FAM40A
Encyclopedia
Protein FAM40A is a protein
that is located on chromosome 1 in humans and is encoded by the FAM40A gene
.
of 5.92 and a molecular weight of 95,575 daltons
. It is predicted to have three transmembrane domains, making it a transmembrane protein
. FAM40A does not contain a signal peptide
and is also predicted to bind to DNA
, possibly making it a membrane protein
in the nuclear membrane.
The secondary structure
of FAM40A is predicted to contain twenty-six alpha helices and two beta sheets. The 5' untranslated region of FAM40A is predicted to contain one stem-loop
and the 3' untranslated region is predicted to contain eight stem-loop structures. Two miRNA
s are predicted to bind to two of the stem-loop structures present in the 3' UTR region.
. It has been suggested that FAM40A is a homolog to the yeast gene FAR11, which is involved in the recovery from cell cycle arrest.
The following table represents a small selection of orthologs found using searches in BLAST
and BLAT
. This is by no means a comprehensive list, however it does show the vast diversity of species where FAM40A orthologs are found.
, eight-cell stage, and fetal stages of development. FAM40A has also been shown to be expressed in high levels in the mammary glands, brain
, thymus
, mouth
and the testes. It has also been shown to be expressed in high levels in mammary gland tumors, leukemia cells, and germ cell tumors.
. The SOX
transcription factors are predicted to bind to the promoter region of the FAM40A gene, possibly indicating a role in sex determination.
with RP6-213H19.1
, STRN
, PDCD10
, TRAF3IP3
, STRN3
, PPP2R1A
, MOBKL3
, CTTNBP2NL
, STK24
and PPP2CA
.
Protein
Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...
that is located on chromosome 1 in humans and is encoded by the FAM40A gene
Gene
A gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
.
Characteristics and secondary structure
FAM40A has an isoelectric pointIsoelectric point
The isoelectric point , sometimes abbreviated to IEP, is the pH at which a particular molecule or surface carries no net electrical charge....
of 5.92 and a molecular weight of 95,575 daltons
Daltons
Daltons Weekly is a newspaper published in England. It is published every Thursday.Established during the late 1860s by Herbert Dalton, Daltons Weekly was initially a single broadsheet listing 'Accommodation for Gentleman' in the then fashionable middle class suburbs around Vauxhall in South London...
. It is predicted to have three transmembrane domains, making it a transmembrane protein
Transmembrane protein
A transmembrane protein is a protein that goes from one side of a membrane through to the other side of the membrane. Many TPs function as gateways or "loading docks" to deny or permit the transport of specific substances across the biological membrane, to get into the cell, or out of the cell as...
. FAM40A does not contain a signal peptide
Signal peptide
A signal peptide is a short peptide chain that directs the transport of a protein.Signal peptides may also be called targeting signals, signal sequences, transit peptides, or localization signals....
and is also predicted to bind to DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, possibly making it a membrane protein
Membrane protein
A membrane protein is a protein molecule that is attached to, or associated with the membrane of a cell or an organelle. More than half of all proteins interact with membranes.-Function:...
in the nuclear membrane.
The secondary structure
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
of FAM40A is predicted to contain twenty-six alpha helices and two beta sheets. The 5' untranslated region of FAM40A is predicted to contain one stem-loop
Stem-loop
Stem-loop intramolecular base pairing is a pattern that can occur in single-stranded DNA or, more commonly, in 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 read in opposite directions,...
and the 3' untranslated region is predicted to contain eight stem-loop structures. Two miRNA
Mirna
Mirna may refer to:geographical entities* Mirna , a river in Istria, Croatia* Mirna , a river in Slovenia, tributary of the river Sava* Mirna , a settlement in the municipality of Mirna in Southeastern Sloveniapeople...
s are predicted to bind to two of the stem-loop structures present in the 3' UTR region.
Homology
FAM40A has no paralogs. However, it does have orthologs stretching all the way back to yeastYeast
Yeasts are eukaryotic micro-organisms classified in the kingdom Fungi, with 1,500 species currently described estimated to be only 1% of all fungal species. Most reproduce asexually by mitosis, and many do so by an asymmetric division process called budding...
. It has been suggested that FAM40A is a homolog to the yeast gene FAR11, which is involved in the recovery from cell cycle arrest.
The following table represents a small selection of orthologs found using searches in BLAST
BLAST
In bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
and BLAT
BLAT (bioinformatics)
Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments.BLAT is a software program developed by Jim Kent at UCSC to identify similarities between DNA sequences and protein sequences. It was developed to assist in the annotation of the human genome sequence...
. This is by no means a comprehensive list, however it does show the vast diversity of species where FAM40A orthologs are found.
| Scientific Name | Common Name | Accession number (from NCBI ) | Sequence Length | Percent Identity | Percent Similarity |
|---|---|---|---|---|---|
| Homo sapiens | Human | NP_149079 | 837 | - | - |
| Pongo abelii | Sumatran orangutan | XP_002810520 | 837 | 99.6% | 100% |
| Sus scrofa | Pig | XP_003125904 | 837 | 98.8% | 100% |
| Equus caballus | Horse | XP_001493762 | 837 | 98.8% | 100% |
| Mus musculus | Mouse | NP_705791 | 837 | 98% | 100% |
| Rattus norvegicus | Rat | XP_001068288 | 837 | 97.8% | 100% |
| Monodelphis domestica | Gray short-tailed opossum | XP_001372588 | 843 | 95.4% | 100% |
| Danio rerio Danio rerio The zebrafish, Danio rerio, is a tropical freshwater fish belonging to the minnow family of order Cypriniformes. It is a popular aquarium fish, frequently sold under the trade name zebra danio, and is an important vertebrate model organism in scientific research.-Taxonomy:The zebrafish are... |
Zebra fish | XP_001918929 | 813 | 83.4% | 98% |
| Canis lupus familiaris | Dog | From BLAT | 812 | 96.1% | 100% |
| Ailuropoda melanoleuca | Panda | From BLAT | 823 | 96.2$ | 100% |
| Oryzias latipes Oryzias latipes Oryzias latipes, also known as Medaka and Japanese killifish, is a member of genus Oryzias , the only genus in the subfamily Oryziinae. This rather small... |
Medaka | From BLAT | 751 | 78.4% | 96% |
| Xenopus (Silurana) tropicalis | Western clawed frog | NP_001027483 | 819 | 86.4% | 96% |
| Aedes aegypti Aedes aegypti The yellow fever mosquito, Aedes aegypti is a mosquito that can spread the dengue fever, Chikungunya and yellow fever viruses, and other diseases. The mosquito can be recognized by white markings on legs and a marking in the form of a lyre on the thorax... |
Yellow-fever mosquito | XP_001658692 | 829 | 51.2% | 97% |
| Tribolium castaneum | Red flour beetle | XP_001815164 | 817 | 57.4% | 97% |
| Hydra magnipapillata | Hydra hydrozoan | XP_002164866 | 830 | 44% | 97% |
| Ciona intestinalis Ciona intestinalis Ciona intestinalis is a urochordata , a tunicate widely distributed in Northern European waters. As an invasive species, it has also spread to other parts of the world.... |
Sea squirt | XP_002130558 | 867 | 46.4% | 97% |
| Pediculus humanus corporis | Human lice | XP_002425964 | 808 | 52.7% | 97% |
| Nasonia vitripennis | Jewel wasp | XP_001603859 | 802 | 52.7% | 97% |
| Drosophila erecta | Fruit fly | XP_001971743 | 882 | 45.2% | 97% |
| Saccharomyces cerevisiae Saccharomyces cerevisiae Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes... |
Bakers yeast | NP_014272 | 953 | 18.9% | 97% |
Expression
FAM40A is expressed in high levels during the blastocystBlastocyst
The blastocyst is a structure formed in the early embryogenesis of mammals, after the formation of the morula. It is a specifically mammalian example of a blastula. It possesses an inner cell mass , or embryoblast, which subsequently forms the embryo, and an outer layer of cells, or trophoblast,...
, eight-cell stage, and fetal stages of development. FAM40A has also been shown to be expressed in high levels in the mammary glands, brain
Brain
The brain is the center of the nervous system in all vertebrate and most invertebrate animals—only a few primitive invertebrates such as sponges, jellyfish, sea squirts and starfishes do not have one. It is located in the head, usually close to primary sensory apparatus such as vision, hearing,...
, thymus
Thymus
The thymus is a specialized organ of the immune system. The thymus produces and "educates" T-lymphocytes , which are critical cells of the adaptive immune system....
, mouth
Mouth
The mouth is the first portion of the alimentary canal that receives food andsaliva. The oral mucosa is the mucous membrane epithelium lining the inside of the mouth....
and the testes. It has also been shown to be expressed in high levels in mammary gland tumors, leukemia cells, and germ cell tumors.
Transcription Regulation
FAM40A is predicted to have a promoter region 789 base pairs upstream of the start of transcriptionTranscription (genetics)
Transcription is the process of creating a complementary RNA copy of a sequence of DNA. Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language that can be converted back and forth from DNA to RNA by the action of the correct enzymes...
. The SOX
SoX
Sound eXchange, abbreviated SoX, is a free cross-platform digital audio editor, licensed under the GNU General Public License, and distributed by Chris Bagwell through SourceForge.net...
transcription factors 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 interactProtein-protein interaction
Protein–protein interactions occur when two or more proteins bind together, often to carry out their biological function. Many of the most important molecular processes in the cell such as DNA replication are carried out by large molecular machines that are built from a large number of protein...
with RP6-213H19.1
RP6-213H19.1
Serine/threonine protein kinase MST4, also known as RP6-213H19.1, is a human gene.-Interactions:RP6-213H19.1 has been shown to interact with STRN, PDCD10, CTTNBP2, STRN3, MOBKL3, CTTNBP2NL and FAM40A.-Further reading:...
, STRN
STRN
Striatin is a protein that in humans is encoded by the STRN gene.-Interactions:STRN has been shown to interact with STK25, PDCD10, CTTNBP2, TRAF3IP3, STRN3, MOBKL3, STK24, PPP2CA, RP6-213H19.1, PPP2R1A, CTTNBP2NL and FAM40A.-Further reading:...
, PDCD10
PDCD10
Programmed cell death protein 10 is a protein that in humans is encoded by the PDCD10 gene.-Interactions:PDCD10 has been shown to interact with RP6-213H19.1, STK25, STRN, STRN3, MOBKL3, CTTNBP2NL, STK24 and FAM40A.-Further reading:...
, TRAF3IP3
TRAF3IP3
TRAF3-interacting JNK-activating modulator is a protein that in humans is encoded by the TRAF3IP3 gene.-Interactions:TRAF3IP3 has been shown to interact with STRN, MOBKL3, STK24 and FAM40A.-Further reading:...
, STRN3
STRN3
Striatin-3 is a protein that in humans is encoded by the STRN3 gene.-Interactions:STRN3 has been shown to interact with PDCD10, CTTNBP2, MOBKL3, STK24, PPP2CA, RP6-213H19.1, STRN, PPP2R1A, CTTNBP2NL and FAM40A.-Further reading:...
, PPP2R1A
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 .- Function :...
, MOBKL3
MOBKL3
Mps one binder kinase activator-like 3 is an enzyme that in humans is encoded by the MOBKL3 gene.-Interactions:MOBKL3 has been shown to interact with STK25, PDCD10, CTTNBP2, TRAF3IP3, STRN3, STK24, PPP2CA, RP6-213H19.1, STRN, CTTNBP2NL and FAM40A....
, CTTNBP2NL
CTTNBP2NL
CTTNBP2 N-terminal-like protein is a protein that in humans is encoded by the CTTNBP2NL gene.-Interactions:CTTNBP2NL has been shown to interact with RP6-213H19.1, STRN, PDCD10, STRN3, PPP2R1A, MOBKL3, STK24, FAM40A and PPP2CA.-Further reading:...
, STK24
STK24
Serine/threonine-protein kinase 24 is an enzyme that in humans is encoded by the STK24 gene.-Interactions:STK24 has been shown to interact with PDCD10, TRAF3IP3, STRN3, MOBKL3, STRN, SLMAP, PPP2R1A, CTTNBP2NL, FAM40A and STRN4.-Further reading:...
and PPP2CA
PPP2CA
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform is an enzyme that in humans is encoded by the PPP2CA gene.-Interactions:...
.