FAM178B

FAM178B
Identifiers
Aliases	FAM178B , family with sequence similarity 178 member B
External IDs	MGI: 3026913 HomoloGene: 87288 GeneCards: FAM178B
Gene location (Human)
Chr.	Chromosome 2 (human)
End	96,986,580 bp
Gene location (Mouse)
Chr.	Chromosome 1 (mouse)
End	36,683,183 bp
Orthologs
	51252
	381337
	ENSG00000168754
	ENSMUSG00000046337
	Q8IXR5
	Q24JP3
	NM_001122646 ; NM_001172667 ; NM_016490
	NM_001126046 ; NM_027957 ; NM_201365 ; NM_001372416 ; NM_001372417 Contents Forms ; Protein structure ; Expression ; DNA Level Regulation ; Protein Level Regulation ; Homology and Evolution ; Interacting Proteins ; References ; Further reading ;
	NP_001116118 ; NP_001166138 ; NP_057574
	NP_001119518 ; NP_082233 ; NP_958753 ; NP_001359345 ; NP_001359346
	Wikidata
View/Edit Human	View/Edit Mouse

Last updated July 01, 2021

FAM178B is a protein coding that is located on the plus strand of chromosome 2.^[5] The locus for the gene is 2q11.2. It is also known by the aliases Family with Sequence Similarity 178, Member B, and HSPC234.^[6] In total there are 24 exons in the gene. FAM178B spans 110,720 base pairs, and contains 827 amino acids.

Forms

There are two isoforms of the gene transcript that exist by alternative splicing, and one gene precursor.^[5]

FAM178B Isoforms from Splice Variation:
Isoform:	Identifier:	Length in Amino Acids:	Mass (Daltons):
1	Q8IXR5-1	827	93,514
2	Q8IXR5-2	119	13,809
3	Q8IXR5-3	679	76,515

SLF2 (FAM178A) is an important paralog of FAM178B. SLF2 is predicted to play a role in the DNA damage response (DDR) pathway by regulating post-replication repair of UV-damaged DNA, and genomic stability maintenance.^[7]

Protein structure

The molecular weight of the protein is 76.5 kilodaltons,^[8] and the isoelectric point is 5.47.The gene has 6 transcript splice variants.^[9] The protein has been phenotypically associated with bipolar disease due to its locus,^[10] as well as body mass index (BMI), and cell adhesion.^[11] A proposed structure for the protein can be found in the images for proposed structures.^[12] The secondary structure for the FAM178B protein is predicted to be primarily alpha helices.^[13] The tertiary structure of the protein may assume a coiled coil structure.^[13]

Expression

FAM178B is most highly expressed in the skeletal muscle and brain tissues^[14].The structure in which it is highly concentrated is in the corpus callosum of the brain.^[14] Additionally, it is of high levels in the trigeminal nerve and spinal cord. Further, there is also high concentrations of the gene found near the heart, testes and olfactory regions.

According to the Allen Brain Atlas,^[15] the olfactory regions, and the hippocampus of the mouse brain showed the greatest expressions of the gene when tested experimentally.

DNA Level Regulation

The proposed promoter region of FAM178B protein is below.^[16] A table of relevant transcription factor binding sites that correspond to the sequence and colors highlighted in the promoter region is also included.

The promoter region of FAM178B is highly conserved across its most related orthologs, and is almost identical across the human, gorilla, chimp, bonobo and gibbon organisms.^[17]

Protein Level Regulation

Below is a table that shows the protein modifications that could be potentially made to FAM178B, and the potential effects of these modifications on the protein itself:.^[18]

Homology and Evolution

An important paralog of the gene is SLF2, which plays a role in the DNA damage response (DDR) pathway by regulating post replication repair of UV-damaged DNA. It also helps maintain genomic stability.^[19] There are 74 known orthologs of the protein, and it can be traced back as far back as crustaceans.^[5] FAM178B is heavily found in both vertebrates and invertebrates. The ortholog space for the protein FAM178B is quite large as it can be traced back 794 millions of years ago (mya) to mollusks with the apple snail, and Pacific Oyster. There are 134 known orthologs of FAM178B. However, the protein is not found in arthropods, or insects, which is interesting because those organisms also existed in that time period meaning that it was conserved across some taxa, but not others. The protein is most readily found in primates, and other non-primate mammals. The protein is also conserved across reptiles, some bony fish, and cartilaginous fish, and birds.

Below is a table illustrating some of the orthologs for FAM178B using BLAST ^[20] and BLAT.^[21]


Scientific Name:	Common Name:	Accession Number from NCBI:	Sequence Length: (Amino Acids)	Date of Divergence from Human Lineage: (millions of years ago)	Percent Identity:	Percent Similarity:
Homo Sapiens	Human	Q8IXR5.2	827	--	--	--
Macaca Mulatta	Macque	XP_014968433	709	28.1	80	83
Chlorocebus Sabaeus	Green Monkey	XP_008006245	724	28.1	91	94
Cebus Capucinus	Capuchin	XP_017379417	808	42.6	88	91
Otolemur Garnettii	Galago	XP_012666502	675	73.0	74	81
Marmota Marmota	Marmot	XP_015355109	692	88.0	74	80
Microtus Ochrogaste r	Vole	XP_026641579	561	88.0	68	75
Felis Catus	Cat	XP_019682636	720	94.0	71	77
Equus Caballus	Horse	XP_023474395	659	94.0	78	84
Panthera Tigris	Tiger	XP_007097881	674	94.0	75	80
Miniopterus Natalensis	Bat	XP_016077151	649	94.0	73	81
Bison Bison	Bison	XP_010828157	664	94.0	65	73
Tursiops Truncatus	Dolphin	JH473473	827	94.0	61	68
Alligator Mississippiensis	Alligator	XP_019343229	802	320.0	34	47
Pogona Vitticeps	Bearded Dragon	XP_020635880	1003	320.0	41	56
Apteryx Rowi	Kiwi	XP_025941058	512	320.0	42	58
Gallus Gallus	Chicken	XP_024998603	547	320.0	37	50
Rhincodon Typus	Whale Shark	XP_020388490	1155	465.0	34	53
Callorhinchus Milii	Australian Ghostshark	XP_007910600	860	465.0	33	50
Crassostrea Gigas	Pacific Oyser	EKC42969	1222	794.0	24	38
Pomacea Canaliculta	Applesnail	PVD30455	1229	794.0	24	45

Timetree^[22] for FAM178B

Interacting Proteins

There are 2 proteins that have high predicted values of interaction with FAM178B: LRSAM 1 and ZNF598.^[23] LRSAM1 ^[24] is also known as leucine rich repeat and sterile alpha motif protein 1. The value for the protein is .29 and the evidence is physical from hybrid pooling approaches. LRSAM1 was previously known as Tsg-associated ligase and is located on the LRSAM1 gene. Mutations have been associated with periphery neuropathy, and sensory disorders. It is highly expressed in the spinal cord, as is FAM178B. There is currently no known structure for the protein. ZNF598 is a zinc finger protein and the value is .13. It plays a key role in ribosome quality control. The predicted structures are below for both proteins.

MENTHA^[23] interacting proteins for FAM178B.

STRING^[25] interacting proteins for FAM178B.

Related Research Articles

Protein ITFG3 also known as family with sequence similarity 234 member A (FAM234A) is a protein that in humans is encoded by the ITFG3 gene. Here, the gene is explored as encoded by mRNA found in Homo sapiens. The FAM234A gene is conserved in mice, rats, chickens, zebrafish, dogs, cows, frogs, chimpanzees, and rhesus monkeys. Orthologs of the gene can be found in at least 220 organisms including the tropical clawed frog, pandas, and Chinese hamsters. The gene is located at 16p13.3 and has a total of 19 exons. The mRNA has a total of 3224 bp and the protein has 552 aa. The molecular mass of the protein produced by this gene is 59660 Da. It is expressed in at least 27 tissue types in humans, with the greatest presence in the duodenum, fat, small intestine, and heart.

KIAA0895 is a protein that in Homo sapiens is encoded by the KIAA0895 gene. The gene encodes a protein commonly known as the KIAA0895 protein. It's aliases include hypothetical protein LOC23366, OTTHUMP00000206979, OTTHUMP00000206980, 9530077C05Rik, and 1110003N12Rik. It is located at 7p14.2.

METTL26, previously designated C16orf13, is a protein-coding gene for Methyltransferase Like 26, also known as JFP2. Though the function of this gene is unknown, various data have revealed that it is expressed at high levels in various cancerous tissues. Underexpression of this gene has also been linked to disease consequences in humans.

Ankyrin repeat domain-containing protein 24 is a protein in humans that is coded for by the ANKRD24 gene. The gene is also known as KIAA1981. The protein's function in humans is currently unknown. ANKRD24 is in the protein family that contains ankyrin-repeat domains.

PRR29 is a protein located on human chromosome 17 that in humans is encoded by the PRR29 gene.

Transmembrane Protein 176B, or TMEM176B is a transmembrane protein that in humans is encoded by the TMEM176B gene. It is thought to play a role in the process of maturation of dendritic cells.

KIAA1211L is a protein that in humans is encoded by the KIAA1211L gene. It is highly expressed in the brain. Furthermore, it is localized to the microtubules and the centrosomes and is subcellularly located in the nucleus. Finally, KIAA1211L is associated with certain mental disorders and various cancers.

Chromosome 21 Open Reading Frame 58 (C21orf58) is a protein that in humans is encoded by the C21orf58 gene.

Zinc finger CCHC-type containing 18 (ZCCHC18) is a protein that in humans is encoded by ZCCHC18 gene. It is also known as Smad-interacting zinc finger protein 2 (SIZN2), para-neoplastic Ma antigen family member 7b (PNMA7B), and LOC644353. Other names such as zinc finger, CCHC domain containing 12 pseudogene 1, P0CG32, ZCC18_HUMAN had been used to describe this protein.

Chromosome 9 open reading frame 25 (C9orf25) is a domain that encodes the FAM219A gene. The terms FAM219A and C9orf25 are aliases and can be used interchangeably. The function of this gene is not yet completely understood.

Chromosome 4 open reading frame 51 (C4orf51) is a protein which in humans is encoded by the C4orf51 gene.

Golgin subfamily A member 8H, also known as GOLGA8H, is a protein that in Homo sapiens is encoded by the GOLGA8H gene. Function of the GOLGA8H involves a process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the Golgi apparatus.

Tubulin epsilon and delta complex 2 (TEDC2), also known as Chromosome 16 open reading frame 59 (C16orf59), is a protein that in humans is encoded by the TEDC2 gene. Its NCBI accession number is NP_079384.2.

Proline-rich protein 16 (PRR16) is a protein coding gene in Homo sapiens. The protein is known by the alias Largen.

Transmembrane protein 155 is a protein that in humans is encoded by the TMEM155 gene. It is located on human chromosome 4, spanning 6,497 bases. It is also referred to as FLJ30834 and LOC132332. This protein is known to be expressed mainly in the brain, placenta, and lymph nodes and is conserved throughout most placental mammals. The function and structure of this protein is still not well understood, but its level of expression has been studied pertaining to various pathologies.

Chromosome 1 Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood.

Leucine rich single-pass membrane protein 2 is a protein that in humans is encoded by the LSMEM2 gene. The LSMEM2 protein is conserved in mammals, aves, and reptiles. In humans, LSMEM2 is found to be highly expressed in the heart and skeletal muscle tissue.

MIF4GD, or MIF4G domain-containing protein, is a protein which in humans is encoded by the MIF4GD gene. It is also known as SLIP1, SLBP -interacting protein 1, AD023, and MIFD. MIF4GD is expressed ubiquitously in humans, and has been found to be involved in activating proteins for histone mRNA translation, alternative splicing and translation of mRNAs, and is a factor in the regulation of cell proliferation.

The FAM214B, also known as protein family with sequence similarity 214, B (FAM214B) is a protein that, in humans, is encoded by the FAM214B gene located on the human chromosome 9. The protein has 538 amino acids. The gene contain 9 exon. There has been studies that there are low expression of this gene in patients with major depression disorder. In most organisms such as mammals, amphibians, reptiles, and birds, there are high levels of gene expression in the bone marrow and blood. For humans in fetal development, FAM214B is mostly expressed in the brains and bone marrow.

FAM120AOS, or family with sequence similarity 120A opposite strand, codes for uncharacterized protein FAM120AOS, which currently has no known function. The gene ontology describes the gene to be protein binding. Overall, it appears that the thyroid and the placenta are the two tissues with the highest expression levels of FAM120AOS across a majority of datasets.

References

1 2 3 GRCh38: Ensembl release 89: ENSG00000168754 - Ensembl, May 2017
1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000046337 - Ensembl, May 2017
↑ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
↑ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
1 2 3 FAM178B - Protein FAM178B - Homo sapiens (Human) - FAM178B gene & protein. (n.d.). Retrieved February 25, 2019, from https://www.uniprot.org/uniprot/Q8IXR5
↑ RecName: Full=Protein FAM178B - Protein - NCBI. (n.d.). Retrieved February 25, 2019, from https://www.ncbi.nlm.nih.gov/protein/Q8IXR5.2
↑ Räschle M, Smeenk G, Hansen RK, Temu T, Oka Y, Hein MY, Nagaraj N, Long DT, Walter JC, Hofmann K, Storchova Z, Cox J, Bekker-Jensen S, Mailand N, Mann M (May 2015). "DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links". Science. 348 (6234): 1253671. doi:10.1126/science.1253671. PMC 5331883 . PMID 25931565.
↑ "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-04-21.
↑ Gene: FAM178B (ENSG00000168754) - Splice variants - Homo sapiens - Ensembl genome browser 95. (n.d.). Retrieved February 25, 2019, from http://useast.ensembl.org/Homo_sapiens/Gene/Splice?db=core;g=ENSG00000168754;r=2:96875882-96986592
↑ Bipolar disorder lithium response (continuous) or schizophrenia - Loci associated with Bipolar disorder lithium response (continuous) or schizophrenia - Homo sapiens - Ensembl genome browser 95. (n.d.). Retrieved February 25, 2019, from http://useast.ensembl.org/Homo_sapiens/Phenotype/Locations?db=core;g=ENSG00000168754;ph=70698;r=2:96875882-96986592
↑ Gene: FAM178B (ENSG00000168754) - Phenotypes - Homo sapiens - Ensembl genome browser 95. (n.d.). Retrieved February 25, 2019, from http://useast.ensembl.org/Homo_sapiens/Gene/Phenotype?db=core;g=ENSG00000168754;r=2:96875882-96986592
↑ SWISS-MODEL Repository | Q8IXR5. (n.d.). Retrieved February 25, 2019, from https://swissmodel.expasy.org/repository/uniprot//Q8IXR5
1 2 "PHYRE2 Protein Fold Recognition Server". www.sbg.bio.ic.ac.uk. Retrieved 2019-04-22.
1 2 "Gene2Promoter". ExPasy.
↑ "Allen Brain Atlas".
↑ "ElDorado Introduction". www.genomatix.de. Retrieved 2019-04-29.
↑ "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-04-29.
↑ "ExPASy: SIB Bioinformatics Resource Portal - Categories". www.expasy.org. Retrieved 2019-04-29.
↑ Räschle, M., Smeenk, G., Hansen, R. K., Temu, T., Oka, Y., Hein, M. Y., … Mann, M. (2015). DNA repair. Proteomics reveals dynamic assembly of repair complexes during bypass of DNA cross-links. Science, 348(6234), 1253671. https://doi.org/10.1126/science.1253671
↑ "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2019-04-21.
↑ "Human BLAT Search". genome.ucsc.edu. Retrieved 2019-04-21.
↑ "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2019-04-29.
1 2 "mentha: the interactome browser". www.mentha.uniroma2.it. Retrieved 2019-04-29.
↑ "LRSAM1 - E3 ubiquitin-protein ligase LRSAM1 - Homo sapiens (Human) - LRSAM1 gene & protein". www.uniprot.org. Retrieved 2019-04-29.
↑ "FAM178B protein (human) - STRING interaction network". string-db.org. Retrieved 2019-04-29.