LRRC40: Difference between revisions

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== Gene ==
== Gene ==
LRRC40 is located on the negative DNA strand (see [[Sense (molecular biology)]]) of [[chromosome 1]] from 70,611,483- 70,671,223.<ref name="Gene">{{cite web | title = NCBI Gene: 55631| url =https://www.ncbi.nlm.nih.gov/gene/55631| accessdate = }}</ref> The gene produces a 2958 [[base pair]] [[mRNA]]. There are 15 predicted [[exons]] in the human gene <ref name="Nucleotide: Hsa"/> with four other splice patterns predicted on GeneCards by the Alternative Splice Database.<ref name="GeneCards">{{cite web | title = GeneCards: LRRC40| url =http://www.genecards.org/cgi-bin/carddisp.pl?gene=LRRC40&search=LRRC40| accessdate = }}</ref>
LRRC40 is located on the negative DNA strand (see [[Sense (molecular biology)]]) of [[chromosome 1]] from 70,611,483- 70,671,223.<ref name="Gene">{{cite web | title = NCBI Gene: 55631| url =https://www.ncbi.nlm.nih.gov/gene/55631| accessdate = }}</ref> The gene produces a 2958 [[base pair]] [[mRNA]]. There are 15 predicted [[exons]] in the human gene <ref name="Nucleotide: Hsa"/> with four other splice patterns predicted on GeneCards by the Alternative Splice Database.<ref name="GeneCards">{{cite web | title = GeneCards: LRRC40| url =https://www.genecards.org/cgi-bin/carddisp.pl?gene=LRRC40&search=LRRC40| accessdate = }}</ref>


=== Gene neighborhood ===
=== Gene neighborhood ===
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=== Properties ===
=== Properties ===
LRRC40 is a 602 amino acid protein with a [[molecular weight]] of 68.254 kDa and an [[isoelectric point]] of 6.04.<ref name="Compute PI/Mw">{{cite web | title = ExPASy: Compute PI/Mw| url =http://expasy.org/cgi-bin/pi_tool| accessdate = }}</ref> LRRC40 is expected to localize to the [[Cell nucleus|nucleus]] <ref name="PSORTII">{{cite web | title = PSORTII: Protein Localization Tool| url =http://psort.hgc.jp/cgi-bin/runpsort.pl| accessdate = }}</ref> and has no transmembrane domains to anchor it to the [[nuclear membrane]]. LRRC40 has many predicted [[phosphorylation]] sites. Of the 19 predicted [[phosphoserine]] sites, only two are conserved within the orthologs.<ref name="NetPhos 2.0">{{cite web | title = NetPhos 2.0 Server: Phosphorylation Prediction| url =http://www.cbs.dtu.dk/services/NetPhos/| accessdate = }}</ref> These two sites are S38 and S391.
LRRC40 is a 602 amino acid protein with a [[molecular weight]] of 68.254 kDa and an [[isoelectric point]] of 6.04.<ref name="Compute PI/Mw">{{cite web| title =ExPASy: Compute PI/Mw| url =http://expasy.org/cgi-bin/pi_tool| accessdate =| archive-url =https://web.archive.org/web/20030723023847/http://www.expasy.org/cgi-bin/pi_tool#| archive-date =2003-07-23| dead-url =yes| df =}}</ref> LRRC40 is expected to localize to the [[Cell nucleus|nucleus]] <ref name="PSORTII">{{cite web| title =PSORTII: Protein Localization Tool| url =http://psort.hgc.jp/cgi-bin/runpsort.pl| accessdate =}}{{dead link|date=December 2017 |bot=InternetArchiveBot |fix-attempted=yes }}</ref> and has no transmembrane domains to anchor it to the [[nuclear membrane]]. LRRC40 has many predicted [[phosphorylation]] sites. Of the 19 predicted [[phosphoserine]] sites, only two are conserved within the orthologs.<ref name="NetPhos 2.0">{{cite web | title = NetPhos 2.0 Server: Phosphorylation Prediction| url =http://www.cbs.dtu.dk/services/NetPhos/| accessdate = }}</ref> These two sites are S38 and S391.


=== Protein structure ===
=== Protein structure ===
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! Abbreviation !! Protein name !! NCBI protein accession !! Cellular location !! Function
! Abbreviation !! Protein name !! NCBI protein accession !! Cellular location !! Function
|-
|-
| [[CDC5L]] || Cell division cycle 5-like protein || NP_001244 || nucleus || transcription regulation and mRNA processing <ref name="MINT: CDC5L">{{cite web | title = MINT: CDC5L| url =http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-133723&dataSet=&| accessdate = }}</ref>
| [[CDC5L]] || Cell division cycle 5-like protein || NP_001244 || nucleus || transcription regulation and mRNA processing <ref name="MINT: CDC5L">{{cite web| title =MINT: CDC5L| url =http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-133723&dataSet=&| accessdate =| archive-url =https://archive.is/20130218153409/http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-133723&dataSet=&#| archive-date =2013-02-18| dead-url =yes| df =}}</ref>
|-
|-
| [[SNW1]] || Ski-interacting protein || NP_036377.1  || nucleus || mRNA processing <ref name="MINT: SNW1">{{cite web | title = MINT: SNW1| url =http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-193944&dataSet=&| accessdate = }}</ref>
| [[SNW1]] || Ski-interacting protein || NP_036377.1  || nucleus || mRNA processing <ref name="MINT: SNW1">{{cite web| title =MINT: SNW1| url =http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-193944&dataSet=&| accessdate =| archive-url =https://archive.is/20130218185926/http://mint.bio.uniroma2.it/mint/search/interactor.do?interactorAc=MINT-193944&dataSet=&#| archive-date =2013-02-18| dead-url =yes| df =}}</ref>
|}
|}


== References ==
== References ==
{{Reflist|2}}
{{Reflist|2}}

Latest revision as of 12:36, 14 November 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

Leucine rich repeat containing 40 (LRRC40) is a protein that in humans is encoded by the LRRC40 gene.[1]

Species distribution

LRRC40 is conserved throughout all of its orthologs. The entire protein is highly conserved in mammals, while conservation is high within the leucine rich repeats in the rest of the orthologs.[2] Orthologs were found all the way back to the scarlet sea anemone and homologs were found in bacteria and Archaea using BLAST.[3] The following table gives information on the homologs of LRRC40.

Genus species Organism common name Divergence from humans (MYA) [4] NCBI mRNA accession Sequence similarity [3] Protein length Common gene name
Homo sapiens[5] Humans -- NM_017768 100% 602 LRRC40
Pan troglodytes[6] Common chimp 6.4 XM_513483 99% 602 Hypothetical protein
Pongo abelii [7] Orangutan 15.8 NM_001131180 99% 602 LRRC40
Macaca fascicularis [8] Long-tailed macaque 30.2 AB179219 99% 602 Full LRRC40
Callithrix jacchus [9] Common marmoset 43.9 XM_002750952.1 99% 602 Predicted: LRRC40
Sus scrofa [10] Wild boar 92.5 XM_003127928 96% 602 Predicted: LRRC40 like protein
Mus musculus [11] Mouse 94.1 NM_024194 92% 602 LRRC40
Monodelphis domestica [12] Opossum 160.2 XM_001379417 86% 598 Hypothetical protein
Gallus gallus [13] Chicken 274.8 NM_001031295 85% 603 LRRC40
Taeniopygia guttata [14] Zebra finch 274.8 XM_002188367 85% 605 Predicted: LRRC40
Xenopus (Silurana) tropicalis [15] Western clawed frog 389.7 NM_001011310 80% 605 LRRC40
Danio rerio [16] Zebrafish 444.3 NM_199862 83% 601 LRRC40
Salmo salar [17] Salmon 444.3 BT043621 82% 600 LRRC40
Nematostella vectensis [18] Scarlet sea anemone 830.3 XM_001640230 66% 602 Predicted protein
Culex quinquefasciatus [19] Southern house mosquito 838.3 XM_001842697.1 58% 612 LRRC40

Gene

LRRC40 is located on the negative DNA strand (see Sense (molecular biology)) of chromosome 1 from 70,611,483- 70,671,223.[20] The gene produces a 2958 base pair mRNA. There are 15 predicted exons in the human gene [5] with four other splice patterns predicted on GeneCards by the Alternative Splice Database.[21]

Gene neighborhood

LRRC40 is neighbored downstream by LRRC7 (70,225,888 - 70,587,570) on the positive DNA strand and upstream by SRSF11 (70,687,320-70,716,488) on the positive DNA strand.

Gene expression

LRRC40 is expressed between the 50th and 100th percentile in almost every tissue in the body.[22]

File:LRRC40 Gene Expression.png
Expression of LRRC40 in 79 human tissues.[22]

Protein

While the exact function of the LRRC40 protein is not yet understood, it is believed to participate in protein-protein interactions because it is a member of the leucine rich repeat family of proteins which are known to participate in protein-protein interactions.[23]

Properties

LRRC40 is a 602 amino acid protein with a molecular weight of 68.254 kDa and an isoelectric point of 6.04.[24] LRRC40 is expected to localize to the nucleus [25] and has no transmembrane domains to anchor it to the nuclear membrane. LRRC40 has many predicted phosphorylation sites. Of the 19 predicted phosphoserine sites, only two are conserved within the orthologs.[26] These two sites are S38 and S391.

Protein structure

The secondary structure of the protein has a pattern within the leucine repeat regions. Each leucine repeat has a β-sheet and α-helix. The image to the right shows the particular horseshoe-like structure of a protein with many leucine rich repeats. Depending on the area where the LRRs are located, other proteins can bind within the curve of the horseshoe or attach to the outside of the protein.

File:Inla S192n Protein Structure.png
Structure of the Inla S192n G194S protein without its binding partner, sHEC1. The binding site was left empty to show the highlights of the leucine rich repeats (in yellow) demonstrating the protein-binding properties of LRRs.[27]

Protein interactions

According to Genecards, LRRC40 has 756 possible protein interactions.[21] These interactions are based on results in the Molecular Interaction database which provided two possible protein interactions. The two proteins are described in the table below.

Abbreviation Protein name NCBI protein accession Cellular location Function
CDC5L Cell division cycle 5-like protein NP_001244 nucleus transcription regulation and mRNA processing [28]
SNW1 Ski-interacting protein NP_036377.1 nucleus mRNA processing [29]

References

  1. ↑ "Entrez Gene: leucine rich repeat containing 40".
  2. ↑ Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD (July 2003). "Multiple sequence alignment with the Clustal series of programs". Nucleic Acids Res. 31 (13): 3497–500. doi:10.1093/nar/gkg500. PMC 168907. PMID 12824352.
  3. ↑ 3.0 3.1 "NCBI BLAST".
  4. ↑ "Time Tree".
  5. ↑ 5.0 5.1 "NCBI Nucleotide: NM_017768.4".
  6. ↑ "NCBI Nucleotide: XP_513483".
  7. ↑ "NCBI Nucleotide: NM_001131180".
  8. ↑ "NCBI Nucleotide: AB179219".
  9. ↑ "NCBI Nucleotide: XM_002750952.1".
  10. ↑ "NCBI Nucleotide: XM_003127928".
  11. ↑ "NCBI Nucleotide: NM_024194".
  12. ↑ "NCBI Nucleotide: XM_001379417".
  13. ↑ "NCBI Nucleotide: NM_001031295".
  14. ↑ "NCBI Nucleotide: XM_002188367".
  15. ↑ "NCBI Nucleotide: NM_001011310".
  16. ↑ "NCBI Nucleotide: NM_199862".
  17. ↑ "NCBI Nucleotide: BT043621".
  18. ↑ "NCBI Nucleotide: XM_001640230".
  19. ↑ "NCBI Nucleotide: XM_001842697.1".
  20. ↑ "NCBI Gene: 55631".
  21. ↑ 21.0 21.1 "GeneCards: LRRC40".
  22. ↑ 22.0 22.1 "GEO Profiles: LRRC40 GDS596".
  23. ↑ Kobe B, Kajava AV (December 2001). "The leucine-rich repeat as a protein recognition motif". Curr. Opin. Struct. Biol. 11 (6): 725–32. doi:10.1016/S0959-440X(01)00266-4. PMID 11751054.
  24. ↑ "ExPASy: Compute PI/Mw". Archived from the original on 2003-07-23.
  25. ↑ "PSORTII: Protein Localization Tool".[permanent dead link]
  26. ↑ "NetPhos 2.0 Server: Phosphorylation Prediction".
  27. ↑ "NCBI MMDB: Inla S192n G194S".
  28. ↑ "MINT: CDC5L". Archived from the original on 2013-02-18.
  29. ↑ "MINT: SNW1". Archived from the original on 2013-02-18.
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