User:988mprv/sandbox
Gene
[edit]Family with sequence simiilarity 180, is a homo sapien protein that is encoded by the FAM180b gene also known as LOC399888.[1] It's located on the positive DNA strand in Chromosome 11p11.2 (47,586,651 - 47,589,194) and is 1403 nucleotides long. The gene also has 3 exons. [2]
Protein
[edit]Composition
[edit]The isoelectric point of FAM180b is 4.74 and has a molecular weight of 20KDa. [3]The protein lacks any prominent amino acids, but does have an increase in acidity due to the negatively charge KR-ED.[4]
Paralog
[edit]FAM180A is the only paralog to FAM180b. The four different isoforms of FAM180b are listed below. [5]
| Name | Accession number | Length | Amino Acid Length |
|---|---|---|---|
| protein FAM180B isoform 1 | NM_001164379 NP_001157851 | 1403 bp | 183 aa |
| protein FAM180B isoform 2 | NM_001367966 NP_001354895 | 1394 bp | 171 aa |
| protein FAM180B isoform 2 | NM_001367967 NP_001354896 | 1359 bp | 133 aa |
| protein FAM180B isoform 4 | NM_001367968 NP_001354897 | 1465 bp | 121 aa |
Orthologs
[edit]FAM180b is found in Primates, Mammalians, and Fungi. But there are no orthologs in plants.[6]
A table indicating the various orthologs:
| Scientific Name | Common Name | Divergence from Humans (MYA) [7] | NCBI Protein Accession Number | Sequence Length (A.A) | Sequence Similarity |
|---|---|---|---|---|---|
| Saimiri boliviensis boliviensis | Black- Capped Squirrel Monkey | 43 | XP_010332662.1 | 188 | 91% |
| Carlito syrichta | Philippine Tarsier | 69 | XP_008067959.1 | 181 | 88% |
| Otolemur garnettii | Northern Greater Galago | 74 | XP_012668472.0 | 183 | 89% |
| Microcebus murinus | Gray Mouse Lemur | 74 | XP_020142069.1 | 186 | 88% |
| Propithecus coquereli | Coquerel's Sifaka | 74 | XP_012500556.1 | 182 | 90% |
| Peromscus leucopus | White-footed Mouse | 89 | XP_028734672.1 | 179 | 73% |
| Peromyscus maniculatus bairdii | Deer Mouse | 89 | XP_006999134.1 | 179 | 74% |
| Cricetulus griseus | Chinese Hamster | 89 | XP_027247094.1 | 217 | 65% |
| Octodon degus | Common Degu | 89 | XP_004627338.2 | 181 | 76% |
| Cavia porcellus | Guinea Pig | 89 | XP_005008583.3 | 183 | 79% |
| Chinchilla lanigera | Long-tailed Chincilla | 89 | XP_005384010.1 | 183 | 81% |
| Phoca vitulina | Harbor Seal | 94 | XP_032270037.1 | 232 | 58.6% |
| Podarcis muralis | Common Wall Lizard | 318 | XP_028581862.1 | 204 | 44% |
| Pogona vitticeps | Central Bearded Dragon | 318 | XP_020655822.1 | 207 | 43% |
| Python bivattatus | Burmese Python | 318 | XP_007431575.1 | 201 | 42% |
| Geecko japonicus | Schlegel's Japanese Gecko | 318 | XP_015271160.1 | 177 | 40% |
| Cyprinus carpio | Common Carp | 433 | XP_018978565.1 | 160 | 36% |
| Erpetoichthys calabaricus | Reedfish | 433 | XP_028649020.1 | 171 | 40% |
| Anarrhichthys ocellatus | Wolf Eel | 433 | XP_031713372.1 | 163 | 39% |
| Trichoderma gamsii | N/A | 1017 | XP_018664307.1 | 182 | 27% |
Secondary & Tertiary Structures
[edit]FAM180b is composed of 63% alpha-helixes and 54.1% beta sheets. [8]Certain amino acids have an overlap in both, hence the percentage exceeding 100% when totaled. The predicted tertiary structure obtained from Phyre 2 can be seen in Figure 3. on the right. [9]
Regulation
[edit]Epigenetic
[edit]FAM180b has a CpG island associated with it's promoter, and has a CpG count of 150. FAM180b also has relatively low levels of H3K4me1, H3K4me3 and H3K27Ac amongst the cell types, MADD, ARFGAP2, FNBP4, C1QTNF4, AGBL2, and PTPRJ.[10]
Subcellular Localization
[edit]The FAM180b protein is predicted to be located in the extracellular region, with a reliability score of 55.6%. [11] The protein contains a signal peptide, which has a cleavage site between 23 and 24 aa. However, FAM180b does not have any ER retention motif in the C-terminus, nor cleavage sites for mitochondria. [12]
Post-Translational
[edit]FAM180b has two cysteine residues located at amino acid (aa) 10 and 16, that are predicted to be palmitoylation sites. [13]FAM180b also has three Threonine residues positioned in aa 4, 22, and 23, and one Glycine residue located in aa 19 that are all predicted to be phosphorylation sites.[14] O-GlcNacylation sites are present in serine residues located in 35 aa , 171 aa and in Threonine residue located in 36 aa. [15]
Domains & Motifs
[edit]FAM180b has one domain listed as Big-1 (bacterial IG-like domain 1) domain at position 1-8. It has an e-value of 1.6 + 0.3. As for the motif, there is an amidation site at position 78-81. [16]
Gene Expression
[edit]In human fetal tissues, FAM180b is expressed in the lungs and stomach at 10 weeks. It's also highly expressed in the intestine at 11 weeks. Amongst various different RNA sequenced tissues, FAM180b is highly expressed in fat, skin, and thyroid. [17]
Clinical Significance
[edit]Currently there are no clinical significances associated with protein FAM180b [18]
Suggested Readings
[edit]Strausberg, Robert L et al. “Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.” Proceedings of the National Academy of Sciences of the United States of America vol. 99,26 (2002): 16899-903. doi:10.1073/pnas.242603899
References
[edit]- ^ "FAM180B (family with sequence similarity 180 member B)". Atlas of Genetics and Cytogenetics in Oncology and Haematology.
- ^ "Homo sapiens family with sequence similarity 180 member B (FAM180B), transcript variant 1, mRNA". NCBI.
- ^ "Compute pI/Mw". Compute pI/Mw. ExPasy.
- ^ "Compositional Analysis". SAPS. ExPasy.
- ^ "FAM180b Gene". GeneCards The Human Gene Database. Retrieved 29 April 2020.
- ^ "NCBI Protein Blast". National Center for Biotechnology Information.
- ^ Kumar, S.; Stecher, G.; Suleski, M.; Hedges, S.B. "TimeTree: a resource for timelines, timetrees,and divergence times". Molecular Biology and Evolution.
- ^ "CFSSP". CFSSP: Chou & Fasman Secondary Structure Prediction Server.
- ^ "Phyre2". Phyre 2 Protein Fold Recognition Server.
- ^ "UCSC Genome Browser on Human Dec. 2013 (GRCh38/hg38) Assembly". USCS Genome Browser.
- ^ "PSORT II Prediction". PSORT WWW Server.
- ^ "PSORT II Prediction". PSORT WWW Server.
- ^ "CSS- Palm Online Service". The Cuckoo Workshop.
- ^ "GPS Web Server". The Cuckoo workshop.
- ^ "YingoYang 1.2 Server- prediction results". YingoYang 1.2 Server.
- ^ "Motif Scan Results". Motif Scan.
- ^ "Expression". National Center for Biotechnology Information.
- ^ "dsNP". National Library of Medicine: National Center for Biotechnology Information. Retrieved 3 May 2020.