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.
Gene
Expression This gene is expressed at a very high level,4.4 times the average gene. The c11orf98 protein is expressed in a wide array of tissues. RNA-seq dat showed this gene to be expressed highest in the appendix, lymph node, and thymus.
An analysis via PSORT II concluded that the C11orf98 gene product is localized to the nucleus 82.6% reliability. This nuclear localization suggests that C11orf98 protein may have a function related to the expression and regulation of genes in the nucleus.
Regulation Several different transcription factors are predicted to regulate the expression of the c11orf98 gene. These transcription factors were predicted based on DNA sequences found in the gene using Genomatix which also provided the name and description. #NameTF Description1V$ZIC3.03Zinc finger protein of the cerebellum (Zic3)2V$SPZ1.01Spermatogenic Zip 1 transcription factor3V$YB1.01Y box binding protein 1, has a preference for binding ssDNA4V$PAX5PAX5 paired domain protein5V$TCF21.02Transcription factor 216V$GFI1B.02Growth factor independence 1 zinc finger protein Gfi-1B7V$SPI1.02SPI-1 proto-oncogene; hematopoietic transcription factor PU.18V$ZKSCAN3.01Zinc finger with KRAB and SCAN domains 39V$EGR2.03Early growth response 210V$ZNF300.01KRAB-containing zinc finger protein 30011V$AP4.03Activating enhancer binding protein 412V$AML2.01RUNX3 (Runt-related transcription factor 3), AML2 (Acute myeloid leukemia 2)13V$WHN.01Winged helix protein, involved in hair keratinization and thymus epithelium differentiation14O$DINR.01Drosophila initiator motifs15V$ZTRE.035' half site of ZTRE motif16V$ZNF35.01Human zinc finger protein ZNF3517V$SP1.02Stimulating protein 1, ubiquitous zinc finger transcription factor18V$DMP1.02Cyclin D binding myb-like transcription factor19V$ETV1.02Ets variant 120V$WT1.02Wilms Tumor Suppressor
Protein The c11orf98 gene encodes a protein that is 123 amino acids long. The predicted molecular weight of the protein is 14.2 kDa. The basal isoelectric point was determined to be 11.53. The protein's subcellular localization was predicted to be in the nucleus.
Domain The c11orf98 protein contains a region of unknown function (DUF5564) that spans from amino acids 1-98. There are also 2 disordered regions within the protein that span from amino acids 1-21 and 32-123. C11orf98 contains 4 bipartite nuclear localization signals (NLS_BP) which indicates the protein will be 'tagged' for import into the cell nucleus by nuclear transport. The NLS_BP sequence usually consists of positively charged arginines, which would also explain the arginine rich region (ARG_RICH).
Structure The secondary structures of the c11orf98 protein was predicted to have multiple alpha helices as well as beta sheets. The tertiary structure was predicted using AlphaFold
Post-translational Modifications C11orf98 protein undergoes modifications following translation. The c11orf98 protein was predicted to have an amidation site. This functions as an active peptide precursor cleavage site. Next, a cAMP- and cGMP-dependent protein kinase phosphorylation site was predicted as well as other phosphorylation sites such as a Casein kinase II phosphorylation site and a protein kinase C phosphorylation site . An N-myristoylation site was predicted as well. Phosphorylation is significant because a phosphoryl group is added to the site, which only can occur in the nucleus or in cytosol. Myristoylation is significant because a myristoyl group (fatty acid group) is added to the site which helps anchor the transmembrane protein or cytosolic protein to the membrane. There were twelve predicted o-beta-GlcNAc glycosylation sites. This is significant because this modification is exclusively found on nuclear and cytoplasmic proteins rather than membrane proteins and secretory proteins. One sumoylation site was predicted. Sumoylation is a post-translational modification involved in nuclear-cytosolic transport, transcriptional regulation, apoptosis, protein stability, response to stress, and progression through the cell cycle.
Interactions
Abbreviated Name Name Basis of ID Score Description JUNC-junProximity-dependent biotin identificationVariousc-Jun, in combination with c-Fos, forms the AP-1 early response transcription factorFBLFibrillarinProximity-dependent biotin identificationVariouscomponent of a nucleolar small nuclear ribonucleoprotein (snRNP) particle thought to participate in the first step in processing pre-ribosomal (r)RNAESR1Estrogen receptor 1 Tandem affinity purification0.35activated by the sex hormone estrogen, is a transcription factor composed of several domains important for hormone binding, DNA binding, and activation of transcriptionSCARB2Scavenger Receptor Class B Member 2Pull Down 0.35protein is primarily found in the membrane of cellular structures called lysosomes, which are specialized compartments that digest and recycle materialsOAS32'-5'-Oligoadenylate Synthetase 3Pull Down 0.35This enzyme is induced by interferons and catalyzes the 2', 5' oligomers of ATP
Homology and evolution
Orthologs The c11orf98 gene has 148 orthologs. The oldest ortholog appeared in invertebrates. Other orthologs were found in birds, reptiles, amphibians, fish, and invertebrates. +Seq #C11orf98Genus, SpeciesCommon NameTaxonomic GroupDivergence Date (Million Years Ago)Accession NumberQuery CoverSequence Length (aa)Sequence Identity (%)Sequence Similarity (%)0MAMMALIAHomo sapienshumanPrimates0NP_0012730151001231001001Pan Paniscusbonobo (pygmy chimpanzee)Primates6.7XP_008952146.110012399.21002Mus musculushouse mouseRodentia90NP_079739.110012382.9391.13AVESDromaius novaehollandiaeemuAves312XP_0259752909620035.643.44Apteryx mantelli North Island brown kiwiAves312XP_0138065429015548.461.95REPTILIAChelydra serpentinacomman snapping turtleReptilia312KAG6938024.19712762.2746AMPHIBIANBufo bufo common toadAmphibian351.8XP_040265882.19813551.5757Ranitomeya imitatormimic poison frogAmphibian351.8CAF5124592.1 599751.256.68FISHDanio reriozebrafishActinoptergyii (bony fish)435XP_009298201.1 6517733.743.79Perca flavescensyellow perchActinoptergyii (bony fish)435XP_028427042.1 9712958.371.210Rhincodon typuswhale sharkChondrichthyes473XP_020392632.1 9512559.173.211Carcharodon carchariasgreat white sharkChondrichthyes473XP_041069108.19513057.674.212Callorhinchus miliielephant sharkChondrichthyes473XP_007910732.16113447.163.613INVERTEBRATESStyela Clavastalked sea squirtChordata676XP_039269774.1 9112536.851.914Branchiostoma belcheribelcher's lanceletChordata684XP_019641031.1 9312739.955.815Priapulus caudatuspenis wormPriapulimorphida797XP_014677581.1 9515728.740.716Owenia fusiformistubewormPolychaeta797CAC9620481.19214834.25017Lingula anatinalingulaBrachiopoda797XP_013399665.16914135.255.618Exaiptasia diaphanasea anemoneAnthozoa 824XP_020906605.17811030.652.419Actinia tenebrosaWaratah anemoneAnthozoa 824XP_031558418.1 7011336.257.520Nematostella vectensisStarlet sea anemoneAnthozoa 824XP_001639221.1 8011234.954
Evolution rate The relative evolution rate for c11orf98 is slower than the rate of fibrinogen alpha, but faster than cytochrome c. This is shown on the graph on the right
Phylogenetic tree
On the right is a phylogenetic tree displaying the evolutionary history of the gene.
Clinical significance Currently, the c11orf98 gene is not associated with any disease or medical condition.
References