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CEFIP

From Wikipedia, the free encyclopedia

Cardiac-enriched FHL2-interacting protein (CEFIP) is a protein encoded by the gene C10orf71 on chromosome 10 open reading frame 71.[1][2] It is primarily understood that this gene is moderately expressed in muscle tissue and cardiac tissue.[3][4]

Gene

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The cytogenic locus is found at 10q11.23.[1] C10orf71 encodes 28294 base pairs (bp) within chromosome 10 at 49299193-49327487 bp.[1] It is located on the plus strand and is flanked by several other genes.[1]

Chromosome 10 representation showing C10orf71 location and other neighboring genes it is flanked by.[5]

mRNA

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The mRNA sequence of C10orf71 has 3 exons and 10 stop codons in the favorable splice form.[1][6] The two alternative splice forms had 47 and 75 stop codons interspersed throughout the sequence so they were not utilized to obtain further sequence information. The main splice form that was analyzed had the ten stop codons interspersed throughout the 5' and 3' UTR, which was why this splice form was utilized to further analyze. The mRNA of the Homo sapiens ortholog of C10orf71was 5286 bp in length.[1][6]

Alternative splice forms of C10orf7
Splice 1 Stop Codons found starting at bp: 4, 150, 247, 310, 4645, 4774, 4783, 4855, 4986, and 5250

Exons found between bp: 431/432, 544/545, and 5285/5286

Kozak site found at bp 332-334

Splice 2 47 Stop Codons found interspersed throughout the entire sequence
Splice 3 75 stop codons found interspersed throughout the entire sequence

The three alternative splice forms found of C10orf71 mRNA sequence and the locations stop codons, exons and the Kozak site found in Splice 1. Splice 1 was utilized to analyze and obtain information about as all of the stop codons found in this splice form were found in the 5' and 3' UTR regions of the sequence. There were three exons found in Splice 1 with a Kozak consensus sequence in the overall sequence as well.[1][6]

Protein

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The mature Homo sapiens homolog of the CEFIP protein encoded by C10orf71 is 1435 amino acids (aa) in length and weighs approximately 156.5 kDa.[6] This homolog has an isoelectric point of 5.94.[6] The range of pH values from Homo sapiens to the latest ortholog analyzed, Rhincodon types, ranged from 5.94-6.93, with it gradually increasing as it went later in the divergence of the ortholog.[6]

Species Length (aa) Molecular Weight (kDa) Isoelectric point
Homo sapiens 1,435 156.5 5.94
Gorilla gorilla 1,435 156.2 5.91
Mus muculus 1,412 154.5 5.81
Gallus gallus 1,521 167.7 6.15
Rhincodon typus 1,253 138.8 6.93

Comparison of some of the orthologs analyzed when compared to Homo sapiens. The orthologs are arranged from species that are most closely related to the Homo sapiens ortholog to least closely related (top to bottom respectively).[6]

Composition of protein

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CEFIP is predicted to be a non-transmembrane, soluble protein.[7] It is predicted to be a nuclear protein with 91.3% confidence with it being fairly confident to be a nuclear protein throughout the orthologs. There was one positive charge cluster found in CEFIP protein sequence, that is located from amino acids 1165–1193.[6] This cluster was moderately conserved throughout the orthologs analyzed. There was also a mixed charge cluster found in the Homo sapiens' sequence of this protein, located from amino acid 750–778, although this cluster was not highly conserved throughout the analyzed orthologs.[6] There was one repeat sequence found as well, TASKPPA, located at amino acids 163-169 and 116–1172. This protein is Proline and Serine rich as well.[6]

Predicted C10orf71 location in orthologs.
Species Nuclear Cytoplasmic Cytoskeletal
Homo sapiens 91.3% 4.3% 4.3%
Gorilla gorilla 91.3% 4.3% 4.3%
Mus musculus 82.6% 13.0% —
Gallus gallus 69.6% 17.4% 4.3%
Rhincodon typus 69.6% 21.7% —
This cartoon represents the basic layout of the CEFIP protein. The overall protein is represented by the orange rectangle, DUF4585 is represented by the blue pentagon, VAC is represented by the green oval, nuclear localization signals are represented by the gray diamonds and N-glycosylation sites are represented by the red diamonds.

Domains and motifs

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One confirmed domain of unknown function (DUF) was found within the CEFIP protein sequence, DUF4585.[1] DUF4585 is located on the Homo sapiens protein sequence from amino acid 311–334. DUF4585 was highly conserved throughout the orthologs that were analyzed. There was also a small vacuolar targeting motif (VAC) found within the analyzed protein sequence spanning amino acids 543–546.

Protein structure

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The mature CEFIP protein contains nuclear localization signals (NLS), pat4 (RKPK at aa 382, RPRK at aa 640, KRRK at aa 1190) and pat7 (PPWRKPK at aa 379 and PWRKPKT at aa 380) with an NLS score of 0.94. A secondary structure was constructed with a 6.1% confidence level.[7]

Predicted CEFIP protein structure.[8]

Post-translational modifications

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There were seven GlcNAc O-glycosylation sites predicted within the protein sequence found at amino acids 116, 120, 139, 165, 468, 470, and 844.[7] There were also several phosphorylation sites found interspersed throughout the sequence. One propeptide cleavage site was predicted at amino acid 38.[7] There were three predicted sumoylation sites found at amino acids 599, 890, and 1176.

Expression

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The C10orf71 mRNA was found to be highly expressed in cardiac, muscle, and liver tissue (biology).[1]

Regulation of expression

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There were 6 possible promoters found in the sequence. Promoter GXP_6729162 is 1403 bp in length.[9] This promoter had several transcription factors of interest including those involved with myocytes.[9]

Function

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There is little scientific information known about the function of CEFIP.

Interacting proteins

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There was a total of 25 proteins generated that were predicted to interact with CEFIP (Homo sapiens ortholog).[10][11] Most of the interactions predicted were physical interactions with CEFIP.[10] These interactions were discovered through a variety of mechanisms including, but not limited to: affinity chromatography, microarray analysis, and tandem mass spectrometry among others.[10][11] Refer to table for details about the interacting proteins of CEFIP.[12]

Interacting Protein Name of Protein Known Function Location Expressed or Associated Diseases
C20orf78 Chromosome 20 Open Reading Frame 78 Unknown Unconfirmed
BPIFA2[13] BPI Fold Containing Family A Member 2 Plays a role in antibacterial resistance in upper respiratory pathway Expressed in salivary glands
PPIL6[14] Peptidyl Prolyl Isomerase Like 6 Accelerates folding of proteins Unconfirmed
KIF17[15] Kinesin Family Member 17 Transports vesicles containing NMDA receptor 2B Expressed in microtubules
KRT78[16] Keratin 78 Forms cytoplasmic network; encodes proteins with intermediate filament domains Expressed in intermediate filaments
TBX4[17] T-box4 Transcription Factor Encode transcription factors involved in regulation of developmental processes; assists with regulation of mesoderm differentiation; could play a role in limb pattern formation Associated with Small Patella Syndrome and Heritable Pulmonary Arterial Hypertension
DNAH8[18] Dynein Axonemal Heavy Chain 8 heavy chain of an axonemal dynein involved in sperm and respiratory cilia motility. Associated with Colchicine Resistance and Mitochondrial Complex V Deficiency, Nuclear Type 1
TSPAN17[19] Tetraspanin 17 Predicted to regulate ADAM10 maturation Unconfirmed
C14orf80[20] Chromosome 14 Open Reading Frame 80 Unknown Unconfirmed
SLC35F4[21] Solute Carrier Family 35 Member F4 Solute transporter Unconfirmed
LHX4[22] LIM Homeobox 4 Predicted to play a role in maturing lungs, development of respiratory mechanisms, and development of the pituitary gland Associated with Pituitary Hormone Deficiency, Combined 4 and Lhx4=Related Combined Pituitary Hormone
FAM53A[23] Family With Sequence Similarity 53 Member A Plays a role in neural development Possibly expressed in ventricle tissue
GRIK5[24] Glutamate Ionotropic Receptor Kainase Type Subunit 5 Forms functional heteromeric kainite-preferring ionic channels Associated with Schizophrenia
FADS2[25] Fatty Acid Denaturase 2 Regulates unsaturation of fatty acids through introduction of double bonds between define Cysteines of the fatty acid chains Associated with Best Vitelliform Macular Dystrophy
GDF2[26] Growth Differentiation Factor 2 Regulates cartilage and bone development; differentiation of cholinergic receptors in CNS Unconfirmed
C17orf77[27] Chromosome 17 Open Reading Frame 77 Unknown Unconfirmed
CFAP45 (CCDC19)[28] Cilia And Flagella Associated Protein 45 Associated with pharynx cancer Unconfirmed
DCST2[29] DC-STAMP Domain Containing 2 Unknown Unconfirmed
CTXN1[30] Cortexin 1 Predicted to play a role in IC or EC signaling of the cortical neurons during the development of the forebrain. Unconfirmed
C19orf68[31] Chromosome 19 Open Reading Frame 68 Unknown Unconfirmed
DCAF7[32] DDB1 And CUL4 Associated Factor 7 It's been shown to function as a scaffold protein in kinase signaling. It's also been known to be involved with craniofacial development Unconfirmed
DYRK1A[33] Dual Specificity YAK1-Related Kinase May play a role in brain development and cell proliferation; nuclear localized protein Associated with Mental Retardation, Autosomal Dominant 7 and Microcephaly
DYRK1B[34] Dual Specificity Tyrosine-(Y)-Phosphorylation Regulated Kinase 1B Plays a role in the cell cycle; nuclear-localized protein Associated with Abdominal Obesity-Metabolic Syndrome 3 and Abdominal Obesity-Metabolic Syndrome
FNTA[35] Protein Farnesyltransferase/Geranylgeranyltransferase Type-1 Subunit Alpha Helps regulate neuromuscular junction development Unconfirmed
FNTB[36] Protein Farnesyltransferase Subunit Beta Catalyzes the transfer of a farnesyl moiety from farnesyl diphosphate to a cysteine Unconfirmed

Interacting proteins, their function if known, and any tissues they have been found or predicted to be expressed in and any diseases they have been associated with.[10][11][12]

Homologs

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Paralogs

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There are currently no known paralogs to the C10orf71 gene.

Orthologs

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C10orf71 is known to have 68 orthologs in various species including primates (11 species), rodents (8 species), Laurasiatheria carnivores (14 species), Placental mammals (38 species), Sauropsida birds and reptiles (7 species), and fish (11 species).[37] The highly conserved sequences are primarily from primates with the identity percentage of these species being >90%, whereas species such as reptiles, birds, and fish had an identity percentage ≤30%.[6] Refer to table for additional information on dates of divergence, sequence length, and sequence identity and similarity for orthologs. C10orf71 is not present in prokaryotes, archaea, or fungi.[37]

Abbreviation (for Phylogenetic Tree) Species Common Name Protein Accession # Estimated Date of Divergence (MYA) Sequence Length (aa) Sequence Identity to Human mRNA/protein (%) Sequence Similarity to Human mRNA/protein (%)
HomS Homo sapiens human NP_001128668.1 1435 100 100
GorG Gorilla gorilla western gorilla XP_018889898.1 9.06 1435 98.3 98.7
RhiR Rhinopithecus roxellana Golden snub-nosed monkey XP_010381152.1 29.44 1435 93.4 95.3
OtoG Otolemur garnettii small-eared galago XP_003801705.1 74 1419 74.9 81.5
TupC Tupaia chinensis Chinese tree shrew XP_014439281.1 82 1186 61.5 67.8
MusM Mus musculus house mouse NP_001182026.1 90 1412 65.4 74.3
OctD Octodon degus Common degu XP_004647022.1 90 1407 63.3 73.1
HetG Heterocephalus glaber Naked mole-rat XP_004874589.1 90 1411 63.2 73.3
CerS Ceratotherium simum simum Southern white rhinoceros XP_004432504.1 96 1436 74 81
OrcO Orcinus orca killer whale XP_004286436 96 1433 72.6 79.4
LoxA Loxodonta Africana African bush elephant XP_003408977.1 105 1438 65.5 74.5
SarH Sarcophilus harrisii Tasmanian devil XP_003755230.2 159 1470 49.0 62.5
GavG Gavialis gangeticus crocodile XP_019358113.1 312 1538 32.8 46.7
TinG Tinamus guttatus White-throated tinamou XP_010216992.1 312 1529 32.4 46.3
PelS Pelodiscus sinensis turtle XP_006118195.1 312 1505 32.0 46.2
GalG Gallus gallus chicken XP_421655.3 312 1521 30.5 44.7
MelU Melopsittacus undulates parrot XP_005153970 312 1538 30.3 45.1
OreN Oreochromis niloticus Nile tilapia XP_019221822 435 661 12.0 18.7
SclF Scleropages formosus Asian arowana XP_018580403 435 3125 11.5 17.9
DanR Danio rerio Zebrafish XP_005157004.1 435 3591 9.2 16.0
CluH Clupea harengus Atlantic herring XP_012687674.1 435 3633 9.1 13.8
RhiT Rhincodon typus whale shark XP_020385611.1 473 1253 40.0 24.8

Ortholog table in descending order to latest ortholog diverged. This table compares the orthologs analyzed, their species names, common names, dates of divergence from Homo sapiens ortholog (MYA), length (aa), and percentage of similarity and identity.[1][6][37][38]

Phylogeny

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A phylogenic tree created from the orthologs. They are grouped in similar animal species. The branches are labeled with the four letter code given to them, full species name and common names of these codes can be found in table above.

A phylogenetic tree was constructed for the orthologs that were analyzed in comparison to Homo sapiens. With the species of latest divergence being Rhincodon types, or the whale shark.[37][38]

Evolutionary rate

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C10orf71's rate of divergence was faster than that of fibrinogen or Cytochrome C.[37]

The corrected % of divergence compared to the date of divergence for the orthologs. The ortholog points on the graph can be identified by referring to table above. C10orf71 (blue line) appears to have diverged faster than both Fibrinogens (red line) and Cytochrome C (green line). The correct % of divergence was calculated using the equation m/100 = –ln(1- n/100) where m= total number of amino acid changes which have occurred in a 100-amino-acid segment of a protein and n=observed number of amino acid changes per 100 residues.

Clinical significance

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There was a microarray experiment that also showed evidence that C10orf71's expression was lowered in skeletal muscle tissues that experienced sepsis.[39] There was clinical significance found in the expression level of C10orf71 in an experiment looking at those with Myotonic dystrophy.[39] One microarray analysis produced results that showed C10orf71's expression level decreased in those with prostate cancer as well.[39]

References

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  1. ^ a b c d e f g h i j "Home - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
  2. ^ "HGNC database of human gene names | HUGO Gene Nomenclature Committee". www.genenames.org. Retrieved 2017-05-07.
  3. ^ "Home - UniGene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
  4. ^ Thierry-Mieg, Danielle; Thierry-Mieg, Jean (2012-10-16). "AceView a comprehensive annotation of human and worm genes with mRNAs or ESTsAceView". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
  5. ^ "National Center for Biotechnology Information". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
  6. ^ a b c d e f g h i j k l Workbench, NCSA Biology. "SDSC Biology Workbench". seqtool.sdsc.edu. Archived from the original on 2003-08-11. Retrieved 2017-05-07.
  7. ^ a b c d "ExPASy: SIB Bioinformatics Resource Portal - Home". www.expasy.org. Retrieved 2017-05-07.
  8. ^ "i-TASSER". zhanglab.ccmb.med.umich.edu. Retrieved 2017-05-07.
  9. ^ a b "Genomatix: Genome Annotation and Browser: Query Input". www.genomatix.de. Retrieved 2017-05-07.
  10. ^ a b c d "GeneMANIA". genemania.org. Retrieved 2017-05-07.
  11. ^ a b c Lab, Mike Tyers. "BioGRID | Database of Protein, Chemical, and Genetic Interactions". thebiogrid.org. Retrieved 2017-05-07.
  12. ^ a b Database, GeneCards Human Gene. "GeneCards - Human Genes | Gene Database | Gene Search". www.genecards.org. Retrieved 2017-05-07.
  13. ^ Database, GeneCards Human Gene. "BPIFA2 Gene - GeneCards | BPIA2 Protein | BPIA2 Antibody". www.genecards.org. Retrieved 2017-05-09.
  14. ^ Database, GeneCards Human Gene. "PPIL6 Gene - GeneCards | PPIL6 Protein | PPIL6 Antibody". www.genecards.org. Retrieved 2017-05-09.
  15. ^ Database, GeneCards Human Gene. "KIF17 Gene - GeneCards | KIF17 Protein | KIF17 Antibody". www.genecards.org. Retrieved 2017-05-09.
  16. ^ Database, GeneCards Human Gene. "KRT78 Gene - GeneCards | K2C78 Protein | K2C78 Antibody". www.genecards.org. Retrieved 2017-05-09.
  17. ^ Database, GeneCards Human Gene. "TBX4 Gene - GeneCards | TBX4 Protein | TBX4 Antibody". www.genecards.org. Retrieved 2017-05-09.
  18. ^ Database, GeneCards Human Gene. "DNAH8 Gene - GeneCards | DYH8 Protein | DYH8 Antibody". www.genecards.org. Retrieved 2017-05-09.
  19. ^ Database, GeneCards Human Gene. "TSPAN17 Gene - GeneCards | TSN17 Protein | TSN17 Antibody". www.genecards.org. Retrieved 2017-05-09.
  20. ^ Database, GeneCards Human Gene. "C14orf80 Gene - GeneCards | CN080 Protein | CN080 Antibody". www.genecards.org. Retrieved 2017-05-09.
  21. ^ Database, GeneCards Human Gene. "SLC35F4 Gene - GeneCards | S35F4 Protein | S35F4 Antibody". www.genecards.org. Retrieved 2017-05-09.
  22. ^ Database, GeneCards Human Gene. "LHX4 Gene - GeneCards | LHX4 Protein | LHX4 Antibody". www.genecards.org. Retrieved 2017-05-09.
  23. ^ Database, GeneCards Human Gene. "FAM53A Gene - GeneCards | FA53A Protein | FA53A Antibody". www.genecards.org. Retrieved 2017-05-09.
  24. ^ Database, GeneCards Human Gene. "GRIK5 Gene - GeneCards | GRIK5 Protein | GRIK5 Antibody". www.genecards.org. Retrieved 2017-05-09.
  25. ^ Database, GeneCards Human Gene. "FADS2 Gene - GeneCards | FADS2 Protein | FADS2 Antibody". www.genecards.org. Retrieved 2017-05-09.
  26. ^ Database, GeneCards Human Gene. "GDF2 Gene - GeneCards | GDF2 Protein | GDF2 Antibody". www.genecards.org. Retrieved 2017-05-09.
  27. ^ Database, GeneCards Human Gene. "C17orf77 Gene - GeneCards | CQ077 Protein | CQ077 Antibody". www.genecards.org. Retrieved 2017-05-09.
  28. ^ Database, GeneCards Human Gene. "CFAP45 Gene - GeneCards | CFA45 Protein | CFA45 Antibody". www.genecards.org. Retrieved 2017-05-09.
  29. ^ Database, GeneCards Human Gene. "DCST2 Gene - GeneCards | DCST2 Protein | DCST2 Antibody". www.genecards.org. Retrieved 2017-05-09.
  30. ^ Database, GeneCards Human Gene. "CTXN1 Gene - GeneCards | CTXN1 Protein | CTXN1 Antibody". www.genecards.org. Retrieved 2017-05-09.
  31. ^ Database, GeneCards Human Gene. "C19orf68 Gene - GeneCards | CS068 Protein | CS068 Antibody". www.genecards.org. Retrieved 2017-05-09.
  32. ^ Database, GeneCards Human Gene. "DCAF7 Gene - GeneCards | DCAF7 Protein | DCAF7 Antibody". www.genecards.org. Retrieved 2017-05-09.
  33. ^ Database, GeneCards Human Gene. "DYRK1A Gene - GeneCards | DYR1A Protein | DYR1A Antibody". www.genecards.org. Retrieved 2017-05-09.
  34. ^ Database, GeneCards Human Gene. "DYRK1B Gene - GeneCards | DYR1B Protein | DYR1B Antibody". www.genecards.org. Retrieved 2017-05-09.
  35. ^ Database, GeneCards Human Gene. "FNTA Gene - GeneCards | FNTA Protein | FNTA Antibody". www.genecards.org. Retrieved 2017-05-09.
  36. ^ Database, GeneCards Human Gene. "FNTB Gene - GeneCards | FNTB Protein | FNTB Antibody". www.genecards.org. Retrieved 2017-05-09.
  37. ^ a b c d e "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
  38. ^ a b "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2017-05-07.
  39. ^ a b c "Home - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2017-05-07.
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