FAM107B

FAM107B
Identifiers
Aliases	FAM107B , C10orf45, family with sequence similarity 107 member B, HITS
External IDs	MGI: 1913790 HomoloGene: 75316 GeneCards: FAM107B
Gene location (Human) Chr. Chromosome 10 (human) [1] Band 10p13 Start 14,518,557 bp [1] End 14,774,897 bp [1]
Gene location (Mouse) Chr. Chromosome 2 (mouse) [2] Band 2|2 A1 Start 3,571,525 bp [2] End 3,783,179 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in corpus callosum inferior ganglion of vagus nerve renal medulla bone marrow trachea medulla oblongata pancreatic ductal cell bone marrow cells external globus pallidus subthalamic nucleus Top expressed in retinal pigment epithelium ciliary body secondary oocyte lacrimal gland thymus spermatocyte iris conjunctival fornix spleen epithelium of stomach More reference expression data BioGPS n/a
Orthologs Species Human Mouse Entrez 83641 66540 Ensembl ENSG00000065809 ENSMUSG00000026655 UniProt Q9H098 Q3TGF2 RefSeq (mRNA) NM_001282695 NM_001282696 NM_001282697 NM_001282698 NM_001282699 NM_001282700 NM_001282701 NM_001282702 NM_001282703 NM_031453 NM_001320735 NM_001320736 NM_001320737 NM_001320738 NM_001320739 NM_001320740 NM_001320741 NM_025626 RefSeq (protein) NP_001269624 NP_001269625 NP_001269626 NP_001269627 NP_001269628 NP_001269629 NP_001269630 NP_001269631 NP_001269632 NP_001307664 NP_001307665 NP_001307666 NP_001307667 NP_001307668 NP_001307669 NP_001307670 NP_113641 NP_079902 Location (UCSC) Chr 10: 14.52 – 14.77 Mb Chr 2: 3.57 – 3.78 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

FAM107B is a gene found in humans. It is located on the minus strand of chromosome 10, p13, which is on the short arm of the chromosome. It has other alias names, such as C10orf45, FLJ45505, MGC11034 and MGC90261. The gene contains a conserved domain, DUF1151, which is a family that consists of several eukaryotic proteins of unknown function. FAM107B is expressed in most tissues in the human body without there being a high frequency in any one tissue. It is found in all stages of human development.

Gene

The mRNA for FAM107B is 3785 base pairs long and contains five exons. The protein for FAM107B is known as LOC83641. It is 306 amino acids long. According to AceView, there are 27 spliced variants with 2 unspliced variants and 27 mRNAs of FAM107B. Of these variants and mRNAs, only 23 spliced and unspliced mRNAs are known to encode proteins of quality. Additionally, there appear to be 17 different isoforms. FAM107B is not a signal peptide, but is thought to be a protein that is exported to the mitochondria. It has the following genes located in its gene neighborhood: FRMD4A (FERM domain containing 4A); LOC100289125 (hypothetical protein LOC100289125); RPSAP7 (ribosomal protein SA pseudogene 7 in Homo sapiens); CDNF (cerebral dopamine neurotrophic factor; HSPA14.

FAM107B has one paralog, FAM107A, and many orthologs in organisms including primates, dogs, cows, mice, and chickens. With these orthologs, there is a high degree of conservation.

Structure

Two structures have a high similarity to that of FAM107B: that of a human septin trimer in Homo sapiens and that of the 3rd HMG-box of mouse UBF1. The septin trimer is that of a Ras-like GTPase superfamily whose members are known to regulate cytoskeletal reorganization, gene expression, vesicle trafficking, nucleocytoplasmic transport, and microtubule organization. The 3rd HMG-box of Mouse Ubf is part of the HMG-box superfamily whose members bind to DNA to bend or distort it where it can cause looping of linear DNA, create four-way DNA junctions, and DNA bulges. Members of this family also include mitochondrial transcription factors that bind at four-way DNA junctions.

Interacting proteins

Proteins exist that interact with the FAM107B protein:

• autophagy proteins that are involved in the transport from the cytoplasm to the vacuole, and specifically Cvt vesicle^{[ clarification needed ]} formation;
• the probable protein kinase, which is a heat shock-like protein as well as an antigen;
• the kinesin-related protein which is a biliary glycoprotein isoantigen;
• the hypothetical protein HP0231, which is a somatostatin receptor, as well as the ISWI complex protein 2, which is a mitochondrial reverse transcriptose-like protein;
• the CG7077-PA open reading frame protein, which is known for the Alu repetitive sequence.

Model organisms

Fam107b knockout mouse phenotype

Characteristic	Phenotype
Homozygote viability	Normal
Homozygous Fertility	Normal
Body weight	Normal
Anxiety	Normal
Neurological assessment	Normal
Grip strength	Normal
Hot plate	Normal
Dysmorphology	Normal
Indirect calorimetry	Normal
Glucose tolerance test	Normal
Auditory brainstem response	Abnormal
DEXA	Normal
Radiography	Normal
Body temperature	Normal
Eye morphology	Normal
Clinical chemistry	Normal
Plasma immunoglobulins	Normal
Haematology	Normal
Peripheral blood lymphocytes	Normal
Micronucleus test	Normal
Heart weight	Normal
Skin Histopathology	Normal
Brain histopathology	Normal
Eye Histopathology	Normal
MicroCT & Quantitative Faxitron	Abnormal
Salmonella infection	Normal [5]
Citrobacter infection	Normal [6]
All tests and analysis from [7] [8]

Model organisms have been used in the study of FAM107B function. A conditional knockout mouse line, called Fam107b^{tm1a(KOMP)Wtsi [9] [10]} was generated as part of the International Knockout Mouse Consortium program — a high-throughput mutagenesis project to generate and distribute animal models of disease to interested scientists. ^{[11] [12] [13]}

Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion. ^{[7] [14]} Twenty six tests were carried out on mutant mice and two significant abnormalities were observed: homozygous animals had abnormal brainstem auditory evoked potential and increased trabecular bone thickness. ^[7]

References

1. GRCh38: Ensembl release 89: ENSG00000065809 - Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000026655 - Ensembl, May 2017
3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
5. "Salmonella infection data for Fam107b". Wellcome Trust Sanger Institute.
6. "Citrobacter infection data for Fam107b". Wellcome Trust Sanger Institute.
7. Gerdin AK (2010). "The Sanger Mouse Genetics Programme: High throughput characterisation of knockout mice". Acta Ophthalmologica. 88: 925–7. doi:10.1111/j.1755-3768.2010.4142.x. S2CID   85911512.
8. Mouse Resources Portal, Wellcome Trust Sanger Institute.
9. "International Knockout Mouse Consortium".
10. "Mouse Genome Informatics".
11. Skarnes, W. C.; Rosen, B.; West, A. P.; Koutsourakis, M.; Bushell, W.; Iyer, V.; Mujica, A. O.; Thomas, M.; Harrow, J.; Cox, T.; Jackson, D.; Severin, J.; Biggs, P.; Fu, J.; Nefedov, M.; De Jong, P. J.; Stewart, A. F.; Bradley, A. (2011). "A conditional knockout resource for the genome-wide study of mouse gene function". Nature. 474 (7351): 337–342. doi:10.1038/nature10163. PMC   3572410 . PMID   21677750.
12. Dolgin E (2011). "Mouse library set to be knockout". Nature. 474 (7351): 262–3. doi: 10.1038/474262a . PMID   21677718.
13. Collins FS, Rossant J, Wurst W (2007). "A Mouse for All Reasons". Cell. 128 (1): 9–13. doi: 10.1016/j.cell.2006.12.018 . PMID   17218247. S2CID   18872015.
14. van der Weyden L, White JK, Adams DJ, Logan DW (2011). "The mouse genetics toolkit: revealing function and mechanism". Genome Biol. 12 (6): 224. doi: 10.1186/gb-2011-12-6-224 . PMC   3218837 . PMID   21722353.

Further reading

1. AceView. NCBI.
2. Pfam. Wellcome Trust Sanger Institute. ^[ permanent dead link ]
3. De Vree, Paula. Application of molecular cytogenetic techniques to clarify apparently balanced complex chromosomal rearrangements in to patients with an abnormal phenotype: case report. Molecular Cytogenetics 2009, 2:15. BioMed Central Ltd.
4. The GeneCards Human Gene Database: Copyright © 1996-2009, Weizmann Institute of Science. All Rights Reserved.
5. Related Structures at NCBI.
6. Sigma Aldrich. FAM107B.
7. Database of Interacting Proteins.
8. Sigma Aldrich.
9. Conserved Domains at NCBI.
10. Marchler-Bauer A et al. (2009), "CDD: specific functional annotation with the Conserved Domain Database.", Nucleic Acids Res.37(D)205-10. Conserved Domains at NCBI.