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TMEM242

December 18, 2023

Transmembrane protein 242 (TMEM242) is a protein that in humans is encoded by the TMEM242 gene.[5] The tmem242 gene is located on chromosome 6, on the long arm, in band 2 section 5.3. This protein is also commonly called C6orf35, BM033, and UPF0463 Transmembrane Protein C6orf35. The tmem242 gene is 35,238 base pairs long, and the protein is 141 amino acids in length. The tmem242 gene contains 4 exons.[6] The function of this protein is not well understood by the scientific community. This protein contains a DUF1358 domain (Domain of Unknown Function 1358).[7]

TMEM242
Identifiers
AliasesTMEM242, BM033, C6orf35, transmembrane protein 242
External IDsMGI: 1917794 HomoloGene: 44020 GeneCards: TMEM242
Orthologs
SpeciesHumanMouse
Entrez

729515

70544

Ensembl

ENSG00000215712

ENSMUSG00000004945

UniProt

Q9NWH2

Q8VCR3

RefSeq (mRNA)

NM_018452

NM_027457

RefSeq (protein)

NP_060922

NP_081733

Location (UCSC)Chr 6: 157.29 – 157.32 MbChr 17: 5.46 – 5.49 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

Associated proteins edit

Several predicted interacting proteins and functional sites on the protein have been identified. One of the predicted interacting protein is MAP2K1IP1, which is a scaffold protein.[8] This protein is known to be involved in the MAP Kinase pathway. The MAP Kinase pathway is associated with the Alzheimer's pathway through a protein called Tau or MAPT. Excessive phosphorylation of this protein leads to aggregation of neurons which can cause Alzheimer's disease. Other associated proteins include GGT7,[9][10] RNF5,[9][10] ELOVL4,[9] GPR42,[9] BCL2L13,[9] HEATR1,[11] IZUMO4,[11] ARID1B,[11] SIAE,[11] EDARADD,[11] URB1,[11] ZDHHC14,[11] KIF11,[11] RRM2,[11] KCTD13,[11] TMEM31,[10] NDUFA3,[10] SGPL1,[10] CNR2,[10] and GJA8.[10] All of the listed proteins have known functions.

Function edit

The tmem242 protein is highly expressed in many tissues, but the most highly expressed in the brain, heart, adrenal, and thyroid.[12]

Homologs and orthologs edit

There are homologs and orthologs of the tmem242 protein in a variety of species. The species have diverged as far back as 794 million years ago.[13] The following species have been found as having orthologs to the tmem242 protein in their genome:[14]

  • TMEM242, H. sapiens
  • TMEM242, P. troglodytes
  • Tmem242, M. musculus
  • C1H6orf35, R. norvegicus
  • TMEM242, C. lupus
  • TMEM242, B. taurus
  • C3H6ORF35, G. gallus
  • tmem242, D. rerio
  • tmem242, X. tropicalis
  • AgaP_AGAP009165, A. gambiae
  • CG11699, D. melanogaster


 
This image shows the corrected divergence for tmem242 compared to fibrinogen and cytochrome C

The image to the right represents the rate of divergence for tmem242 (blue) compared to fibrinogen (red) and cytochrome C (green). This graph shows that tmem242 is evolving at a rate that is in between that of fibrinogen, which evolves quickly, and cytochrome C, which evolves slowly.

Regulation edit

Gene level edit

The promoter for the tmem242 gene is located upstream, but includes the transcription and translational start sites. This promoter was found using ElDorado by Genomatix.[15] This promoter has many transcription factor binding sites. Some of these transcription factors include TFIIB, Mouse Krueppel like factor, and NKX homeodomain factors. One notable transcription factor is the Retinoblastoma-binding protein with demethylase activity. There are ubiquitous basal level expression of tmem242 in all tissues in human[6] and mouse.[16] There are other tissues with increase expression levels such as the cerebellum and the hippocampus. There is increase expression levels in many parts of the brain along with kidney and prostate.[17] Tmem242 is also expressed in smaller amounts such as heart, adrenal gland, and thyroid.[6]

Transcriptional level edit

Tmem242 has several predicted post-transcriptional stem loop structures in the 5' UTR.[18] These structures use binding, both traditional and modified, to create stem loop structures in the untranslated regions of the mRNA.

Protein level edit

There are various forms of protein level regulation for tmem242. Tmem242 is found in a membrane within the cell. It is likely tmem242 is found in the cellular membrane[19] or the mitochondrial membrane,[20] but other sub cellular locations are possible. These include the endoplasmic reticulum and the nuclear membrane. There are various phosphorylation sites present on tmem242. These sites include cAMP and cGMP dependent protein kinase phosphorylation sites, casein kinase II phosphorylation sites, and a protein kinase C phosphorylation site.[21] These site all favor the phosphorylation of serine and threonine residues.[22] Other post-translational modifications include a N-myristoylation site, which covalently adds a myristate molecule.[22]

Structure edit

There are various single nucleotide polymorphisms (SNPs) that can occur in tmem242. A few cause stop codons, others make either silent mutations or missense mutations.

The TMEM242 protein has a conserved domain of unknown function pfam 07096, DUF 1358., which covers the first 121 aa of the protein. This domain is conserved in eukaryotes.

Tmem242 is 141 amino acids long, and contains at least one residue of each amino acid. There are two transmembrane domains, one spanning from approximately the 28th residue to the 48th reside. The second domain spans from approximately the 82nd residue to the 102nd residue.[23] These amino acid residues are approximate as various sources have approximations for the transmembrane domains.

Secondary edit

Tmem242 has several secondary structures. The two transmembrane domains have alpha helices.[24] These helices are formed from uncharged residues that are buried in the membrane. These helices are not exposed for binding. Other parts of the tmem242 protein may form secondary structures.

Tertiary edit

The tmem242 protein further folds to its final structure to embed in a membrane. It is likely tmem242 is embedded in the cellular membrane,[25] there is also potential for tmem242 to embed in the mitochondrial membrane or the endoplasmic reticulum membrane.

Post-translational modification edit

Tmem242 undergoes various post-translational modification. There are 11 serine residues that have a potential to be phosphorylated. Those sites occur in residue numbers 13, 20, 51, 57, 65, 74, 76, 77, 119, 128, and 130.[26] There are also four threonine residues that have the potential to be phosphorylated. Those site are residue numbers 36, 49, 123, and 137.[26] Other post-translational modifications that potentially happen occur at specific motif sites. There are 12 motif sites in tmem242 that correlate to 4 different motif types. The four types are cAMP and cGMP dependent protein kinase phosphorylation site, casein kinase II phosphorylation site, N-myristoylation site, and protein kinase C phosphorylation site.[22] There is one cAMP and cGMP dependent protein kinase phosphorylation site in tmem242, and this motif has a preference for phosphorylation of threonine and serine residues.[22] There are four casein kinase II phosphorylation sites, and this motif is a serine/threonine kinase. There are six N-myristoylation sites in tmem242, and this motif signals a covalent attachment of myristate.[22] There is one protein kinase C phosphorylation site which signals phosphorylation of serine or threonine resides.[22]

References edit

  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000215712 - Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000004945 - 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: chromosome 6 open reading frame 35".
  6. ^ a b c "transmembrane protein 242 [Homo sapiens]". Protein - NCBI. National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2019-02-26.
  7. ^ "Pfam Family: DUF1358 (PF07096)". Pfam.
  8. ^ "C6orf35 protein (Homo sapiens)". STRING interaction network.[permanent dead link]
  9. ^ a b c d e Calderone A. "TMEM242". Mentha: the intercome browser. Rome, Italy: University of Tor Vergata.
  10. ^ a b c d e f g "48 binary interactions found for search term tmem242". IntAct Molecular Interaction Database. EMBL-EBI.
  11. ^ a b c d e f g h i j "STRING: functional protein association networks". string-db.org. Retrieved 2019-04-22.
  12. ^ "TMEM242 transmembrane protein 242 [Homo sapiens (human)]". Gene - NCBI. National Center for Biotechnology Information, U.S. National Library of Medicine. Retrieved 2019-02-26.
  13. ^ "TimeTree :: The Timescale of Life". timetree.org. Retrieved 2019-03-04.
  14. ^ "HomoloGene:44020". HomoloGene. National Center for Biotechnology Information, U.S. National Library of Medicine.
  15. ^ "Genomatix - NGS Data Analysis & Personalized Medicine". www.genomatix.de. Retrieved 2019-05-15.
  16. ^ "Experiment Detail :: Allen Brain Atlas: Mouse Brain". mouse.brain-map.org. Retrieved 2019-05-15.
  17. ^ Hu P, Li G, Zhao X, Zhao F, Li L, Zhou H (2018). "Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria × ananassa)". PeerJ. 6: e4976. doi:10.7717/peerj.4976. PMC 6026456. PMID 29967718.
  18. ^ Kayal E, Bentlage B, Cartwright P, Yanagihara AA, Lindsay DJ, Hopcroft RR, Collins AG (2015). "Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription". PeerJ. 3: e1403. doi:10.7717/peerj.1403. PMC 4655093. PMID 26618080. Figure S10: Putative secondary structures of the four IGRs (A-D correspond to IGRs in Fig. 2 from left to right) from the filiferan Hydractinia symbiolongicarpus the RNA Folding Form of the mfold Web Server
  19. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2019-05-15.
  20. ^ "PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features". predictprotein.org. Retrieved 2019-05-15.
  21. ^ "Motif Scan". myhits.isb-sib.ch. Retrieved 2019-05-15.
  22. ^ a b c d e f "SIB myhits". SIB.
  23. ^ "The European Bioinformatics Institute < EMBL-EBI". www.ebi.ac.uk. Retrieved 2019-04-22.
  24. ^ "PredictProtein - Protein Sequence Analysis, Prediction of Structural and Functional Features". predictprotein.org. Retrieved 2019-04-22.
  25. ^ "PSORT WWW Server". psort.hgc.jp. Retrieved 2019-04-22.
  26. ^ a b "ExPaSy (Expert Protein Analysis System)", Encyclopedic Dictionary of Genetics, Genomics and Proteomics, John Wiley & Sons, Inc., 2004-07-15, doi:10.1002/0471684228.egp04300, ISBN 978-0471684220

External links edit

Further reading edit

  • Bonaldo MF, Lennon G, Soares MB (September 1996). "Normalization and subtraction: two approaches to facilitate gene discovery". Genome Research. 6 (9): 791–806. doi:10.1101/gr.6.9.791. PMID 8889548.
  • Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, et al. (January 2006). "Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes". Genome Research. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC 1356129. PMID 16344560.

December 18, 2023
tmem242, transmembrane, protein, protein, that, humans, encoded, gene, tmem242, gene, located, chromosome, long, band, section, this, protein, also, commonly, called, c6orf35, bm033, upf0463, transmembrane, protein, c6orf35, tmem242, gene, base, pairs, long, p. Transmembrane protein 242 TMEM242 is a protein that in humans is encoded by the TMEM242 gene 5 The tmem242 gene is located on chromosome 6 on the long arm in band 2 section 5 3 This protein is also commonly called C6orf35 BM033 and UPF0463 Transmembrane Protein C6orf35 The tmem242 gene is 35 238 base pairs long and the protein is 141 amino acids in length The tmem242 gene contains 4 exons 6 The function of this protein is not well understood by the scientific community This protein contains a DUF1358 domain Domain of Unknown Function 1358 7 TMEM242IdentifiersAliasesTMEM242 BM033 C6orf35 transmembrane protein 242External IDsMGI 1917794 HomoloGene 44020 GeneCards TMEM242Gene location Human Chr Chromosome 6 human 1 Band6q25 3Start157 289 025 bp 1 End157 323 601 bp 1 Gene location Mouse Chr Chromosome 17 mouse 2 Band17 17 A1Start5 461 145 bp 2 End5 490 534 bp 2 RNA expression patternBgeeHumanMouse ortholog Top expressed invena cavaright ventricleponspericardiumbody of tongueprefrontal cortexbiceps brachiisynovial jointparotid glandcardiaTop expressed inyolk sacintercostal muscleright ventriclesoleus muscleskeletal muscle tissuemedial ganglionic eminencespermatocytedigastric muscleseminiferous tubuleextraocular muscleMore reference expression dataBioGPSn aOrthologsSpeciesHumanMouseEntrez72951570544EnsemblENSG00000215712ENSMUSG00000004945UniProtQ9NWH2Q8VCR3RefSeq mRNA NM 018452NM 027457RefSeq protein NP 060922NP 081733Location UCSC Chr 6 157 29 157 32 MbChr 17 5 46 5 49 MbPubMed search 3 4 WikidataView Edit HumanView Edit Mouse Contents 1 Associated proteins 2 Function 3 Homologs and orthologs 4 Regulation 4 1 Gene level 4 2 Transcriptional level 4 3 Protein level 5 Structure 5 1 Secondary 5 2 Tertiary 5 3 Post translational modification 6 References 7 External links 8 Further readingAssociated proteins editSeveral predicted interacting proteins and functional sites on the protein have been identified One of the predicted interacting protein is MAP2K1IP1 which is a scaffold protein 8 This protein is known to be involved in the MAP Kinase pathway The MAP Kinase pathway is associated with the Alzheimer s pathway through a protein called Tau or MAPT Excessive phosphorylation of this protein leads to aggregation of neurons which can cause Alzheimer s disease Other associated proteins include GGT7 9 10 RNF5 9 10 ELOVL4 9 GPR42 9 BCL2L13 9 HEATR1 11 IZUMO4 11 ARID1B 11 SIAE 11 EDARADD 11 URB1 11 ZDHHC14 11 KIF11 11 RRM2 11 KCTD13 11 TMEM31 10 NDUFA3 10 SGPL1 10 CNR2 10 and GJA8 10 All of the listed proteins have known functions Function editThe tmem242 protein is highly expressed in many tissues but the most highly expressed in the brain heart adrenal and thyroid 12 Homologs and orthologs editThere are homologs and orthologs of the tmem242 protein in a variety of species The species have diverged as far back as 794 million years ago 13 The following species have been found as having orthologs to the tmem242 protein in their genome 14 TMEM242 H sapiens TMEM242 P troglodytes Tmem242 M musculus C1H6orf35 R norvegicus TMEM242 C lupus TMEM242 B taurus C3H6ORF35 G gallus tmem242 D rerio tmem242 X tropicalis AgaP AGAP009165 A gambiae CG11699 D melanogaster nbsp This image shows the corrected divergence for tmem242 compared to fibrinogen and cytochrome CThe image to the right represents the rate of divergence for tmem242 blue compared to fibrinogen red and cytochrome C green This graph shows that tmem242 is evolving at a rate that is in between that of fibrinogen which evolves quickly and cytochrome C which evolves slowly Regulation editGene level edit The promoter for the tmem242 gene is located upstream but includes the transcription and translational start sites This promoter was found using ElDorado by Genomatix 15 This promoter has many transcription factor binding sites Some of these transcription factors include TFIIB Mouse Krueppel like factor and NKX homeodomain factors One notable transcription factor is the Retinoblastoma binding protein with demethylase activity There are ubiquitous basal level expression of tmem242 in all tissues in human 6 and mouse 16 There are other tissues with increase expression levels such as the cerebellum and the hippocampus There is increase expression levels in many parts of the brain along with kidney and prostate 17 Tmem242 is also expressed in smaller amounts such as heart adrenal gland and thyroid 6 Transcriptional level edit Tmem242 has several predicted post transcriptional stem loop structures in the 5 UTR 18 These structures use binding both traditional and modified to create stem loop structures in the untranslated regions of the mRNA Protein level edit There are various forms of protein level regulation for tmem242 Tmem242 is found in a membrane within the cell It is likely tmem242 is found in the cellular membrane 19 or the mitochondrial membrane 20 but other sub cellular locations are possible These include the endoplasmic reticulum and the nuclear membrane There are various phosphorylation sites present on tmem242 These sites include cAMP and cGMP dependent protein kinase phosphorylation sites casein kinase II phosphorylation sites and a protein kinase C phosphorylation site 21 These site all favor the phosphorylation of serine and threonine residues 22 Other post translational modifications include a N myristoylation site which covalently adds a myristate molecule 22 Structure editThere are various single nucleotide polymorphisms SNPs that can occur in tmem242 A few cause stop codons others make either silent mutations or missense mutations The TMEM242 protein has a conserved domain of unknown function pfam 07096 DUF 1358 which covers the first 121 aa of the protein This domain is conserved in eukaryotes Tmem242 is 141 amino acids long and contains at least one residue of each amino acid There are two transmembrane domains one spanning from approximately the 28th residue to the 48th reside The second domain spans from approximately the 82nd residue to the 102nd residue 23 These amino acid residues are approximate as various sources have approximations for the transmembrane domains Secondary edit Tmem242 has several secondary structures The two transmembrane domains have alpha helices 24 These helices are formed from uncharged residues that are buried in the membrane These helices are not exposed for binding Other parts of the tmem242 protein may form secondary structures Tertiary edit The tmem242 protein further folds to its final structure to embed in a membrane It is likely tmem242 is embedded in the cellular membrane 25 there is also potential for tmem242 to embed in the mitochondrial membrane or the endoplasmic reticulum membrane Post translational modification edit Tmem242 undergoes various post translational modification There are 11 serine residues that have a potential to be phosphorylated Those sites occur in residue numbers 13 20 51 57 65 74 76 77 119 128 and 130 26 There are also four threonine residues that have the potential to be phosphorylated Those site are residue numbers 36 49 123 and 137 26 Other post translational modifications that potentially happen occur at specific motif sites There are 12 motif sites in tmem242 that correlate to 4 different motif types The four types are cAMP and cGMP dependent protein kinase phosphorylation site casein kinase II phosphorylation site N myristoylation site and protein kinase C phosphorylation site 22 There is one cAMP and cGMP dependent protein kinase phosphorylation site in tmem242 and this motif has a preference for phosphorylation of threonine and serine residues 22 There are four casein kinase II phosphorylation sites and this motif is a serine threonine kinase There are six N myristoylation sites in tmem242 and this motif signals a covalent attachment of myristate 22 There is one protein kinase C phosphorylation site which signals phosphorylation of serine or threonine resides 22 References edit a b c GRCh38 Ensembl release 89 ENSG00000215712 Ensembl May 2017 a b c GRCm38 Ensembl release 89 ENSMUSG00000004945 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 chromosome 6 open reading frame 35 a b c transmembrane protein 242 Homo sapiens Protein NCBI National Center for Biotechnology Information U S National Library of Medicine Retrieved 2019 02 26 Pfam Family DUF1358 PF07096 Pfam C6orf35 protein Homo sapiens STRING interaction network permanent dead link a b c d e Calderone A TMEM242 Mentha the intercome browser Rome Italy University of Tor Vergata a b c d e f g 48 binary interactions found for search term tmem242 IntAct Molecular Interaction Database EMBL EBI a b c d e f g h i j STRING functional protein association networks string db org Retrieved 2019 04 22 TMEM242 transmembrane protein 242 Homo sapiens human Gene NCBI National Center for Biotechnology Information U S National Library of Medicine Retrieved 2019 02 26 TimeTree The Timescale of Life timetree org Retrieved 2019 03 04 HomoloGene 44020 HomoloGene National Center for Biotechnology Information U S National Library of Medicine Genomatix NGS Data Analysis amp Personalized Medicine www genomatix de Retrieved 2019 05 15 Experiment Detail Allen Brain Atlas Mouse Brain mouse brain map org Retrieved 2019 05 15 Hu P Li G Zhao X Zhao F Li L Zhou H 2018 Transcriptome profiling by RNA Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries Fragaria ananassa PeerJ 6 e4976 doi 10 7717 peerj 4976 PMC 6026456 PMID 29967718 Kayal E Bentlage B Cartwright P Yanagihara AA Lindsay DJ Hopcroft RR Collins AG 2015 Phylogenetic analysis of higher level relationships within Hydroidolina Cnidaria Hydrozoa using mitochondrial genome data and insight into their mitochondrial transcription PeerJ 3 e1403 doi 10 7717 peerj 1403 PMC 4655093 PMID 26618080 Figure S10 Putative secondary structures of the four IGRs A D correspond to IGRs in Fig 2 from left to right from the filiferan Hydractinia symbiolongicarpus the RNA Folding Form of the mfold Web Server PSORT II Prediction psort hgc jp Retrieved 2019 05 15 PredictProtein Protein Sequence Analysis Prediction of Structural and Functional Features predictprotein org Retrieved 2019 05 15 Motif Scan myhits isb sib ch Retrieved 2019 05 15 a b c d e f SIB myhits SIB The European Bioinformatics Institute lt EMBL EBI www ebi ac uk Retrieved 2019 04 22 PredictProtein Protein Sequence Analysis Prediction of Structural and Functional Features predictprotein org Retrieved 2019 04 22 PSORT WWW Server psort hgc jp Retrieved 2019 04 22 a b ExPaSy Expert Protein Analysis System Encyclopedic Dictionary of Genetics Genomics and Proteomics John Wiley amp Sons Inc 2004 07 15 doi 10 1002 0471684228 egp04300 ISBN 978 0471684220External links editHuman TMEM242 genome location and TMEM242 gene details page in the UCSC Genome Browser Further reading editBonaldo MF Lennon G Soares MB September 1996 Normalization and subtraction two approaches to facilitate gene discovery Genome Research 6 9 791 806 doi 10 1101 gr 6 9 791 PMID 8889548 Kimura K Wakamatsu A Suzuki Y Ota T Nishikawa T Yamashita R et al January 2006 Diversification of transcriptional modulation large scale identification and characterization of putative alternative promoters of human genes Genome Research 16 1 55 65 doi 10 1101 gr 4039406 PMC 1356129 PMID 16344560 Retrieved from https en wikipedia org w index php title TMEM242 amp oldid 1187413359, wikipedia, wiki, book, books, library,

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