. (2006). DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature, 440(787), 1045-11049
  6. ^ PSORT II entry on c17orf98 https://psort.hgc.jp/form2.html
  7. ^ NCBI Conserved Domains entry C17orf98
  8. ^ ENMBL-EBI SAPS entry on c17orf98 https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=saps-I20180419-1415
  9. ^ https://blast.ncbi.nlm.nih.gov/Blast.cgi
  10. ^ https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
  11. ^ Human protein atlas entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489-C17orf98/tissue
  12. ^ Human protein atlas entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489-C17orf98/tissue
  13. ^ Human protein atlas entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489-C17orf98/tissue
  14. ^ Genomatix El Derado etnry on c17orf98 https://www.genomatix.de/cgibin/eldorado/eldorado.pl?s=0c99e39acf1f2c9dd47191b5b7f412b;SHOW_ANNOTATION=C17 orf98;ELDORADO_VERSION=E33R1705
  15. ^ TissGDB entry on c17orf98 https://bioinfo.uth.edu/TissGDB/gene_search_result.cgi?page=page&type=quick_search&quick_search=388381
  16. ^ http://www.genecards.org/cgi-bin/carddisp.pl?gene=C17orf98
  17. ^ Genomatix El Derado etnry on c17orf98 https://www.genomatix.de/cgibin/eldorado/eldorado.pl?s=0c99e39acf1f2c9dd47191b5b7f412b;SHOW _ANNOTATION=C17orf98;ELDORADO_VERSION=E33R1705
  18. ^ YinOyang entry on c17orf98 http://www.cbs.dtu.dk/services/YinOYang/
  19. ^ Acieview entry on c17orf98 https://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=human&term=c17orf98&submit=Go
  20. ^ Target Scan entry on c17orf98 http://www.targetscan.org/cgibin/targetscan/vert_71/view_gene.cgi?rs=ENST00000398575.4&taxid=9606&showc nc=0&shownc=0&shownc_nc=&showncf1=&showncf2=&subset=1
  21. ^ ClustalW entry on c17orf98 5’ UTR https://www.ebi.ac.uk/Tools/msa/clustalo/
  22. ^ NCBI Blast entry on c17orf98 5’ UTR https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blastho me
  23. ^ ENMBL-EBI SAPS entry on c17orf98 https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=saps-I20180419-1415
  24. ^ ExPASy pI/mW entry on c17orf98 https://web.expasy.org/cgi-bin/compute_pi/pi_tool
  25. ^ PSort II entry on C17orf98 https://psort.hgc.jp/cgi-bin/runpsort.pl
  26. ^ PSort II entry on C17orf98 https://psort.hgc.jp/cgi-bin/runpsort.pl
  27. ^ DTU Bioinformatics entry on c17orf98 http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=5AD7D62200000C8DFA04286C&wait=20
  28. ^ Expasy Sosui entry on C17orf98 http://harrier.nagahama-i-bio.ac.jp/sosui/cgi-bin/adv_sosui.cgi
  29. ^ Bio Cockoo GPS entry on C17orf98 http://gps.biocu
  30. ^ Enzim entry on c17orf98 http://www.enzim.hu/hmmtop/html/submit.html
  31. ^ BioGrid entry on c17orf98 https://thebiogrid.org/132666/summary/homo-sapiens/c17orf98.html
  32. ^ MINT entry on c17orf98 https://mint.bio.uniroma2.it/index.php/results-interactions/?id=c17orf98
  33. ^ STRING entry on C17orf98 https://string-db.org/cgi/network.pl?taskId=V780xrKjRDdJ
  34. ^ PSICQUIC View entry on c17orf98 http://www.ebi.ac.uk/Tools/webservices/psicquic/view/results.xhtml?conversationContext=3
  35. ^ pax-db entry on c17orf98 https://pax-db.org/protein/1858623#
  36. ^ NCBI GeoProfiles entry on c17orf98 https://www.ncbi.nlm.nih.gov/geoprofiles/?term=c17orf98
  37. ^ Human Protein Atlas (sigma) entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489‐C17orf98/cell
  38. ^ Sigma Aldrich entry on c17orf98 https://www.sigmaaldrich.com/catalog/product/sigma/hpa051696?lang=en&region=US
  39. ^ PSORT II entry on c17orf98 amino acid sequence https://psort.hgc.jp/form2.html
  40. ^ Protein Atlas entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489-C17orf98/cell
  41. ^  NCBI Unigene entry on c17orf98  www.ncbi.nlm.nih.gov/UniGene/clust.cgi?UGID=169593&TAXID=9606&SEARCH=c17orf98 
  42. ^ Human Protein Atlas (sigma) entry on c17orf98 https://www.proteinatlas.org/ENSG00000275489-C17orf98/cell
  43. ^ NCBI GeoProfiles entry on c17orf98 https://www.ncbi.nlm.nih.gov/geoprofiles
  44. ^ Phosphosite entry on c17orf98 https://www.phosphosite.org/proteinAction.action?id=5156341&showAllSites=true
  45. ^ TissGDB entry on c17orf98 https://bioinfo.uth.edu/TissGDB/gene_search_result.cgi?page=page&type=quick_search&quick_search=388381
  46. ^ TissGDB entry on c17orf98 https://bioinfo.uth.edu/TissGDB/gene_search_result.cgi?page=page&type=quick_search&quick_search=388381
  47. ^ https://www.nature.com/scitable/topicpage/the-molecular-clock-and-estimating-species-divergence-41971
  48. ^ Blast entry on c17orf98 https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
  49. ^ https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
  50. ^ https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
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