Protein FAM40A is a

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...

that is located on

chromosome 1 Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which ar ...

in humans and is encoded by the ''FAM40A''

gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...

Characteristics and secondary structure

FAM40A has an

isoelectric point The isoelectric point (pI, pH(I), IEP), is the pH at which a molecule carries no net electrical charge or is electrically neutral in the statistical mean. The standard nomenclature to represent the isoelectric point is pH(I). However, pI is also u ...

of 5.92 and a

molecular weight A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioch ...

of 95,575 daltons.pI/MW Tool
/ref> It is predicted to have three

transmembrane domain A transmembrane domain (TMD) is a membrane-spanning protein domain. TMDs generally adopt an alpha helix topological conformation, although some TMDs such as those in porins can adopt a different conformation. Because the interior of the lipid bil ...

s, making it a

transmembrane protein A transmembrane protein (TP) is a type of integral membrane protein that spans the entirety of the cell membrane. Many transmembrane proteins function as gateways to permit the transport of specific substances across the membrane. They frequentl ...

.Transmembrane domain prediction
/ref> FAM40A does not contain a

signal peptide A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16-30 amino acids long) present at the N-ter ...

and is also predicted to bind to DNA, possibly making it a

membrane protein Membrane proteins are common proteins that are part of, or interact with, biological membranes. Membrane proteins fall into several broad categories depending on their location. Integral membrane proteins are a permanent part of a cell membrane ...

in the

nuclear membrane The nuclear envelope, also known as the nuclear membrane, is made up of two lipid bilayer membranes that in eukaryotic cells surround the nucleus, which encloses the genetic material. The nuclear envelope consists of two lipid bilayer membrane ...

.SignalP 3.0 Server
/ref>
/ref> Transmembrane

The

secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, alpha helices and beta ...

of FAM40A is predicted to contain twenty-six

alpha helices The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues ear ...

and two

beta sheets The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a gen ...

.Phyre v. 2.0
/ref> The 5'

untranslated region In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5' side, it is called the 5' UTR (or leader sequence), or if it is foun ...

of FAM40A is predicted to contain one

stem-loop Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded RNA. The structure is also known as a hairpin or hairpin loop. It occurs when two regions of the same strand, usually complementary in nucleotide sequence when ...

and the 3' untranslated region is predicted to contain eight stem-loop structures. Two

miRNA MicroRNA (miRNA) are small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides. Found in plants, animals and some viruses, miRNAs are involved in RNA silencing and post-transcriptional regulation of gene expression. miRN ...

s are predicted to bind to two of the stem-loop structures present in the 3' UTR region.miRBase
/ref>

Homology

FAM40A has no

paralogs Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...

. However, it does have

orthologs Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a spec ...

stretching all the way back to

yeast Yeasts are eukaryotic, single-celled microorganisms classified as members of the fungus kingdom. The first yeast originated hundreds of millions of years ago, and at least 1,500 species are currently recognized. They are estimated to constitut ...

. It has been suggested that FAM40A is a

homolog In biology, homology is similarity due to shared ancestry between a pair of structures or genes in different taxa. A common example of homologous structures is the forelimbs of vertebrates, where the wings of bats and birds, the arms of prima ...

to the yeast gene FAR11, which is involved in the recovery from cell cycle arrest.Yeast Gene FAR11 from Saccharomyces Genome Database
/ref>National Center for Biotechnology Information (NCBI) Protein
/ref> The following table represents a small selection of orthologs found using searches in

BLAST Blast or The Blast may refer to: * Explosion, a rapid increase in volume and release of energy in an extreme manner *Detonation, an exothermic front accelerating through a medium that eventually drives a shock front Film * ''Blast'' (1997 film) ...

NCBI BLAST: Basic Local Alignment Search Tool
/ref> and BLAT.BLAT Search Genome
/ref> This is by no means a comprehensive list, however it does show the vast diversity of species where FAM40A orthologs are found.

Expression

FAM40A is expressed in high levels during the

blastocyst The blastocyst is a structure formed in the early embryonic development of mammals. It possesses an inner cell mass (ICM) also known as the ''embryoblast'' which subsequently forms the embryo, and an outer layer of trophoblast cells called the t ...

eight-cell stage In embryology, cleavage is the division of cells in the early development of the embryo, following fertilization. The zygotes of many species undergo rapid cell cycles with no significant overall growth, producing a cluster of cells the same size ...

, and

fetal A fetus or foetus (; plural fetuses, feti, foetuses, or foeti) is the unborn offspring that develops from an animal embryo. Following embryonic development the fetal stage of development takes place. In human prenatal development, fetal develo ...

stages of development.European Bioinformatics Institute
/ref> FAM40A has also been shown to be expressed in high levels in the

mammary glands A mammary gland is an exocrine gland in humans and other mammals that produces milk to feed young offspring. Mammals get their name from the Latin word ''mamma'', "breast". The mammary glands are arranged in organs such as the breasts in prima ...

brain A brain is an organ that serves as the center of the nervous system in all vertebrate and most invertebrate animals. It is located in the head, usually close to the sensory organs for senses such as vision. It is the most complex organ in a v ...

thymus The thymus is a specialized primary lymphoid organ of the immune system. Within the thymus, thymus cell lymphocytes or ''T cells'' mature. T cells are critical to the adaptive immune system, where the body adapts to specific foreign invaders. ...

mouth In animal anatomy, the mouth, also known as the oral cavity, or in Latin cavum oris, is the opening through which many animals take in food and issue vocal sounds. It is also the cavity lying at the upper end of the alimentary canal, bounded on ...

and the

testes A testicle or testis (plural testes) is the male reproductive gland or gonad in all bilaterians, including humans. It is homologous to the female ovary. The functions of the testes are to produce both sperm and androgens, primarily testoster ...

.EST Profile for FAM40A
/ref> It has also been shown to be expressed in high levels in mammary gland tumors, leukemia cells, and

germ cell tumors Germ cell tumor (GCT) is a neoplasm derived from germ cells. Germ-cell tumors can be cancerous or benign. Germ cells normally occur inside the gonads (ovary and testis). GCTs that originate outside the gonads may be birth defects resulting from er ...

Transcription Regulation

FAM40A is predicted to have a

promoter region In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA), or can have a function in and of i ...

789 base pairs upstream of the start of

transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...

.Genomatix
/ref> The

SOX Sox most often refers to: * Boston Red Sox, an MLB team * Chicago White Sox, an MLB team * An alternate spelling of socks Sox may also refer to: Places * SOX, Sogamoso Airport's IATA airport code, an airport in Colombia Computing and technolo ...

transcription factors In molecular biology, a transcription factor (TF) (or sequence-specific DNA-binding factor) is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The func ...

are predicted to bind to the promoter region of the FAM40A gene, possibly indicating a role in sex determination.

Interactions

FAM40A has been shown to

interact Advocates for Informed Choice, dba interACT or interACT Advocates for Intersex Youth, is a 501(c)(3) nonprofit organization using innovative strategies to advocate for the legal and human rights of children with intersex traits. The organizati ...

with

RP6-213H19.1 Serine/threonine protein kinase MST4, also known as mammalian STE20-like protein kinase 4 (MST-4), is a protein that in humans is encoded by the ''MST4'' gene. Function The product of this gene is a member of the GCK group III family of kinas ...

STRN Striatin is a protein that in humans is encoded by the ''STRN'' gene. Interactions STRN has been shown to interact with: * CTTNBP2NL, * CTTNBP2, * FAM40A, * MOBKL3, * PDCD10, * PPP2CA, * PPP2R1A, * RP6-213H19.1, * STK24, * STK25, * ...

PDCD10 Programmed cell death protein 10 is a protein that in humans is encoded by the ''PDCD10'' gene. Function This gene encodes a protein, originally identified in a premyeloid cell line, with similarity to proteins that participate in apoptosis. Th ...

TRAF3IP3 TRAF3-interacting JNK-activating modulator is a protein that in humans is encoded by the ''TRAF3IP3'' gene. Model organisms Model organisms have been used in the study of TRAF3IP3 function. A conditional knockout mouse line, called ''Traf3ip3tm1 ...

STRN3 Striatin-3 is a protein that in humans is encoded by the ''STRN3'' gene. Interactions STRN3 has been shown to interact with: * CTTNBP2NL, * CTTNBP2, * FAM40A, * MOBKL3, * PDCD10, * PPP2CA, * PPP2R1A, * RP6-213H19.1, * STK24, and * S ...

PPP2R1A Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform is an enzyme that in humans is encoded by the ''PPP2R1A'' gene. In the plant Arabidopsis thaliana a similar enzyme is encoded by the RCN1 gene (At1g25490). Functio ...

MOBKL3 Mps one binder kinase activator-like 3 is an enzyme that in humans is encoded by the ''MOBKL3'' gene. Function This gene was identified based on its similarity with the mouse counterpart. Studies of the mouse counterpart suggest that the expres ...

CTTNBP2NL CTTNBP2 N-terminal-like protein is a protein that in humans is encoded by the ''CTTNBP2NL'' gene. It is a substrate for phosphorylation. Interactions CTTNBP2NL has been shown to interact with: * FAM40A, and * MOBKL3, * PDCD10, * PPP2CA, * ...

STK24 Serine/threonine-protein kinase 24 is an enzyme that in humans is encoded by the ''STK24'' gene located in the chromosome 13, band q32.2. It is also known as Mammalian STE20-like protein kinase 3 (MST-3). The protein is 443 amino acids long and its ...

and

PPP2CA Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform is an enzyme that (in humans) is encoded by the ''PPP2CA'' gene. Function This gene encodes the phosphatase 2A catalytic subunit. Protein phosphatase 2A is one of the fou ...

Characteristics and secondary structure

Homology

Expression

Transcription Regulation

Interactions

References

Further reading