ITFG3: Difference between revisions

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{{Infobox_gene}}
{{Infobox_gene}}
'''Protein ITFG3''' is a [[protein]] that in humans is encoded by the ''ITFG3'' [[gene]].<ref name="entrez">{{cite web | title = Entrez Gene: ITFG3 integrin alpha FG-GAP repeat containing 3| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=83986| accessdate = }}</ref>
'''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]].<ref name="entrez">{{cite web | title = Entrez Gene: ITFG3 integrin alpha FG-GAP repeat containing 3| url = https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=83986| access-date = }}</ref><ref>{{Cite web|url=https://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=14163|title=FAM234A Symbol Report {{!}} HUGO Gene Nomenclature Committee|website=www.genenames.org|access-date=2018-02-20}}</ref>  Here, the gene is explored as encoded by [[Messenger RNA|mRNA]] found in ''Homo sapiens''.  The FAM234A gene is conserved in mice, rats, chickens, zebrafish, dogs, cows, frogs, chimpanzees, and rhesus monkeys.<ref name="Entrez_gene">{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene?cmd=retrieve&list_uids=83986|title=FAM234A family with sequence similarity 234 member A [Homo sapiens (human)] - Gene - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-02-20}}</ref> [[Orthologs]] of the gene can be found in at least 220 organisms including the tropical clawed frog, pandas, and Chinese hamsters.<ref>{{Cite web|url=https://www.ncbi.nlm.nih.gov/gene/?Term=ortholog_gene_83986[group|title=NCBI GENE Ortholog Search|last=|first=|date=|website=|access-date=}}</ref> The gene is located at [[Chromosome 16 (human)|16]]p13.3 and has a total of 19 exons.  The mRNA has a total of 3224 bp and the protein has 552 aa.<ref>{{Cite web|url=https://www.ncbi.nlm.nih.gov/protein/14042970|title=protein FAM234A [Homo sapiens] - Protein - NCBI|website=www.ncbi.nlm.nih.gov|access-date=2018-02-20}}</ref><ref name="Entrez_gene" />  The molecular mass of the protein produced by this gene is 59660 Da.<ref name=":1">{{Cite web|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=FAM234A|title=FAM234A Gene - GeneCards {{!}} F234A Protein {{!}} F234A Antibody|last=Database|first=GeneCards Human Gene|website=www.genecards.org|access-date=2018-02-20}}</ref> It is expressed in at least 27 tissue types in humans, with the greatest presence in the [[duodenum]], [[fat]], [[small intestine]], and [[heart]].<ref name="Entrez_gene" />
<!-- The PBB_Summary template is automatically maintained by Protein Box Bot.  See Template:PBB_Controls to Stop updates. -->
 
{{PBB_Summary
A “Newfoundland deletion” or a<sup>0</sup>-thalassemia deletion has been found within the second intervening sequence of the FAM234A gene.<ref>{{cite journal | vauthors = Waye JS, Eng B, Hanna M, Hohenadel BA, Nakamura L, Walker L | title = α0-Thalassemia Due to a 90.7 kb Deletion (-/-NFLD) | journal = Hemoglobin | volume = 41 | issue = 3 | pages = 218–219 | date = May 2017 | pmid = 28838269 | doi = 10.1080/03630269.2017.1369987 }}</ref> The gene is associated with multiple [[red blood cell]] phenotypes in [[African Americans]] – though the exact function or effect of the gene was not entirely clear.<ref>{{cite journal | vauthors = Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, Li J, Lu Y, Yanek LR, Keating B, Meng Y, van Rooij FJ, Okada Y, Kubo M, Rasmussen-Torvik L, Keller MF, Lange L, Evans M, Bottinger EP, Linderman MD, Ruderfer DM, Hakonarson H, Papanicolaou G, Zonderman AB, Gottesman O, Thomson C, Ziv E, Singleton AB, Loos RJ, Sleiman PM, Ganesh S, McCarroll S, Becker DM, Wilson JG, Lettre G, Reiner AP | display-authors = 6 | title = Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network | journal = Human Molecular Genetics | volume = 22 | issue = 12 | pages = 2529–38 | date = June 2013 | pmid = 23446634 | pmc = 3658166 | doi = 10.1093/hmg/ddt087 | url = https://www.ncbi.nlm.nih.gov/pubmed/?term=ITFG3 }}</ref>  Review of [[GeneCards|GeneCards’]] current database on the FAM234A gene provided no additional elucidation on the function of the gene.<ref name=":1" />
| section_title =  
 
| summary_text =  
== Gene ==
}}
FAM234A is located on [[Chromosome 16 open reading frame 13|Chromosome 16]] (234,546 - 269, 943). It is 35,398 bases long, contains 11 exons, and is oriented on the plus strand in the 5' to 3' direction. Other aliases include ITFG3, C16orf9, and gs19.
 
There are no known paralogs of FAM234A.
 
The FAM234A gene is conserved in at least 220 organisms, with no evidence for conservation of the gene in single celled organisms. Listed below is a selection of [[Homology (biology)|orthologs]] with the estimated date of divergence from human lineage in million years ago (MYA), the accession number, and the % identity to human FAM234A. This list does not contain all of the known orthologs.
{| class="wikitable"
|+Selection of Organisms with FAM234A Orthologs
!Common Name
!Divergence from Human Lineage (MYA)
!Accession Number
!Identity to Human (%)
|-
|Rhesus Monkey
|28.1
|NP_001253283.1
|95
|-
|White-tufted-ear marmoset
|42.6
|XP_009007067.1
|86
|-
|House mouse
|88
|NP_001344823.1
|86
|-
|Chinese Hamster
|88
|XP_003501607.1
|77
|-
|Upper Galilee mountains blind mole  rat
|88
|XP_008849023.1
|74
|-
|Golden Hamster
|88
|XP_005081607.1
|76
|-
|Giant Panda
|94
|XP_011224429.1
|73
|-
|Horse
|94
|XP_014585783.1
|74
|-
|Beluga Whale
|94
|XP_022450014.1
|73
|-
|Chicken
|320
|XP_414950.2
|45
|-
|Blue Tit
|320
|XP_023792271.1
|43
|-
|Bengalese Finch
|320
|XP_021404267.1
|44
|-
|Central Bearded Dragon
|320
|XP_020667631.1
|43
|-
|Australian saltwater crocodile
|320
|XP_019395600.1
|47
|-
|Tropical Clawed Frog
|353
|NP_001121517.1
|35
|-
|Zebrafish
|432
|XP_001336768.2
|31
|-
|Barramundi Perch
|432
|XP_018520114.1
|34
|-
|Japanese Medaka
|432
|XP_020567870.1
|33
|-
|Elephant Shark
|465
|XP_007906598.1
|37
|-
|Rat
|88
|NP_001009701.1
|72
|}
 
== mRNA ==
There are at least 11 FAM234A [[Protein isoform|isoforms]]. Aside from the longest transcript, the other isoforms differ by truncation, primarily at the 3' end. This results in a wide variation in sequence length between isoforms.


==References==
== Protein ==
[[File:Predicted Secondary Structure of FAM234A.png|thumb|400px|'''Predicted Features of FAM234A Secondary Structure.''' Numbered according to amino acid in the FAM234A protein, areas where there is a predicted alpha-helix are highlighted in yellow.  Areas that are predicted to be beta-strands are highlighted in green.]]
The FAM234A gene encodes a [[serine]] and [[leucine]] rich protein titled the "FAM234A Protein" or ITFG3. The encoded protein is 552 amino acids in length with a predicted molecular weight of 59,660Da and a basal isoelectric point of 5.84.<ref>{{Cite web|url=https://www.phosphosite.org/proteinAction?id=24315&showAllSites=true)|title=ITFG3 (human)|website=www.phosphosite.org|access-date=2018-05-06}}</ref> The FAM234A protein has a notable hydrophobic region from position 49-70 in the amino acid sequence that correlates with one of the two trans-membrane regions found on FAM234A.<ref name=":2">{{Cite web|url=https://www.ebi.ac.uk/Tools/seqstats/saps/|title=SAPS < Sequence Statistics < EMBL-EBI|last=EMBL-EBI|website=www.ebi.ac.uk|language=en|access-date=2018-05-06}}</ref> FAM234A has membrane topology type 3a, indicating multiple trans-membrane regions with it's N-terminus facing the cytosol. The protein is predicted to be located in the [[endoplasmic reticulum]], with portions of it found within the endoplasmic reticulum lumen.<ref name=":2" /> Within the cell, FAM234A has also been localized to the [[ribosome]]s and [[Cell nucleus|nucleus]].<ref>{{Cite web|url=https://www.proteinatlas.org/ENSG00000167930-FAM234A/cell|title=Cell atlas - FAM234A - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2018-05-06}}</ref>
 
== References ==
{{reflist}}
{{reflist}}


==Further reading==
== Further reading ==
{{refbegin | 2}}
{{refbegin | 2}}
{{PBB_Further_reading
* {{cite journal | vauthors = Flint J, Thomas K, Micklem G, Raynham H, Clark K, Doggett NA, King A, Higgs DR | title = The relationship between chromosome structure and function at a human telomeric region | journal = Nature Genetics | volume = 15 | issue = 3 | pages = 252–7 | date = March 1997 | pmid = 9054936 | doi = 10.1038/ng0397-252 }}
| citations =
* {{cite journal | vauthors = Hartley JL, Temple GF, Brasch MA | title = DNA cloning using in vitro site-specific recombination | journal = Genome Research | volume = 10 | issue = 11 | pages = 1788–95 | date = November 2000 | pmid = 11076863 | pmc = 310948 | doi = 10.1101/gr.143000 }}
*{{cite journal   |vauthors=Flint J, Thomas K, Micklem G, etal |title=The relationship between chromosome structure and function at a human telomeric region. |journal=Nat. Genet. |volume=15 |issue= 3 |pages= 252–7 |year= 1997 |pmid= 9054936 |doi= 10.1038/ng0397-252 }}
* {{cite journal | vauthors = Daniels RJ, Peden JF, Lloyd C, Horsley SW, Clark K, Tufarelli C, Kearney L, Buckle VJ, Doggett NA, Flint J, Higgs DR | title = Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16 | journal = Human Molecular Genetics | volume = 10 | issue = 4 | pages = 339–52 | date = February 2001 | pmid = 11157797 | doi = 10.1093/hmg/10.4.339 }}
*{{cite journal |vauthors=Hartley JL, Temple GF, Brasch MA |title=DNA cloning using in vitro site-specific recombination. |journal=Genome Res. |volume=10 |issue= 11 |pages= 1788–95 |year= 2001 |pmid= 11076863 |doi=10.1101/gr.143000 | pmc=310948  }}
* {{cite journal | vauthors = Wiemann S, Arlt D, Huber W, Wellenreuther R, Schleeger S, Mehrle A, Bechtel S, Sauermann M, Korf U, Pepperkok R, Sültmann H, Poustka A | title = From ORFeome to biology: a functional genomics pipeline | journal = Genome Research | volume = 14 | issue = 10B | pages = 2136–44 | date = October 2004 | pmid = 15489336 | pmc = 528930 | doi = 10.1101/gr.2576704 }}
*{{cite journal   |vauthors=Daniels RJ, Peden JF, Lloyd C, etal |title=Sequence, structure and pathology of the fully annotated terminal 2 Mb of the short arm of human chromosome 16. |journal=Hum. Mol. Genet. |volume=10 |issue= 4 |pages= 339–52 |year= 2001 |pmid= 11157797 |doi=10.1093/hmg/10.4.339 }}
* {{cite journal | vauthors = Mehrle A, Rosenfelder H, Schupp I, del Val C, Arlt D, Hahne F, Bechtel S, Simpson J, Hofmann O, Hide W, Glatting KH, Huber W, Pepperkok R, Poustka A, Wiemann S | title = The LIFEdb database in 2006 | journal = Nucleic Acids Research | volume = 34 | issue = Database issue | pages = D415-8 | date = January 2006 | pmid = 16381901 | pmc = 1347501 | doi = 10.1093/nar/gkj139 }}
*{{cite journal   |vauthors=Wiemann S, Weil B, Wellenreuther R, etal |title=Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. |journal=Genome Res. |volume=11 |issue= 3 |pages= 422–35 |year= 2001 |pmid= 11230166 |doi= 10.1101/gr.GR1547R  | pmc=311072 }}
*{{cite journal  |vauthors=Strausberg RL, Feingold EA, Grouse LH, etal |title=Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue= 26 |pages= 16899–903 |year= 2003 |pmid= 12477932 |doi= 10.1073/pnas.242603899  | pmc=139241 }}
*{{cite journal  |vauthors=Ota T, Suzuki Y, Nishikawa T, etal |title=Complete sequencing and characterization of 21,243 full-length human cDNAs. |journal=Nat. Genet. |volume=36 |issue= 1 |pages= 40–5 |year= 2004 |pmid= 14702039 |doi= 10.1038/ng1285 }}
*{{cite journal  |vauthors=Gerhard DS, Wagner L, Feingold EA, etal |title=The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). |journal=Genome Res. |volume=14 |issue= 10B |pages= 2121–7 |year= 2004 |pmid= 15489334 |doi= 10.1101/gr.2596504  | pmc=528928 }}
*{{cite journal  |vauthors=Wiemann S, Arlt D, Huber W, etal |title=From ORFeome to biology: a functional genomics pipeline. |journal=Genome Res. |volume=14 |issue= 10B |pages= 2136–44 |year= 2004 |pmid= 15489336 |doi= 10.1101/gr.2576704 | pmc=528930 }}
*{{cite journal   |vauthors=Mehrle A, Rosenfelder H, Schupp I, etal |title=The LIFEdb database in 2006. |journal=Nucleic Acids Res. |volume=34 |issue= Database issue |pages= D415–8 |year= 2006 |pmid= 16381901 |doi= 10.1093/nar/gkj139 | pmc=1347501 }}
}}
{{refend}}
{{refend}}
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{{gene-16-stub}}

Latest revision as of 06:26, 28 July 2018

VALUE_ERROR (nil)
Identifiers
Aliases
External IDsGeneCards: [1]
Orthologs
SpeciesHumanMouse
Entrez

n/a

n/a

Ensembl

n/a

n/a

UniProt

n/a

n/a

RefSeq (mRNA)

n/a

n/a

RefSeq (protein)

n/a

n/a

Location (UCSC)n/an/a
PubMed searchn/an/a
Wikidata
View/Edit Human

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.[1][2] 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.[3] Orthologs of the gene can be found in at least 220 organisms including the tropical clawed frog, pandas, and Chinese hamsters.[4] 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.[5][3] The molecular mass of the protein produced by this gene is 59660 Da.[6] It is expressed in at least 27 tissue types in humans, with the greatest presence in the duodenum, fat, small intestine, and heart.[3]

A “Newfoundland deletion” or a0-thalassemia deletion has been found within the second intervening sequence of the FAM234A gene.[7] The gene is associated with multiple red blood cell phenotypes in African Americans – though the exact function or effect of the gene was not entirely clear.[8] Review of GeneCards’ current database on the FAM234A gene provided no additional elucidation on the function of the gene.[6]

Gene

FAM234A is located on Chromosome 16 (234,546 - 269, 943). It is 35,398 bases long, contains 11 exons, and is oriented on the plus strand in the 5' to 3' direction. Other aliases include ITFG3, C16orf9, and gs19.

There are no known paralogs of FAM234A.

The FAM234A gene is conserved in at least 220 organisms, with no evidence for conservation of the gene in single celled organisms. Listed below is a selection of orthologs with the estimated date of divergence from human lineage in million years ago (MYA), the accession number, and the % identity to human FAM234A. This list does not contain all of the known orthologs.

Selection of Organisms with FAM234A Orthologs
Common Name Divergence from Human Lineage (MYA) Accession Number Identity to Human (%)
Rhesus Monkey 28.1 NP_001253283.1 95
White-tufted-ear marmoset 42.6 XP_009007067.1 86
House mouse 88 NP_001344823.1 86
Chinese Hamster 88 XP_003501607.1 77
Upper Galilee mountains blind mole rat 88 XP_008849023.1 74
Golden Hamster 88 XP_005081607.1 76
Giant Panda 94 XP_011224429.1 73
Horse 94 XP_014585783.1 74
Beluga Whale 94 XP_022450014.1 73
Chicken 320 XP_414950.2 45
Blue Tit 320 XP_023792271.1 43
Bengalese Finch 320 XP_021404267.1 44
Central Bearded Dragon 320 XP_020667631.1 43
Australian saltwater crocodile 320 XP_019395600.1 47
Tropical Clawed Frog 353 NP_001121517.1 35
Zebrafish 432 XP_001336768.2 31
Barramundi Perch 432 XP_018520114.1 34
Japanese Medaka 432 XP_020567870.1 33
Elephant Shark 465 XP_007906598.1 37
Rat 88 NP_001009701.1 72

mRNA

There are at least 11 FAM234A isoforms. Aside from the longest transcript, the other isoforms differ by truncation, primarily at the 3' end. This results in a wide variation in sequence length between isoforms.

Protein

File:Predicted Secondary Structure of FAM234A.png
Predicted Features of FAM234A Secondary Structure. Numbered according to amino acid in the FAM234A protein, areas where there is a predicted alpha-helix are highlighted in yellow. Areas that are predicted to be beta-strands are highlighted in green.

The FAM234A gene encodes a serine and leucine rich protein titled the "FAM234A Protein" or ITFG3. The encoded protein is 552 amino acids in length with a predicted molecular weight of 59,660Da and a basal isoelectric point of 5.84.[9] The FAM234A protein has a notable hydrophobic region from position 49-70 in the amino acid sequence that correlates with one of the two trans-membrane regions found on FAM234A.[10] FAM234A has membrane topology type 3a, indicating multiple trans-membrane regions with it's N-terminus facing the cytosol. The protein is predicted to be located in the endoplasmic reticulum, with portions of it found within the endoplasmic reticulum lumen.[10] Within the cell, FAM234A has also been localized to the ribosomes and nucleus.[11]

References

  1. ↑ "Entrez Gene: ITFG3 integrin alpha FG-GAP repeat containing 3".
  2. ↑ "FAM234A Symbol Report | HUGO Gene Nomenclature Committee". www.genenames.org. Retrieved 2018-02-20.
  3. ↑ 3.0 3.1 3.2 "FAM234A family with sequence similarity 234 member A [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-02-20.
  4. ↑ "NCBI GENE Ortholog Search".
  5. ↑ "protein FAM234A [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2018-02-20.
  6. ↑ 6.0 6.1 Database, GeneCards Human Gene. "FAM234A Gene - GeneCards | F234A Protein | F234A Antibody". www.genecards.org. Retrieved 2018-02-20.
  7. ↑ Waye JS, Eng B, Hanna M, Hohenadel BA, Nakamura L, Walker L (May 2017). "α0-Thalassemia Due to a 90.7 kb Deletion (-/-NFLD)". Hemoglobin. 41 (3): 218–219. doi:10.1080/03630269.2017.1369987. PMID 28838269.
  8. ↑ Chen Z, Tang H, Qayyum R, Schick UM, Nalls MA, Handsaker R, et al. (June 2013). "Genome-wide association analysis of red blood cell traits in African Americans: the COGENT Network". Human Molecular Genetics. 22 (12): 2529–38. doi:10.1093/hmg/ddt087. PMC 3658166. PMID 23446634.
  9. ↑ "ITFG3 (human)". www.phosphosite.org. Retrieved 2018-05-06.
  10. ↑ 10.0 10.1 EMBL-EBI. "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2018-05-06.
  11. ↑ "Cell atlas - FAM234A - The Human Protein Atlas". www.proteinatlas.org. Retrieved 2018-05-06.

Further reading

Retrieved from "https://www.wikidoc.org/index.php?title=ITFG3&oldid=1541991"