QRICH1: Difference between revisions
Content deleted Content added
Removing links to deleted file File:CARD Domain.jpg |
Theopolisme (talk | contribs) m general cleanup |
||
| Line 24: | Line 24: | ||
The QRICH1 gene is 64,363 [[base pairs]] long, encoding an [[mRNA]] transcript that is 3331 bp in length.<ref name="Gene">{{cite web | title = Gene: 54780| url = http://www.ncbi.nlm.nih.gov/gene/54870|accessdate = 2-February-2011}}</ref> QRICH1 is located on chromosome 3p21.31 and contains 11 [[exons]].<ref name="GenBank">{{cite web | title = GenBank: Homo Sapiens glutamine-rich 1 (QRICH1), transcript variant 1, mRNA| url = http://www.ncbi.nlm.nih.gov/nuccore/38570096?report=genbank|accessdate = 29-January-2011}}</ref> The genomic sequence begins at base pair 49,057,531 and ends at base pair 49,141,201.<ref name="Gene"/> |
The QRICH1 gene is 64,363 [[base pairs]] long, encoding an [[mRNA]] transcript that is 3331 bp in length.<ref name="Gene">{{cite web | title = Gene: 54780| url = http://www.ncbi.nlm.nih.gov/gene/54870|accessdate = 2-February-2011}}</ref> QRICH1 is located on chromosome 3p21.31 and contains 11 [[exons]].<ref name="GenBank">{{cite web | title = GenBank: Homo Sapiens glutamine-rich 1 (QRICH1), transcript variant 1, mRNA| url = http://www.ncbi.nlm.nih.gov/nuccore/38570096?report=genbank|accessdate = 29-January-2011}}</ref> The genomic sequence begins at base pair 49,057,531 and ends at base pair 49,141,201.<ref name="Gene"/> |
||
[[File:QRICH1 Gene Neighborhood.jpg|thumb|The gene neighborhood of QRICH1 constructed by NCBI Gene.<ref name= |
[[File:QRICH1 Gene Neighborhood.jpg|thumb|The gene neighborhood of QRICH1 constructed by NCBI Gene.<ref name=autogenerated1>{{cite web | title = NCBI Gene: 54870| url =http://www.ncbi.nlm.nih.gov/gene/54870| accessdate = 2-February-2011 }}</ref>]] |
||
==Function== |
==Function== |
||
| Line 33: | Line 33: | ||
The glutamine-rich protein 1 is 776 [[amino acids]] in length. [[Glutamine]] residues are abundant, comprising 109 of the amino acids or 14% of the protein.<ref name ="SAPS">{{cite web | title = SAPS: Biology Workbench| url = http://workbench.sdsc.edu/|accessdate = 19-April-2011}}</ref> The protein contains three distinct domains. The first, a CARD domain, is a member of the [[death fold]] superfamily and is involved in apoptosis signaling pathways, immune signaling, inflammation, and host-defense mechanisms.<ref name="UniprotKB"/> The second domain is a glutamine-rich domain which comprises a majority of the protein and is highly conserved among orthologs.<ref name="UniprotKB"/> The final domain is a Domain of Unknown Function (DUF3504) found near the end of the protein sequence.<ref name="UniprotKB"/> All three of these domains are well conserved throughout strict orthologs. |
The glutamine-rich protein 1 is 776 [[amino acids]] in length. [[Glutamine]] residues are abundant, comprising 109 of the amino acids or 14% of the protein.<ref name ="SAPS">{{cite web | title = SAPS: Biology Workbench| url = http://workbench.sdsc.edu/|accessdate = 19-April-2011}}</ref> The protein contains three distinct domains. The first, a CARD domain, is a member of the [[death fold]] superfamily and is involved in apoptosis signaling pathways, immune signaling, inflammation, and host-defense mechanisms.<ref name="UniprotKB"/> The second domain is a glutamine-rich domain which comprises a majority of the protein and is highly conserved among orthologs.<ref name="UniprotKB"/> The final domain is a Domain of Unknown Function (DUF3504) found near the end of the protein sequence.<ref name="UniprotKB"/> All three of these domains are well conserved throughout strict orthologs. |
||
<!-- Deleted image removed: [[File:CARD Domain.jpg|thumb| CARD Domains feature an arrangement of six to seven antiparallel alpha helices with a hydrophobic core and an outer face composed of charged residues.<ref name= |
<!-- Deleted image removed: [[File:CARD Domain.jpg|thumb| CARD Domains feature an arrangement of six to seven antiparallel alpha helices with a hydrophobic core and an outer face composed of charged residues.<ref name=autogenerated3>{{cite web | title = Apoptosis: CARD Domain| url = http://www.cellsignal.com/reference/domain/card.html | accessdate = 23-April-2011}}</ref>]] --> |
||
===Predicted Features=== |
===Predicted Features=== |
||
Properties of QRICH1 that were predicted using [[Bioinformatics]] tools: |
Properties of QRICH1 that were predicted using [[Bioinformatics]] tools: |
||
* Molecular Weight: 86.5 KDa<ref name= |
* Molecular Weight: 86.5 KDa<ref name=autogenerated2>{{cite journal | author = Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S | title = Methods and algorithms for statistical analysis of protein sequences | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 6 | pages = 2002–6 | year = 1992 | month = March | pmid = 1549558 | pmc = 48584 | doi = 10.1073/pnas.89.6.2002| url = | issn = | accessdate = 11-April-2011 }}</ref> |
||
* Isoelectric Point: 5.59<ref name=PI>{{cite web |title= Computer pI/Mw |url= http://expasy.org/tools/pi_tool.html | accessdate = 11-April-2011}}</ref> |
* Isoelectric Point: 5.59<ref name=PI>{{cite web |title= Computer pI/Mw |url= http://expasy.org/tools/pi_tool.html | accessdate = 11-April-2011}}</ref> |
||
*[[Posttranslational modification|Post-translational modification]]: Multiple phosphorylation sites are predicted. [[PhosphoSitePlus]] predicted three phosphorylated serines at amino acids 343, 345, and 659.<ref name=Phosphorylation>{{cite web |title= PhosphoSitePlus |url= http://www.phosphosite.org/proteinAction.do?id=12819&showAllSites=true | accessdate = 13-April-2011}}</ref> The NetPhos program on [[ExPASy]] predicted 45 phosphorylation sites on multiple serine, threonine, and tyrosine residues.<ref name=Phosphorylations>{{cite web |title= NetPhos |url= http://www.cbs.dtu.dk/services/NetPhos/ | accessdate = 13-April-2011}}</ref> There is one predicted sulfinated tyrosine at amino acid 725.<ref name=Sulfination>{{cite web |title= Sulfinator |url= http://www.expasy.org/tools/sulfinator/ | accessdate = 11-April-2011}}</ref> |
*[[Posttranslational modification|Post-translational modification]]: Multiple phosphorylation sites are predicted. [[PhosphoSitePlus]] predicted three phosphorylated serines at amino acids 343, 345, and 659.<ref name=Phosphorylation>{{cite web |title= PhosphoSitePlus |url= http://www.phosphosite.org/proteinAction.do?id=12819&showAllSites=true | accessdate = 13-April-2011}}</ref> The NetPhos program on [[ExPASy]] predicted 45 phosphorylation sites on multiple serine, threonine, and tyrosine residues.<ref name=Phosphorylations>{{cite web |title= NetPhos |url= http://www.cbs.dtu.dk/services/NetPhos/ | accessdate = 13-April-2011}}</ref> There is one predicted sulfinated tyrosine at amino acid 725.<ref name=Sulfination>{{cite web |title= Sulfinator |url= http://www.expasy.org/tools/sulfinator/ | accessdate = 11-April-2011}}</ref> |
||
Revision as of 23:25, 22 February 2013
QRICH1, also known as Glutamine-rich protein 1, is a protein that in humans is encoded by the QRICH1 gene.[1] One notable feature of this protein is that it contains a Caspase Activation Recruitment Domain, also known as a CARD domain.[2] As a result of having this domain, QRICH1 is believed to be involved in apoptotic, inflammatory, and host-immune response pathways.[3]
| Accession Numbers | Location | Identifiers | M.W. | pI |
|---|---|---|---|---|
| mRNA: NM_017730.2
protein: NP_060200.2 |
3p21.31 | FLJ20259, MFC131838[1] | 86.4 kDa | 5.59 |
Gene
The QRICH1 gene is 64,363 base pairs long, encoding an mRNA transcript that is 3331 bp in length.[4] QRICH1 is located on chromosome 3p21.31 and contains 11 exons.[5] The genomic sequence begins at base pair 49,057,531 and ends at base pair 49,141,201.[4]
Function
The exact function of QRICH1 is not well understood by the scientific community. It is, however, thought to be involved in processes such as inflammation and apoptosis due to the presence of a CARD domain near the beginning of the protein sequence.[3] This protein is predicted to localize to the nucleus and is known to interact with the ATXN1 and ATF7IP proteins shown in the image below.[7]
Protein
The glutamine-rich protein 1 is 776 amino acids in length. Glutamine residues are abundant, comprising 109 of the amino acids or 14% of the protein.[8] The protein contains three distinct domains. The first, a CARD domain, is a member of the death fold superfamily and is involved in apoptosis signaling pathways, immune signaling, inflammation, and host-defense mechanisms.[2] The second domain is a glutamine-rich domain which comprises a majority of the protein and is highly conserved among orthologs.[2] The final domain is a Domain of Unknown Function (DUF3504) found near the end of the protein sequence.[2] All three of these domains are well conserved throughout strict orthologs.
Predicted Features
Properties of QRICH1 that were predicted using Bioinformatics tools:
- Molecular Weight: 86.5 KDa[9]
- Isoelectric Point: 5.59[10]
- Post-translational modification: Multiple phosphorylation sites are predicted. PhosphoSitePlus predicted three phosphorylated serines at amino acids 343, 345, and 659.[11] The NetPhos program on ExPASy predicted 45 phosphorylation sites on multiple serine, threonine, and tyrosine residues.[12] There is one predicted sulfinated tyrosine at amino acid 725.[13]
- No predicted Signal Peptide or signal peptide cleavage.[14]
- Interacting Proteins: ATXN1, Spinocerebellar ataxia type 1 protein, and ATF7IP, activating transcription factor 7-interacting protein 1.[15] ATXN1 is involved in binding RNA in vitro and may be involved in RNA metabolism.[16] ATF7IP is a recruiter protein that couples transcriptional factors to the general transcription apparatus, thereby modulating transcription regulation and chromatin formation.[17]
Expression
QRICH1 is expressed at a high level, 3.3 times the average gene.[18] It is expressed ubiquitously throughout the human body, although EST Profile data reveal that QRICH1 is expressed particularly high in tissues such as the thymus, testis, cerebellar cortex and other areas of the brain, trachea, and in embryonic tissue. Health states such as germ cell tumors, leukemia, lymphoma, and chondrosarcoma have also reported high QRICH1 expression.
Homology
Orthologs
QRICH1 is highly conserved among mammalian orthologs, along with other chordates such as fish, birds, and amphibians. The gene has some conservation among insects, but there were no orthologs found in plants, fungi, or yeast.[19]
| Genus/Species | Organism Common Name | Accession Number | Sequence Identity | Sequence Similarity | Length (AAs) | |
| Pan troglodytes | Chimpanzee | XP_001161499.1 | 99% | 99% | 766 | |
| Macaca mulatta | Rhesus Macaque | XP_001110386.2 | 99% | 99% | 659 | |
| Pongo abelii | Orangutan | XP_002813809.1 | 99% | 99% | 777 | |
| Mus musculus | House Mouse | NP_780352.2 | 99% | 99% | 777 | |
| Rattus norvegicus | Norway rat | NP_001128004.1 | 99% | 99% | 687 | |
| Canis familiaris | Dog | XP_850904.1 | 99% | 99% | 780 | |
| Bos taurus | Cow | NP_001091484.1 | 99% | 99% | 779 | |
| Sus scrofa | Wild Boar | XP_003132250.1 | 99% | 99% | 781 | |
| Oryctolagus cuniculus | European Rabbit | XP_002713458.1 | 99% | 99% | 777 | |
| Ailuropoda melanoleuca | Giant Panda | XP_002920598.1 | 99% | 99% | 780 | |
| Callithrix jacchus | Marmoset | XP_002758378.1 | 99% | 99% | 777 | |
| Equus caballus | Horse | XP_001498380.2 | 98% | 98% | 780 | |
| Monodelphis domestica | Opossum | XP_001367745.1 | 95% | 97% | 776 | |
| Gallus gallus | Chicken | XP_001233527.1 | 94% | 96% | 773 | |
| Ornithorhynchus anatinus | Platypus | XP_001505372.1 | 94% | 95% | 741 | |
| Taeniopygia guttata | Zebra finch | XP_002187824.1 | 93% | 97% | 772 | |
| Xenopus laevis | African clawed frog | NP_001083416.1 | 79% | 85% | 755 | |
| Tetraodon nigroviridis | Pufferfish | CAG11318.1 | 71% | 80% | 729 | |
| Danio rerio | Zebra fish | NP_001020633.1 | 63% | 73% | 717 | |
| Apis mellifera | Bee | XP_624959.2 | 47% | 64% | 1356 | |
| Camponotus floridanus | Carpenter ant | EFN71787.1 | 45% | 63% | 1724 | |
Paralogs
QRICH1 has five paralogs all of which encode a zinc finger protein.[20]
References
- ^ a b "Entrez Gene: QRICH1 glutamine-rich 1". Retrieved 22-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ a b c d "UniprotKB". Retrieved 3-March-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ a b "The Pawson Lab: CARD Domain". Retrieved 28-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ a b "Gene: 54780". Retrieved 2-February-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "GenBank: Homo Sapiens glutamine-rich 1 (QRICH1), transcript variant 1, mRNA". Retrieved 29-January-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "NCBI Gene: 54870". Retrieved 2-February-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ db.org/newstring_cgi/show_network_section.pl "Predicted Functional Partners". Retrieved 22-April-2011.
{{cite web}}: Check|url=value (help); Check date values in:|accessdate=(help) - ^ "SAPS: Biology Workbench". Retrieved 19-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ Brendel V, Bucher P, Nourbakhsh IR, Blaisdell BE, Karlin S (1992). "Methods and algorithms for statistical analysis of protein sequences". Proceedings of the National Academy of Sciences of the United States of America. 89 (6): 2002–6. doi:10.1073/pnas.89.6.2002. PMC 48584. PMID 1549558.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|accessdate=(help); Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ "Computer pI/Mw". Retrieved 11-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "PhosphoSitePlus". Retrieved 13-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "NetPhos". Retrieved 13-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "Sulfinator". Retrieved 11-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004). "Improved prediction of signal peptides: SignalP 3.0". Journal of Molecular Biology. 340 (4): 783–95. doi:10.1016/j.jmb.2004.05.028. PMID 15223320.
{{cite journal}}:|access-date=requires|url=(help); Check date values in:|accessdate=(help); Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link) - ^ "STRING8.3". Retrieved 22-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "Spinocerebellar ataxia type 1". Retrieved 22-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "Activating Transcription Factor 7 Interacting Protein". Retrieved 23-April-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "AceView: Homo sapiens complex locus QRICH1, encoding glutamine-rich 1". Retrieved 16-February-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "BLAST". Retrieved 16-February-2011.
{{cite web}}: Check date values in:|accessdate=(help) - ^ "GeneCards". Retrieved 18-April-2011.
{{cite web}}: Check date values in:|accessdate=(help)
This article incorporates text from the United States National Library of Medicine, which is in the public domain.