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.
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 pairmRNA. 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 neighborhoodedit
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 expressionedit
LRRC40 is expressed between the 50th and 100th percentile in almost every tissue in the body.[26]
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]
Propertiesedit
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 structureedit
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 interactionsedit
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.
^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.
^"MINT: CDC5L". Archived from the original on 2013-02-18.
^"MINT: SNW1". Archived from the original on 2013-02-18.
January 01, 1970
lrrc40, leucine, rich, repeat, containing, protein, that, humans, encoded, gene, identifiersaliases, dj677h15, leucine, rich, repeat, containing, 40external, idsmgi, 1914394, homologene, 9825, genecards, gene, location, human, chromosome, human, band1p31, 1sta. Leucine rich repeat containing 40 LRRC40 is a protein that in humans is encoded by the LRRC40 gene 5 LRRC40IdentifiersAliasesLRRC40 dJ677H15 1 leucine rich repeat containing 40External IDsMGI 1914394 HomoloGene 9825 GeneCards LRRC40Gene location Human Chr Chromosome 1 human 1 Band1p31 1Start70 144 805 bp 1 End70 205 579 bp 1 Gene location Mouse Chr Chromosome 3 mouse 2 Band3 3 H4Start157 742 299 bp 2 End157 774 124 bp 2 RNA expression patternBgeeHumanMouse ortholog Top expressed injejunal mucosaoocytesecondary oocyteendothelial cellBrodmann area 23embryooral cavitysynovial jointcerebellar vermissuperficial temporal arteryTop expressed inuretermedullary collecting ductsecondary oocytecumulus cellrenal corpuscleprimitive streakendocardial cushionmaxillary prominenceabdominal wallsuperior cervical ganglionMore reference expression dataBioGPSn aOrthologsSpeciesHumanMouseEntrez5563167144EnsemblENSG00000066557ENSMUSG00000063052UniProtQ9H9A6Q9CRC8RefSeq mRNA NM 017768NM 001289524NM 001289525NM 024194NM 001359763RefSeq protein NP 060238NP 001276453NP 001276454NP 077156NP 001346692Location UCSC Chr 1 70 14 70 21 MbChr 3 157 74 157 77 MbPubMed search 3 4 WikidataView Edit HumanView Edit Mouse Contents 1 Species distribution 2 Gene 2 1 Gene neighborhood 2 2 Gene expression 3 Protein 3 1 Properties 3 2 Protein structure 4 Protein interactions 5 ReferencesSpecies distribution editLRRC40 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 LRRC40Gene editLRRC40 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 edit 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 edit LRRC40 is expressed between the 50th and 100th percentile in almost every tissue in the body 26 nbsp Expression of LRRC40 in 79 human tissues 26 Protein editWhile 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 b sheet and a 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 nbsp 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 editAccording 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 edit a b c GRCh38 Ensembl release 89 ENSG00000066557 Ensembl May 2017 a b c GRCm38 Ensembl release 89 ENSMUSG00000063052 Ensembl May 2017 Human PubMed Reference National Center for Biotechnology Information U S National Library of Medicine Mouse PubMed Reference National Center for Biotechnology Information U S National Library of Medicine Entrez Gene leucine rich repeat containing 40 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 a b NCBI BLAST Time Tree a b NCBI Nucleotide NM 017768 4 24 June 2018 NCBI Nucleotide XP 513483 20 March 2018 NCBI Nucleotide NM 001131180 19 February 2022 NCBI Nucleotide AB179219 6 October 2006 NCBI Nucleotide XM 002750952 1 18 May 2010 NCBI Nucleotide XM 003127928 13 May 2017 NCBI Nucleotide NM 024194 13 August 2022 NCBI Nucleotide XM 001379417 27 April 2016 NCBI Nucleotide NM 001031295 9 March 2022 NCBI Nucleotide XM 002188367 12 February 2013 NCBI Nucleotide NM 001011310 19 June 2021 NCBI Nucleotide NM 199862 20 November 2021 NCBI Nucleotide BT043621 24 November 2009 NCBI Nucleotide XM 001640230 31 January 2009 NCBI Nucleotide XM 001842697 1 December 2009 NCBI Gene 55631 a b GeneCards LRRC40 a b GEO Profiles LRRC40 GDS596 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 ExPASy Compute PI Mw Archived from the original on 2003 07 23 PSORTII Protein Localization Tool permanent dead link NetPhos 2 0 Server Phosphorylation Prediction NCBI MMDB Inla S192n G194S MINT CDC5L Archived from the original on 2013 02 18 MINT SNW1 Archived from the original on 2013 02 18 Retrieved from https en wikipedia org w index php title LRRC40 amp oldid 1197427825, wikipedia, wiki, book, books, library,
