LRRC40

LRRC40
Identifiers
AliasesLRRC40, dJ677H15.1, leucine rich repeat containing 40
External IDsMGI: 1914394 HomoloGene: 9825 GeneCards: LRRC40
Gene location (Human)
Chr.Chromosome 1 (human)[1]
Band1p31.1Start70,144,805 bp[1]
End70,205,620 bp[1]
Orthologs
SpeciesHumanMouse
Entrez

55631

67144

Ensembl

ENSG00000066557

ENSMUSG00000063052

UniProt

Q9H9A6

Q9CRC8

RefSeq (mRNA)

NM_017768

NM_001289524
NM_001289525
NM_024194
NM_001359763

RefSeq (protein)

NP_060238

NP_001276453
NP_001276454
NP_077156
NP_001346692

Location (UCSC)Chr 1: 70.14 – 70.21 MbChr 3: 158.04 – 158.07 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Leucine rich repeat containing 40 (LRRC40) is a protein that in humans is encoded by the LRRC40 gene.[5]

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.[6] Orthologs were found all the way back to the scarlet sea anemone and homologs were found in bacteria and Archaea using BLAST.[7] The following table gives information on the homologs of LRRC40.

Genus speciesOrganism common nameDivergence from humans (MYA) [8]NCBI mRNA accessionSequence similarity [7]Protein lengthCommon gene name
Homo sapiens[9]Humans--NM_017768100%602LRRC40
Pan troglodytes[10]Common chimp6.4XM_51348399%602Hypothetical protein
Pongo abelii [11]Orangutan15.8NM_00113118099%602LRRC40
Macaca fascicularis [12]Long-tailed macaque30.2AB17921999%602Full LRRC40
Callithrix jacchus [13]Common marmoset43.9XM_002750952.199%602Predicted: LRRC40
Sus scrofa [14]Wild boar92.5XM_00312792896%602Predicted: LRRC40 like protein
Mus musculus [15]Mouse94.1NM_02419492%602LRRC40
Monodelphis domestica [16]Opossum160.2XM_00137941786%598Hypothetical protein
Gallus gallus [17]Chicken274.8NM_00103129585%603LRRC40
Taeniopygia guttata [18]Zebra finch274.8XM_00218836785%605Predicted: LRRC40
Xenopus (Silurana) tropicalis [19]Western clawed frog389.7NM_00101131080%605LRRC40
Danio rerio [20]Zebrafish444.3NM_19986283%601LRRC40
Salmo salar [21]Salmon444.3BT04362182%600LRRC40
Nematostella vectensis [22]Scarlet sea anemone830.3XM_00164023066%602Predicted protein
Culex quinquefasciatus [23]Southern house mosquito838.3XM_001842697.158%612LRRC40

Gene

LRRC40 is located on the negative DNA strand (see Sense (molecular biology)) of chromosome 1 from 70,611,483- 70,671,223.[24] The gene produces a 2958 base pair mRNA. There are 15 predicted exons in the human gene [9] with four other splice patterns predicted on GeneCards by the Alternative Splice Database.[25]

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.[26]

Expression of LRRC40 in 79 human tissues.[26]

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.[27]

Properties

LRRC40 is a 602 amino acid protein with a molecular weight of 68.254 kDa and an isoelectric point of 6.04.[28] LRRC40 is expected to localize to the nucleus [29] 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.[30] 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.

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.[31]

Protein interactions

According to Genecards, LRRC40 has 756 possible protein interactions.[25] 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.

AbbreviationProtein nameNCBI protein accessionCellular locationFunction
CDC5LCell division cycle 5-like proteinNP_001244nucleustranscription regulation and mRNA processing [32]
SNW1Ski-interacting proteinNP_036377.1nucleusmRNA processing [33]

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000066557 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000063052 - Ensembl, May 2017
  3. ↑ "Human PubMed Reference:".
  4. ↑ "Mouse PubMed Reference:".
  5. ↑ "Entrez Gene: leucine rich repeat containing 40".
  6. ↑ 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.
  7. 1 2 "NCBI BLAST".
  8. ↑ "Time Tree".
  9. 1 2 "NCBI Nucleotide: NM_017768.4".
  10. ↑ "NCBI Nucleotide: XP_513483".
  11. ↑ "NCBI Nucleotide: NM_001131180".
  12. ↑ "NCBI Nucleotide: AB179219".
  13. ↑ "NCBI Nucleotide: XM_002750952.1".
  14. ↑ "NCBI Nucleotide: XM_003127928".
  15. ↑ "NCBI Nucleotide: NM_024194".
  16. ↑ "NCBI Nucleotide: XM_001379417".
  17. ↑ "NCBI Nucleotide: NM_001031295".
  18. ↑ "NCBI Nucleotide: XM_002188367".
  19. ↑ "NCBI Nucleotide: NM_001011310".
  20. ↑ "NCBI Nucleotide: NM_199862".
  21. ↑ "NCBI Nucleotide: BT043621".
  22. ↑ "NCBI Nucleotide: XM_001640230".
  23. ↑ "NCBI Nucleotide: XM_001842697.1".
  24. ↑ "NCBI Gene: 55631".
  25. 1 2 "GeneCards: LRRC40".
  26. 1 2 "GEO Profiles: LRRC40 GDS596".
  27. ↑ 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.
  28. ↑ "ExPASy: Compute PI/Mw".
  29. ↑ "PSORTII: Protein Localization Tool".
  30. ↑ "NetPhos 2.0 Server: Phosphorylation Prediction".
  31. ↑ "NCBI MMDB: Inla S192n G194S".
  32. ↑ "MINT: CDC5L".
  33. ↑ "MINT: SNW1".
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