Biology:Fam221b

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Short description: Protein-coding gene in the species Mus musculus


A representation of the 3D structure of the protein myoglobin showing turquoise α-helices.
Generic protein structure example


FAM221B is a protein that in humans is encoded by the FAM221B gene [1] . FAM221B is also known by the alias C9orf128, is expressed at low level, and is defined by 17 GenBank accessions [2] . It is predicted to function in transcription regulation as a transcription factor.

Gene

Locus

FAM221B can be found around the end of the short arm of human chromosome 9.

General position of FAM221B on Human Chromosome 9 (marked by red line)
Gene neighborhood of FAM221B

Expression patterns

FAM221B is expressed at low levels in human and mouse tissues. Expression is highest in germ cell tissues and cells. This differential expression is most pronounced in testes tissue. Compared to Homo sapiens, Mus musculus shows more differential expression of FAM221B in testes tissue [3] [4] [5] [6] . Mature beta cells express FAM221B at higher rates than do fetal beta cells [7] .

mRNA

Alternative splicing and isoforms

FAM221B has a total of 5 transcript variants: the putative sequence, Isoform X1 [8] , Isoform X2 [9] , Isoform X3 [10] , and Isoform X4. Isoform X4 does not exist in humans but is found in various primates.

Exons

Various FAM221B spliced isoforms and their exons as shown in AceView

There are a total of six exons in the putative sequence of FAM221B. However, a total of seven exons exist for FAM221B, as the seventh exon is an alternative exon.

Protein

PHYRE2 prediction for FAM221B secondary structure with alpha-helix regions with strongest evidence for presence circled in red [11]
Predicted phosphorylation sites annotated on FAM221B transcript determined by analysis of various program outputs [12] [13]

General characteristics

The putative sequence for FAM221B is 402 amino acids long and weighs 45.4 kilodaltons. Amino acids expressed at abnormal rates include Histidine, Cysteine, Glutamic acid, and Tyrosine. When compared to typical proteins, FAM221B expresses Histidine at a much higher frequency at 6.0% of protein, Cysteine at a slightly higher frequency at 4.7% of protein, Glutamic acid at a slightly higher frequency at 11.4% of protein, and Tyrosine at a slightly lower frequency at 1.0% of protein [14] . The isoelectric point of FAM221B is 5.264, suggesting FAM221B is an acidic protein at a normal physiological pH (7.4) [14] . There is strong evidence that FAM221B is a protein found within the nucleus [15] .

Compositional features

FAM221B is predicted to have two distinct alpha helices in its secondary structure [16] [17] [18] . Secondary structure predicting programs predict beta sheets but are not as consistent as the two alpha helices.

Post-translational modifications

FAM221B is predicted to have a high number of phosphorylation sites.

Protein interactions

There is evidence that FAM221B interacts with the proteins Autophagy related 13 (KIAA0652), RB1-inducible coiled-coil 1 (RB1CC1), and Ephrin-B3 (EFNB3) [19] . These proteins are predicted to be localized in the nucleus at the same confidence level as FAM221B.

Homology and evolution

FAM221B is conserved in Eutheria. However, both orthologous and paralogous transcripts predating ancestral Boroeutheria can be found.

Paralogs

One paralog exists for FAM221B in humans: FAM221A [20] . FAM221A and FAM221B's ancestral gene is predicted to have diverged in prokarya.

Gene name Accession number Sequence length (aa) Sequence identity to human protein Sequence similarity to human protein Notes
FAM221A NP_954587.2 402 28% 46% Exists in other organisms

Orthologs

Genus and species Common name Divergence from human liineage (MYA) Accession number Sequence length (aa) Sequence identity to human protein Sequence similarity to human protein
Rhinopithecus roxellana Golden Snub-nosed Monkey 29.1 XP_010374448.1 402 92% 95%
Saimiri boliviensis Black-capped Squirrel Monkey 43.1 XP_003943837.1 402 92% 93%
Tsuga chinensis Chinese Tree Shrew 85.9 XP_006143215.1 518 78% 88%
Cavia porcellus Guinea Pig 90.9 XP_003470749.1 415 72% 83%
Odobenus rosmarus divergens Pacific Walrus 97.5 XP_004392324.1 398 72% 81%
Orcinus orca Killer Whale 97.5 XP_004271469.1 410 70% 78%
Felis catus Feral Cat 97.5 XP_006939339.1 429 68% 75%
Loxodonta africana African Bush Elephant 105 XP_003407335.1 414 66% 78%
Ornithorhynchus anatinus Platypus 179.2 XP_007656406.1 262 65% 75%
Anolis carolinensis Carolina Anole 320.5 XP_008122390.1 550 63% 69%
Thamnophis sirtalis Common Garter Snake 320.5 XP_013924342.1 411 62% 74%
Lepisosteus oculatus Alligator Gar 429.6 XP_015222126.1 272 62% 74%
Callorhinchus milii Australian Ghostshark 482.9 XP_007895354.1 326 58% 76%
Strongylocentrotus purpuratus Sea Urchin 747.8 XP_781628.1 409 57% 73%
Crassostrea gigas Pacific Oyster 847 EKC20817.1 420 56% 70%
Clonorchis sinensis Chinese Liver Fluke 847 GAA48218.1 359 42% 55%
Nematostella vectensis Startlet Sea Anemone 936 XP_001628705.1 244 42% 57%

Homologous domains

There are three conserved domains within FAM221B: DUF4475 super family [21] , PRCC super family [22] , and Caprin-1_C [23] . DUF4475 is the most conserved domain of the three.

Clinical significance

FAM221B is linked to mutations in the RNA component of RNase MRP, which causes pleiotropic human disease cartilage–hair hypoplasia. Also, as patients with acute lymphoblastic leukemia often carry genetic alterations in the short arm of human chromosome 9, FAM221B has two consistent non-synonymous amino acid variations associated with the disease. In acute lymphoblastic leukemia patients, Histidine is substituted for an Arginine at position 345, and a Leucine is substituted for a Phenylalanine at position 277 of the protein.

References

  1. "FAM221B Gene - GeneCards". https://www.genecards.org/cgi-bin/carddisp.pl?gene=FAM221B. 
  2. "AceView entry on FAM221B". https://www.ncbi.nlm.nih.gov/ieb/research/acembly/av.cgi?db=human&c=mrna&q=C9orf128.c%20Aug10. 
  3. "GEO GDS 3113 entry on FAM221B in Homo sapiens". https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS3113. 
  4. "GEO GDS 3142 entry on FAM221B in Mus musculus". https://www.ncbi.nlm.nih.gov/sites/GDSbrowser?acc=GDS3142. 
  5. "BioGPS entry on FAM221B in Homo sapiens". http://biogps.org/#goto=genereport&id=392307. 
  6. "BioGPS entry on FAM221B in Mus musculus". http://biogps.org/#goto=genereport&id=242408. 
  7. "Markers for mature beta-cells and methods of using the same". http://www.patentsencyclopedia.com/app/20140329704. 
  8. "FAM221B Homo sapiens Isoform X1". https://www.ncbi.nlm.nih.gov/protein/XP_005251513.2. 
  9. "FAM221B Homo sapiens Isoform X2". https://www.ncbi.nlm.nih.gov/protein/XP_011516174.1. 
  10. "FAM221B Homo sapiens Isoform X3". https://www.ncbi.nlm.nih.gov/protein/XP_006716831.1. 
  11. "PHYRE2 secondary structure prediction for FAM221B". http://www.sbg.bio.ic.ac.uk/phyre2/phyre2_output/1682b17b2dd539de/summary.html. 
  12. "MyHits motif scan for post-translational modifications". http://myhits.isb-sib.ch/cgi-bin/motif_scan. 
  13. "NetPhos 2.0 phosphorylation site predictor". http://www.cbs.dtu.dk/cgi-bin/webface2.fcgi?jobid=57204735000027F8A5BCEF30&wait=20. 
  14. 14.0 14.1 "General protein characteristics from SDSC Biology WorkBench SAPS tool". http://seqtool.sdsc.edu/CGI/BW.cgi#!. 
  15. "PSORT II predictions on FAM221B". http://psort.hgc.jp/form2.html. 
  16. "LOMETS prediction for FAM221B". http://zhanglab.ccmb.med.umich.edu/LOMETS/output/S77068. 
  17. "MUSTER prediction for FAM221B". http://zhanglab.ccmb.med.umich.edu/MUSTER/output/S31524. 
  18. "SWISS-model prediction and constructor for FAM221B". http://swissmodel.expasy.org/interactive/k2msAF/models/. 
  19. "BioGrid summary for protein interactions for FAM221B". http://thebiogrid.org/134170/summary/homo-sapiens/fam221b.html. 
  20. "FAM221A Gene - GeneCards". https://www.genecards.org/cgi-bin/carddisp.pl?gene=FAM221A. 
  21. "NCBI entry on DUF 4475 super family". http://www.ncbi.nlm.nih.giv/Structure/cdd/cddsrv.cgi?uid=258890. 
  22. "NCBI entry on PRCC super family". http://www.ncbi.nlm.nih.giv/Structure/cdd/cddsrv.cgi?uid=255852. 
  23. "NCBI entry on Caprin-1_C". http://www.ncbi.nlm.nih.giv/Structure/cdd/cddsrv.cgi?uid=256956. 

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