Biology:CEFIP

Short description: Mammalian protein found in Homo sapiens

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

Gene

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

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

mRNA

The mRNA sequence of C10orf71 has 3 exons and 10 stop codons in the favorable splice form. 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.

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.

Protein

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. This homolog has an isoelectric point of 5.94. 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.

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).

Composition of protein

CEFIP is predicted to be a non-transmembrane, soluble protein. 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. 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. 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.

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

One confirmed domain of unknown function (DUF) was found within the CEFIP protein sequence, DUF4585. 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

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.

Predicted CEFIP protein structure.

Post-translational modifications

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

Expression

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

Regulation of expression

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

Function

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

Interacting proteins

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

Interacting Protein	Name of Protein	Known Function	Location Expressed or Associated Diseases
C20orf78	Chromosome 20 Open Reading Frame 78	Unknown	Unconfirmed
BPIFA2	BPI Fold Containing Family A Member 2	Plays a role in antibacterial resistance in upper respiratory pathway	Expressed in salivary glands
PPIL6	Peptidyl Prolyl Isomerase Like 6	Accelerates folding of proteins	Unconfirmed
KIF17	Kinesin Family Member 17	Transports vesicles containing NMDA receptor 2B	Expressed in microtubules
KRT78	Keratin 78	Forms cytoplasmic network; encodes proteins with intermediate filament domains	Expressed in intermediate filaments
TBX4	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	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	Tetraspanin 17	Predicted to regulate ADAM10 maturation	Unconfirmed
C14orf80	Chromosome 14 Open Reading Frame 80	Unknown	Unconfirmed
SLC35F4	Solute Carrier Family 35 Member F4	Solute transporter	Unconfirmed
LHX4	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	Family With Sequence Similarity 53 Member A	Plays a role in neural development	Possibly expressed in ventricle tissue
GRIK5	Glutamate Ionotropic Receptor Kainase Type Subunit 5	Forms functional heteromeric kainite-preferring ionic channels	Associated with Schizophrenia
FADS2	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	Growth Differentiation Factor 2	Regulates cartilage and bone development; differentiation of cholinergic receptors in CNS	Unconfirmed
C17orf77	Chromosome 17 Open Reading Frame 77	Unknown	Unconfirmed
CFAP45 (CCDC19)	Cilia And Flagella Associated Protein 45	Associated with pharynx cancer	Unconfirmed
DCST2	DC-STAMP Domain Containing 2	Unknown	Unconfirmed
CTXN1	Cortexin 1	Predicted to play a role in IC or EC signaling of the cortical neurons during the development of the forebrain.	Unconfirmed
C19orf68	Chromosome 19 Open Reading Frame 68	Unknown	Unconfirmed
DCAF7	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	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	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	Protein Farnesyltransferase/Geranylgeranyltransferase Type-1 Subunit Alpha	Helps regulate neuromuscular junction development	Unconfirmed
FNTB	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.

Homologs

Paralogs

There are currently no known paralogs to the C10orf71 gene.

Orthologs

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). 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%. 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.

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.

Phylogeny

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.

Evolutionary rate

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

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

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