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LRRC40

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LRRC40
Identifiers
AliasesLRRC40, dJ677H15.1, leucine rich repeat containing 40
External IDsMGI: 1914394; HomoloGene: 9825; GeneCards: LRRC40; OMA:LRRC40 - orthologs
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: 157.74 – 157.77 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

[edit]

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 species Organism common name Divergence from humans (MYA) [8] NCBI mRNA accession Sequence similarity [7] Protein length Common gene name
Homo sapiens[9] Humans -- NM_017768 100% 602 LRRC40
Pan troglodytes[10] Common chimp 6.4 XM_513483 99% 602 Hypothetical protein
Pongo abelii [11] Orangutan 15.8 NM_001131180 99% 602 LRRC40
Macaca fascicularis [12] Long-tailed macaque 30.2 AB179219 99% 602 Full LRRC40
Callithrix jacchus [13] Common marmoset 43.9 XM_002750952.1 99% 602 Predicted: LRRC40
Sus scrofa [14] Wild boar 92.5 XM_003127928 96% 602 Predicted: LRRC40 like protein
Mus musculus [15] Mouse 94.1 NM_024194 92% 602 LRRC40
Monodelphis domestica [16] Opossum 160.2 XM_001379417 86% 598 Hypothetical protein
Gallus gallus [17] Chicken 274.8 NM_001031295 85% 603 LRRC40
Taeniopygia guttata [18] Zebra finch 274.8 XM_002188367 85% 605 Predicted: LRRC40
Xenopus (Silurana) tropicalis [19] Western clawed frog 389.7 NM_001011310 80% 605 LRRC40
Danio rerio [20] Zebrafish 444.3 NM_199862 83% 601 LRRC40
Salmo salar [21] Salmon 444.3 BT043621 82% 600 LRRC40
Nematostella vectensis [22] Scarlet sea anemone 830.3 XM_001640230 66% 602 Predicted protein
Culex quinquefasciatus [23] Southern house mosquito 838.3 XM_001842697.1 58% 612 LRRC40

Gene

[edit]

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

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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

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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

[edit]

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

[edit]

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

[edit]

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

[edit]

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.

Abbreviation Protein name NCBI protein accession Cellular location Function
CDC5L Cell division cycle 5-like protein NP_001244 nucleus transcription regulation and mRNA processing [32]
SNW1 Ski-interacting protein NP_036377.1 nucleus mRNA processing [33]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000066557 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000063052 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  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. ^ a b "NCBI BLAST".
  8. ^ "Time Tree".
  9. ^ a b "NCBI Nucleotide: NM_017768.4". 24 June 2018.
  10. ^ "NCBI Nucleotide: XP_513483". 20 March 2018.
  11. ^ "NCBI Nucleotide: NM_001131180". 19 February 2022.
  12. ^ "NCBI Nucleotide: AB179219". 6 October 2006.
  13. ^ "NCBI Nucleotide: XM_002750952.1". 18 May 2010.
  14. ^ "NCBI Nucleotide: XM_003127928". 13 May 2017.
  15. ^ "NCBI Nucleotide: NM_024194". 13 August 2022.
  16. ^ "NCBI Nucleotide: XM_001379417". 27 April 2016.
  17. ^ "NCBI Nucleotide: NM_001031295". 9 March 2022.
  18. ^ "NCBI Nucleotide: XM_002188367". 12 February 2013.
  19. ^ "NCBI Nucleotide: NM_001011310". 19 June 2021.
  20. ^ "NCBI Nucleotide: NM_199862". 20 November 2021.
  21. ^ "NCBI Nucleotide: BT043621". 24 November 2009.
  22. ^ "NCBI Nucleotide: XM_001640230". 31 January 2009.
  23. ^ "NCBI Nucleotide: XM_001842697.1". December 2009.
  24. ^ "NCBI Gene: 55631".
  25. ^ a b "GeneCards: LRRC40".
  26. ^ a b "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". Archived from the original on 2003-07-23.
  29. ^ "PSORTII: Protein Localization Tool".[permanent dead link]
  30. ^ "NetPhos 2.0 Server: Phosphorylation Prediction".
  31. ^ "NCBI MMDB: Inla S192n G194S".
  32. ^ "MINT: CDC5L". Archived from the original on 2013-02-18.
  33. ^ "MINT: SNW1". Archived from the original on 2013-02-18.
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